cpt codes for Genomic Sequencing procedures, Genomic Sequencing cpt codes, cpt code for Genomic Sequencing, Genomic Sequencing cpt code

CPT Codes For Genomic Sequencing Procedures | Descriptions & Billing Guidelines

Below are the most frequent used CPT codes for genomic sequencing procedures. The official descriptions and billing guidelines can be found below.

1. CPT Code 81410

CPT 81410 can be billed when a lab analyst evaluates the patient’s specimen with a genomic sequence analysis panel for genetic sequences with a minimum of 9 genes that can relate to aortic dilation or dysfunction.

1.1 Description

CPT code 81410 is officially described by the manual of CPT as follows: “Aortic dysfunction or dilation (eg, Marfan syndrome, Loeys Dietz syndrome, Ehler Danlos syndrome type IV, arterial tortuosity syndrome); genomic sequence analysis panel, must include sequencing of at least 9 genes, including FBN1, TGFBR1, TGFBR2, COL3A1, MYH11, ACTA2, SLC2A10, SMAD3, and MYLK.”

1.2 Procedure

Using a patient specimen, such as blood, the lab analyst performs a genomic sequence analysis of at least the nine genes that the code descriptor lists.

The 81410 CPT code procedure involves using specialized equipment such as a next-generation gene sequencer, which is an automated instrument that determines the order of nucleotides in DNA.

The instrument reports the sequence as a string of letters, called a read, which the analyst compares to a reference genome of the same genes, which is like a library of normal and variant gene sequences associated with certain conditions.

Although not limited to testing for a specific condition, clinicians may order this test to aid in the diagnosis of certain aortic dysfunction and dilation conditions, and especially to help distinguish between various genetic disorders such as Marfan syndrome, Loeys Dietz syndrome, Ehler Danlos syndrome type IV, and arterial tortuosity syndrome.

These conditions affect connective tissue and may be associated with many symptoms, including aortic valve disorders.

1.3 Billing Guidelines

Be sure to distinguish CPT 81410 from CPT 81411. Compare the two codes and choose one or report both if the lab analyst performs both analyses. 

2. CPT Code 81411

CPT 81411 can be billed if a patient’s specimen is evaluated by a lab analyst for genetic deletions or duplications with a minimum of 4 genes listed in the official description that could relate to aortic dilation or dysfunction.

2.1 Description

CPT code 81411 is described by CPT and is defined in its manual as: “Aortic dysfunction or dilation (e.g., Marfan syndrome, Loeys Dietz syndrome, Ehler Danlos syndrome type IV, arterial tortuosity syndrome); duplication/deletion analysis panel, must include analyses for TGFBR1, TGFBR2, MYH11, and COL3A1.”

2.2 Procedure

Using a patient specimen, such as blood, the lab analyst performs a duplication and deletion analysis of at least the four genes that the CPT code 81411 descriptor lists.

The lab analyst may perform a method such as Multiplex Ligation dependent Probe Amplification, or MLPA, which is a test designed to detect large deletions and duplications of nucleotide sequences that normal DNA sequencing methods do not detect.

Although not limited to testing for a specific condition, clinicians may order this test to aid in the diagnosis of certain aortic dysfunction and dilation conditions. Specifically, clinicians may order CPT 81411 as a follow-up test for symptomatic patients with negative results from a gene sequencing test such as parent code CPT 81410.

That’s because a small percentage of patients with normal test results from a gene sequencing analysis for aortic dysfunction may harbor a duplication or deletion mutation that the initial test does not detect.

Such mutations may involve various genetic disorders such as Marfan syndrome, Loeys-Dietz syndrome, Ehler-Danlos syndrome type IV, and arterial tortuosity syndrome. These conditions affect connective tissue and may involve many symptoms, including aortic valve disorders.

2.3 Billing Guidelines

CPT code 81410 is similar to CPT code 81411. Distinguish the two codes and choose one, or report both if the lab analyst performs both analyses. 

3. CPT Code 81415

CPT 81415 can be used when a lab analyst does an exome gene sequence analysis. The analysis was used to look for genetic changes which might cause an unexplained syndrome or disorder.

3.1 Description

CPT code 81415 is officially described by CPT as follows: “Exome (e.g., unexplained constitutional or heritable disorder or syndrome); sequence analysis.”

3.2 Procedure

Using a patient specimen, such as blood, the lab analyst performs an exome gene sequence analysis. Although the exome is a small subset of the genome, it accounts for the most known mutations that impact human disease.

The 81415 CPT code procedure involves using specialized equipment such as a next-generation gene sequencer, which is an automated instrument that determines the order of nucleotides in DNA.

This test examines only the genes that form exons, which are DNA sequences that transcribe into mature RNA in cells, which code for proteins.

The gene sequencer reports the patient exome gene sequence as a string of letters, called a read, which the analyst compares to a reference exome.

The goal of the test described by CPT 81415 is to compare the patient exome to a family member’s exomes as the reference. Each exome gene sequencing test for a family member warrants a separate CPT code 81416.

Although not limited to testing for a specific condition, clinicians may order this test to aid in the diagnosis of an unexplained set of patient symptoms that could be associated with a constitutional or genetic disorder or syndrome, particularly if some family members evidence similar symptoms with no evident diagnosis.

3.3 Billing Guidelines

Some payers may pay separately for collecting the specimen using a code such as CPT 36415.

CPT code 81415 is in a code family with CPT 81416 and CPT 81417. You may report any or all of the codes together depending on the various tests that the lab analyst performs.

Make sure to distinguish the CPT 81415, CPT 81416, and CPT81417 for an exome analysis from the CPT 81425, CPT 81426, or CPT 81427 for whole genome analysis.

4. CPT Code 81416

CPT 81416 may be billed for when an exome gene sequence analysis of a patient’s relative is performed by a lab analyst. This is done to create an exome gene sequence reference so the lab analyst can compare it with the patient’s exome.

4.1 Description

CPT code 81416 is an add-on code from CPT, and the official descriptor is: “Exome (e.g., unexplained constitutional or heritable disorder or syndrome); sequence analysis, each comparator exome (e.g., parents, siblings) (List separately in addition to code for primary procedure).”

4.2 Procedure

For add-on CPT code 81416, the gene sequencer reports the comparator exome gene sequence as a string of letters, called a read, which the analyst compares to the patient exome.

The goal of this test is to use the family member’s exome as a reference to compare with the patient exome. If the lab analyst also performs the exome gene sequencing test for the patient, report that service with a separate CPT 81415.

4.3 Billing Guidelines

Because the 81416 CPT code is an add–on code, payers will not reimburse you if you report it without an appropriate primary CPT code, 81415.

5. CPT Code 81417

CPT 81417 can be used for a re-evaluation of an existing patient exome gene sequence because of new information that was unavailable during the initial evaluation. This can be evidence or clinical information, or an unrelated condition. 

5.1 Description

The 81417 CPT code is defined by the CPT manual as: “Exome (e.g., unexplained constitutional or heritable disorder or syndrome); re-evaluation of previously obtained exome sequence (e.g., updated knowledge or unrelated condition/syndrome).”

5.2 Procedure

The 81417 CPT code procedure involves evaluating the existing patient exome gene sequence analysis with reference exome gene sequences at some point after the initial evaluation.

To use this CPT code 81417, the lab analyst may compare the existing patient exome gene sequence with an existing reference exome gene sequence in light of new information, or the lab analyst may compare the existing patient exome gene sequence with a new reference exome gene sequence analysis.

Report each additional comparator exome gene sequence procedure with CPT 81416.

5.3 Billing Guidelines

You can not report this code for incidental findings. Use CPT 81228 or CPT 81229 for cytogenomic (genome-wide) copy number assessment.

6. CPT Code 81419

CPT 81419 can be billed when a lab analyst performs a technical lab test on a patient’s specimen (blood, for example) and conducts a genomic sequence analysis panel to evaluate the genetic sequences of 24 genes or more that are listed in the official description.

The test can help to indicate or diagnose genetic predisposition to epilepsy.

6.1 Description

The 81419 CPT code is defined in the manual of CPT as: “Epilepsy genomic sequence analysis panel, must include analyses for ALDH7A1, CACNA1A, CDKL5, CHD2, GABRG2, GRIN2A, KCNQ2, MECP2, PCDH19, POLG, PRRT2, SCN1A, SCN1B, SCN2A, SCN8A, SLC2A1, SLC9A6, STXBP1, SYNGAP1, TCF4, TPP1, TSC1, TSC2, and ZEB2.” 

6.2 Procedure

The procedure described by CPT 81419 starts with a technical lab test performed by a lab analyst.

He or she extracts nucleic acids from a specimen such as blood, amplifies target genes using methods such as polymerase chain reaction (PCR), and performs genomic sequence analysis of at least 24 genes related to epilepsy listed by the official description of CPT code 81419.

A common procedure for this test is a next-generation sequencing (NGS), which uses an automated instrument that can simultaneously determine the order of DNA nucleotides in many genes.

The instrument identifies each sequence as a string of letters, called a read, and compares the sequences to a library of normal and variant gene sequences associated with certain conditions.

Although not limited to testing for a specific condition, clinicians may order this test to help diagnose and distinguish forms of epilepsy, which is a neurologic disorder resulting in recurrent seizures due to abnormal electrical brain activity.

Clinicians may also order the test to identify gene mutations associated with inherited epilepsy to aid in predictive testing for family members.

6.3 Billing Guidelines

CPT provides multiple other codes that describe individual gene sequence analyses that might be part of the 81419 CPT code panel, such as codes for CACNA1A, as well as Tier 2 molecular pathology codes for some of the other genes such as ALDH7A1 and CDKL5.

CPT code 81419 describes the entire panel, and you should not separately report any individual gene codes in addition to the 81419 CPT code.

7. CPT Code 81420

CPT 81420 can be billed when a lab analyst evaluates circulating cell-free fetal DNA in maternal blood with a genomic sequence analysis panel to analyze genetic sequences on genes that can relate to fetal chromosomal aneuploidy. 

You can find the complete billing guide for the 81420 CPT code here. 

8. CPT Code 81422

CPT 81422 may be reported when a lab analyst used a genomic sequence analysis panel to analyze maternal blood for circulating cell-free fetal DNA to look for chromosomal microdeletion/microdeletions that are associated with syndromes like DiGeorge or Cri–du–chat.

8.1 Description

The 81422 CPT code is defined by CPT. It is officially described as follows: “Fetal chromosomal microdeletion(s) genomic sequence analysis (eg, DiGeorge syndrome, Cri-du-chat syndrome), circulating cell-free fetal DNA in maternal blood.”

8.2 Procedure

During the procedure described by CPT 81422, a lab analyst performed the necessary steps to isolate the specimen, which is circulating cell-free fetal DNA, called cffDNA, from maternal blood.

CffDNA occurs in small quantities in maternal blood, typically as fragments smaller than maternal DNA, so isolating cffDNA may use methods to separate components by sizes, such as centrifugation or column separation.

Using cffDNA, the lab analyst performs a genomic sequence analysis for chromosome microdeletion(s) such as 22q11.2 deletion indicating DiGeorge syndrome and 5P deletion indicating cri–du–chat syndrome.

The 81422 CPT code procedure involves using specialized equipment such as a next-generation gene sequencer, which is an automated instrument that determines the order of nucleotides in DNA.

The instrument reports the sequence as a string of letters, called a read, which the analyst compares to a reference genome of the same genes, which is like a library of normal and variant gene sequences associated with certain conditions.

Although not limited to testing for a specific condition, clinicians may order this test to aid in the diagnosis of certain fetal conditions associated with chromosome microdeletions, such as DiGeorge syndrome.

This may entail poor development of multiple body systems such as heart defects, delayed development, and compromised immune function; or cri–du–chat syndrome (Lejeune’s syndrome), which may include symptoms such as severe cognitive delays, poor growth and distinctive facial features and infant’s cry.

8.3 Billing Guidelines

Distinguish CPT 81422 for genomic sequence analysis of circulating cell-free fetal DNA in maternal blood for chromosomal microdeletion(s) from CPT 81420 for a similar procedure used to evaluate fetal chromosomal aneuploidy, which is an abnormal chromosome number such as trisomy 21.

9. CPT Code 81425

CPT 81425 may be billed when a lab analyst performed a gene sequence analysis patient’s entire genome. This is done to look for genetic changes that might cause an unexplained syndrome or disorder.

9.1 Description

The 81425 CPT code description can be found in the manual of CPT and is officially defined as: “Genome (e.g., unexplained constitutional or heritable disorder or syndrome); sequence analysis.”

9.2 Procedure

Using a patient specimen, such as blood, the lab analyst performs a whole genome sequence analysis. The procedure involves using specialized equipment such as a next-generation gene sequencer, which is an automated instrument that determines the order of nucleotides in DNA.

The gene sequencer reports the patient genome gene sequence as a string of letters, called a read, which the analyst compares to a reference genome. The goal of this test is to compare the patient genome to family member genomes as the reference. Each genome gene sequencing test for a family member warrants a separate CPT code, 81426.

9.3 Billing Guidelines

Make sure to distinguish CPT 81415, CPT 81416, or CPT 81417 for an exome analysis from CPT 81425 for whole genome analysis.

CPT code 81425 is in a family with add-on CPT codes 81426 and CPT 81427. You may report any or all of the codes together depending on the various tests that the lab analyst performs.

10. CPT Code 81426

CPT 81426 is an add-on code and can be billed when a lab analyst performs a gene sequence analysis of the entire genome of a patient relative to compare the genomes.

10.1 Description

The add-on code CPT 81426 is described by CPT as: “Genome (e.g., unexplained constitutional or heritable disorder or syndrome); sequence analysis, each comparator genome (e.g., parents, siblings) (List separately in addition to code for primary procedure).”

10.2 Procedure

Using a specimen, such as blood, the lab analyst performs a full genomic sequence analysis for an individual other than the patient, such as a sibling or parent, to compare with the patient’s genome.

The 81426 CPT code procedure involves using specialized equipment such as a next-generation gene sequencer, which is an automated instrument that determines the order of nucleotides in DNA.

For the add-on code 81426, the gene sequencer reports the comparator genome gene sequence as a string of letters, called a read, which the analyst compares to the patient genome.

The goal of the test described by CPT 81426 is to use the family member genome as a reference to compare with the patient genome. If the lab analyst also performs the genome gene sequencing test for the patient, report that service with a separate CPT code 81425.

10.3 Billing Guidelines

Because CPT 81426 is an add-on code, payers will not reimburse you if you report it without an appropriate primary CPT code 81425.

11. CPT Code 81427

CPT 81427 can be reported when a lab analyst has to reevaluate a full genomic sequence of a patient because of new information that wasn’t available before. This can be an unrelated condition, new evidence, or clinical information.

11.1 Description

The official description of CPT code 81427 can be found in the CPT manual and is as follows: “Genome (eg, unexplained constitutional or heritable disorder or syndrome); re-evaluation of the previously obtained genome sequence (eg, updated knowledge or unrelated condition/syndrome).” 

11.2 Procedure

The 81427 CPT code procedure involves evaluating the existing patient whole genome sequence analysis with reference genomic sequences at some time after the initial evaluation.

To use CPT code 81427, the lab analyst may compare the existing patient genome sequence analysis with an existing reference genome in light of new information, or the lab analyst may compare the existing patient genomic sequence analysis with a new reference whole genome sequence analysis.

11.3 Billing Guidelines

Report each additional comparator genome sequencing procedure with CPT code 81426.

You can not use this code for incidental findings.

12. CPT Code 81430

CPT 81430 can be billed when a genomic sequence analysis panel was performed by a lab analyst to evaluate the specimen of a patient for genetic sequences of 60 genes or more. The genes from the official description are included and can be related to hearing loss.

12.1 Description

The 81430 CPT code is defined by CPT and described in its manual as: “Hearing loss (e.g., non-syndromic hearing loss, Usher syndrome, Pendred syndrome); genomic sequence analysis panel, must include sequencing of at least 60 genes, including CDH23, CLRN1, GJB2, GPR98, MTRNR1, MYO7A, MYO15A, PCDH15, OTOF, SLC26A4, TMC1, TMPRSS3, USH1C, USH1G, USH2A, and WFS1.”

12.2 Procedure

Using a patient specimen, such as blood, the lab analyst performs a genomic sequence analysis of at least 60 genes, including 16 genes that the code descriptor lists.

The procedure involves using specialized equipment such as a next-generation gene sequencer, which is an automated instrument that determines the order of nucleotides in DNA.

The instrument reports the sequence as a string of letters, called a read, which the analyst compares to a reference genome of the same genes, which is like a library of normal and variant gene sequences associated with certain conditions.

12.3 Billing Guidelines

CPT code 81430’s descriptor is similar to CPT code 81431. Distinguish the two codes and choose one or report both if the lab analyst performs both analyses. 

13. CPT Code 81431

The 81431 CPT code can be billed when a lab analyst performed a duplication/deletion analysis panel for the evaluation of the specimen of a patient for copy number changes in DFNB1 and STRC genes. It can also be used for deletions in GJB6 or GJB2 genes.

13.1 Description

The CPT manual describes CPT 81431 as: “Hearing loss (e.g., non-syndromic hearing loss, Usher syndrome, Pendred syndrome); duplication/deletion analysis panel, must include copy number analyses for STRC and DFNB1 deletions in GJB2 and GJB6 genes.”

13.2 Procedure

The 81431 CPT code procedure starts with a lab analyst using a patient specimen, such as blood, to perform copy number analyses of STRC and DFNB1 genes, and deletion analyses of GJB2 and GJB6 genes.

The lab analyst may perform a method such as Multiplex Ligation dependent Probe Amplification, or MLPA, which is a test designed to detect deletions and other copy number changes in nucleotide sequences that normal DNA sequencing methods do not detect.

13.3 Billing Guidelines

Although not limited to testing for a specific condition, clinicians may commonly order this test for patients with a suspected hereditary hearing loss who have tested negative for mutations using the full gene sequencing test, which is CPT 81430.

The description of CPT code 81431 is similar to CPT 81430. Make sure that you can distinguish the differences between these two codes if the lab analyst performs both analyses. 

Although most mutations associated with hereditary hearing loss will show up on the full gene sequence analysis, some patients have duplication or deletion mutations that normal sequencing methods don’t detect.

This test may help distinguish between various genetic disorders such as non-syndromic hearing loss, Usher syndrome, characterized by hearing loss and progressive vision loss, and Pendred syndrome, characterized by hearing loss and thyroid disease.

14. CPT Code 81432

CPT 81432 is used for performs a genomic sequence analysis panel performed by a lab analyst to evaluate a specimen of a patient for the genetic sequence of 10 genes or more. The genes are related to disorders that are associated with hereditary breast cancer mutations and are listed in the official description below.

14.1 Description

The manual of CPT described the 81432 CPT code as follows: “Hereditary breast cancer-related disorders (e.g., hereditary breast cancer, hereditary ovarian cancer, hereditary endometrial cancer); genomic sequence analysis panel, must include sequencing of at least ten genes, always including BRCA1, BRCA2, CDH1, MLH1, MSH2, MSH6, PALB2, PTEN, STK11, and TP53.”

14.2 Procedure

Using a patient specimen, such as blood, the lab analyst performs a genomic sequence analysis of at least the 10 genes that the code descriptor lists.

The 81432 CPT code procedure involves using specialized equipment such as a next-generation gene sequencer, which is an automated instrument that determines the order of nucleotides in DNA.

The instrument reports the sequence as a string of letters, called a read, which the analyst compares to a reference genome of the same genes, which is like a library of normal and variant gene sequences associated with certain conditions.

14.3 Billing Guidelines

CPT provides various other molecular pathology codes for tests involving several of the genes included in the test described by CPT 81432.

You should not additionally report a code for the single test because CPT code 81432 includes gene sequencing of each of the genes,

CPT code 81432 is a parent code for CPT 81433. Distinguish the two codes and choose one, or report both if the two were performed.

15. CPT Code 81433

CPT 81433 may be reported when a lab analyst evaluates a specimen of a patient with a duplication/deletion analysis panel to look into genetic deletions or duplications in five genes or more that are listed in the official description below. The genes can relate to disorders that are associated with hereditary breast cancer mutations.

15.1 Description

CPT 81433 can be found in the CPT manual and is officially defined as: “Hereditary breast cancer-related disorders (eg, hereditary breast cancer, hereditary ovarian cancer, hereditary endometrial cancer); duplication/deletion analysis panel, must include analyses for BRCA1, BRCA2, MLH1, MSH2, and STK11.”

15.2 Procedure

Using a patient specimen, such as blood, the lab analyst performs a duplication and deletion analysis during the 81433 CPT code procedure of at least the five genes BRCA1, BRCA2, MLH1, MSH2, and STK11.

The lab analyst may perform a method such as Multiplex Ligation dependent Probe Amplification, or MLPA, which is a test designed to detect large deletions and duplications of nucleotide sequences that normal DNA sequencing methods do not detect.

15.3 Billing Guidelines

Although not limited to testing for a specific condition, clinicians may order this test to aid in the diagnosis of hereditary breast cancer-related disorders.

Specifically, clinicians may order CPT 81433 for patients with known familial BRCA1 or BRCA2 large deletions or duplications or as a follow-up test for symptomatic patients with negative results from a gene sequencing test such as parent CPT 81432 for sequencing of at least ten genes.

That’s because a small percentage of patients with normal test results from a gene sequencing analysis for hereditary breast cancer–related disorders may harbor a duplication or deletion mutation that the initial test does not detect. 

CPT 81432 is a parent code for CPT 81433.

CPT provides various other molecular pathology codes for tests involving several of the genes included in the test described by CPT 81433. Because this code includes duplication and deletion analysis of each of the genes, you should not additionally report a code for the single test.

16. CPT Code 81436

CPT 81436 may be reported when the panel is performed by a lab analyst for the evaluation of the specimen of a patient to look for deletion and duplication mutations of five genes or more.

The genes are defined as the official description and may relate to hereditary colon cancer syndromes.

16.1 Description

The official description of CPT 81436, as defined in its manual, is: “Hereditary colon cancer disorders (e.g., Lynch syndrome, PTEN hamartoma syndrome, Cowden syndrome, familial adenomatosis polyposis); duplication/deletion analysis panel, must include analysis of at least five genes, including MLH1, MSH2, EPCAM, SMAD4, and STK11.”

16.2 Procedure

Using a patient specimen, such as blood, the lab analyst performs duplication and deletion analysis for the five genes, including MLH1, MSH2, EPCAM, SMAD4, and STK11.

The lab analyst may perform a method such as multiplex–ligation-dependent probe amplification, or MLPA, which is a test designed to detect duplications and deletions in nucleotide sequences that normal DNA sequencing methods do not detect.

16.3 Billing Guidelines

Although not limited to testing for a specific condition, clinicians may commonly order this test for patients with a suspected hereditary colon cancer syndrome who have tested negative for mutations using the full gene sequencing test, which is CPT 81435.

Although most mutations associated with hereditary colon cancer will show up on the full gene sequence analysis, some patients have duplication or deletion mutations that normal sequencing methods don’t detect.

CPT provides various other molecular pathology codes for tests involving several of the genes included in the CPT code 81436 test.

Because this procedure includes duplication and deletion analysis of each of the genes, you should not additionally report a code for the single test. The other tests include CPT 81292, CPT 81293, or CPT 81294 for MLH1, or you can use CPT 81295, CPT 81296, or CPT 81297 for MSH2.

17. CPT Code 81437

CPT 81437 can be used when a lab analyst performs a genomic sequence analysis panel that includes genes that are associated with hereditary neuroendocrine tumors; MAX, SDHB, SDHC, SDHD, TMEM127, and VHL. The panel is performed to look for genetic sequences.

17.1 Description

The 81437 CPT code description can be found in the CPTs manual and is defined as: “Hereditary neuroendocrine tumor disorders (e.g., medullary thyroid carcinoma, parathyroid carcinoma, malignant pheochromocytoma or paraganglioma); genomic sequence analysis panel, must include sequencing of at least six genes, including MAX, SDHB, SDHC, SDHD, TMEM127, and VHL.”

17.2 Procedure

Using a patient specimen, such as blood, the lab analyst performs a genomic sequence analysis of at least the six genes MAX, SDHB, SDHC, SDHD, TMEM127, and VHL.

The 81437 CPT code procedure involves using specialized equipment such as a next-generation gene sequencer, which is an automated instrument that determines the order of nucleotides in DNA.

The instrument reports the sequence as a string of letters, called a read, which the analyst compares to a reference genome of the same genes, which is like a library of normal and variant gene sequences associated with certain conditions.

17.3 Billing Guidelines

Although not limited to testing for a specific condition, clinicians may order the 81437 CPT code test as part of genetic counseling and evaluation of patients for susceptibility to certain heritable neuroendocrine tumor disorders such as medullary thyroid cancer, parathyroid cancer, and malignant pheochromocytoma or paraganglioma, tumors that release bursts of too much adrenalin, the “fight or flight” hormone. 

CPT provides various other molecular pathology codes for tests involving several of the genes included in the 81437 CPT code test. Because CPT 81437 includes gene sequencing of each of the genes, you should not additionally report a code for the single test.

18. CPT Code 81438

The 81437 CPT code describes a duplication/deletion analysis panel by a lab analyst for the evaluation of the specimen of a patient for genetic deletions or duplications of four genes or more that might involve mutations and are generally associated with hereditary neuroendocrine tumor disorders.

18.1 Description

The official description of the 81437 CPT is: “Hereditary neuroendocrine tumor disorders (e.g., medullary thyroid carcinoma, parathyroid carcinoma, malignant pheochromocytoma or paraganglioma); duplication/deletion analysis panel, must include analyses for SDHB, SDHC, SDHD, and VHL.”

18.2 Procedure

Using a patient specimen, such as blood, the lab analyst performs a duplication and deletion analysis of at least the four genes SDHB, SDHC, SDHD, and VHL.

The lab analyst may perform a method such as Multiplex Ligation dependent Probe Amplification, or MLPA, which is a test designed to detect large deletions and duplications of nucleotide sequences that normal DNA sequencing methods do not detect.

18.3 Billing Guidelines

Although not limited to testing for a specific condition, clinicians may order this test to aid in the diagnosis of hereditary neuroendocrine tumor disorders.

Specifically, clinicians may order CPT code 81438 for patients with known familial neuroendocrine tumor large deletions or duplications or as a follow-up test for symptomatic patients with negative results from a gene sequencing test such as parent CPT code 81437.

The follow-up testing allows evaluation of the small percentage of patients with normal test results from a gene sequencing analysis for hereditary neuroendocrine tumors that may harbor a duplication or deletion mutation that the initial test does not detect.

CPT provides various other molecular pathology codes for tests involving several of the genes included in the test described by CPT code 81438. Because this code includes duplication and deletion analysis of each of the genes, you should not additionally report a code for the single test.

19. CPT Code 81439

Report CPT 81439 when a lab analyst performed a genomic sequence analysis panel of the specimen of a patient to evaluate it for genetic sequences of five or more cardiomyopathy–related genes. These genes can be related to hereditary cardiomyopathy conditions like;

  • Arrhythmogenic right ventricular cardiomyopathy;
  • Dilated cardiomyopathy; or
  • Hypertrophic cardiomyopathy.

19.1 Description

The 81439 CPT code is maintained by CPT and officially described in its manual as: “Hereditary cardiomyopathy (e.g., hypertrophic cardiomyopathy, dilated cardiomyopathy, arrhythmogenic right ventricular cardiomyopathy), genomic sequence analysis panel, must include sequencing of at least five cardiomyopathy-related genes (e.g., DSG2, MYBPC3, MYH7, PKP2, TTN).”

19.2 Procedure

The 81439 CPT code procedure starts with a lab analyst taking a specimen from a patient to perform a genomic sequence analysis of at least five cardiomyopathy–related genes.

The lab analyst can use a next-generation gene sequencer to determine the order of nucleotides in the patient’s DNA.

A next-generation gene sequencer reports a read (a sequence as a string of letters) so a reference genome can be compared by the lab analyst.

19.3 Billing Guidelines

The 81439 CPT code procedure can be used by clinicians for identifying potential genetic components of cardiomyopathy.

CPT provides various other molecular pathology codes for tests involving most of the genes, including the CPT code 81439. Because CPT 81439 includes gene sequencing of each gene, you should not additionally report a code for the single gene analysis.

You can not report CPT code 81439 with CPT 81413 or CPT 81414 if these services are provided on the same date.

20. CPT Code 81440

CPT 81440 describes a procedure in which lab analysts perform a genomic sequence analysis panel for the evaluation of the specimen of a patient for genetic sequences of 100 mitochondrial genes or more that are encoded in the nucleus.

They include the 19 genes that are defined by the official description and relate to muscle or nerve pathologies.  

20.1 Description

The 81440 CPT code descriptions can be found in the CPTs manual and are as follows: “Nuclear encoded mitochondrial genes (e.g., neurologic or myopathic phenotypes), genomic sequence panel, must include analysis of at least 100 genes, including BCS1L, C10orf2, COQ2, COX10, DGUOK, MPV17, OPA1, PDSS2, POLG, POLG2, RRM2B, SCO1, SCO2, SLC25A4, SUCLA2, SUCLG1, TAZ, TK2, and TYMP.”

20.2 Procedure

Blood is taken from the patient, so the lab analyst can perform a genomic sequence analysis panel of 100 genes or more, including the 19 genes from the official description, from the nucleus that involves mitochondrial processes.

The CPT code 81440 procedure is performed by the lab analyst with specialized equipment. This can be a generation gene sequencer to determine the order of nucleotides in DNA.

The sequence is reported as a string of letters (a read). This is compared to the reference genome of the same genes.

20.3 Billing Guidelines

Report CPT 81440 for nuclear-encoded mitochondrial DNA and the CPT 81460 until CPT 81465 for mDNA in the mitochondria.

Although not limited to testing for a specific condition, clinicians may order the 81460 CPT code test to help evaluate disorders of the mitochondria, which can affect nerve and muscle function.

Symptoms of mitochondrial disorders vary widely, from asymptomatic to fatal, but often involve muscle weakness, organ diseases such as liver, kidney, heart, and lungs, neurological problems, and vision or hearing loss.

21. CPT Code 81442

CPT 81442 may be used when a genomic sequence analysis panel is performed by a lab analyst to evaluate a specimen of a patient for genetic sequences of 12 or more genes.

The genes are defined by the official description and related to NSD disorders (Noonan–Spectrum Disorders).

21.1 Description

The 81442 CPT code descriptor is officially described in the CPT manual as: “Noonan spectrum disorders (e.g., Noonan syndrome, cardio-facio-cutaneous syndrome, Costello syndrome, LEOPARD syndrome, Noonan-like syndrome), genomic sequence analysis panel, must include sequencing of at least 12 genes, including BRAF, CBL, HRAS, KRAS, MAP2K1, MAP2K2, NRAS, PTPN11, RAF1, RIT1, SHOC2, and SOS1.”

21.2 Procedure

The CPT 81442 procedure starts with a lab analyst taking blood from a patient. This is used to perform genomic sequence analysis of 12 or more genes defined by the official code description.

The lab analyst can use a next-generation gene sequencer to determine the order of nucleotides in the DNA of the patient. This is then compared to a reference genome of the same genes.

21.3 Billing Guidelines

CPT provides various other molecular pathology codes for tests involving many of the genes included in the 81442 CPT code test. Because CPT 81442 includes gene sequencing of each of the genes, you should not additionally report a code for the single test.

The other tests include CPT 81210 for BRAF, CPT 81275 for KRAS, and various Tier 2 molecular pathology codes in the range CPT 81400 until CPT 81406 for gene analysis for HRAS, BRAF, KRAS, MAP2K1, MAP2K2, NRAS, PTPN11, RAF1, RIT1, SHOC2, and SOS1.

22. CPT Code 81443

CPT 81443 describes another genomic sequence analysis panel for the evaluation of the specimen of a patient for genetic sequences of 15 genes or more.

The genes are defined by the official description of this code. These genes are related to inherited conditions of a severe nature and are often found in people that are Ashkenazi Jewish descendants.

22.1 Description

The 81443 CPT code is defined and described by CPT as follows: “Genetic testing for severe inherited conditions (eg, cystic fibrosis, Ashkenazi Jewish-associated disorders [eg, Bloom syndrome, Canavan disease, Fanconi anemia type C, mucolipidosis type VI, Gaucher disease, Tay-Sachs disease], beta hemoglobinopathies, phenylketonuria, galactosemia), genomic sequence analysis panel, must include sequencing of at least 15 genes (eg, ACADM, ARSA, ASPA, ATP7B, BCKDHA, BCKDHB, BLM, CFTR, DHCR7, FANCC, G6PC, GAA, GALT, GBA, GBE1, HBB, HEXA, IKBKAP, MCOLN1, PAH).”

22.2 Procedure

Using a patient specimen, such as blood, the lab analyst performs a genomic sequence analysis of at least 15 genes related to severe inherited conditions, such as the 20 gene examples that can be found in the official description above.

The 81443 CPT code procedure involves using specialized equipment such as a next-generation gene sequence to report a sequence as a string of letters to compare to a reference genome of the same genes.

Although not limited to testing for a specific condition, clinicians may order the 81443 CPT code test as part of genetic counseling and evaluation of patients for susceptibility to certain severe, heritable conditions.

These conditions are common in people of Ashkenazi (German or Eastern European) Jewish descent, such as cystic fibrosis, characterized by thick, sticky mucus that blocks pancreatic ducts and clogs the lungs;

  • Bloom syndrome: characterized by dilated blood vessels in a butterfly-shaped distribution on the face, light sensitivity, and susceptibility to certain cancers, particularly leukemia;
  • Canavan disease: characterized by a loss of white matter in the brain, starting in infancy, and leading to death;
  • Fanconi anemia group C: an inherited blood disorder that results in dwarfism and susceptibility to certain cancers;
  • Gaucher disease: characterized by spleen and liver enlargement and anemia;
  • Tay–Sachs disease: characterized by a build-up of fatty proteins in the brain that causes spasticity, loss of sight and hearing, and death in childhood; and
  • Mucolipidosis type IV: characterized by vision loss and delayed mental and motor skills often leading to blindness and inability to walk or talk.

The test used in the 81443 CPT code procedure also interrogates genes for the basis of conditions such as beta hemoglobinopathies, phenylketonuria, and galactosemia.

22.3 Billing Guidelines

Report CPT 81329 with this code if testing for spinal muscular atrophy separately.

Be sure to distinguish CPT 81443 from CPT 81412, which involves testing for nine genes for Ashkenazi–Jewish–associated disorders, many of which CPT code 81443 also includes.

CPT provides multiple other codes that describe individual gene sequence analyses that might be part of the 81443 CPT code panel, such as;

  • CPT 81200 for ASPA;
  • CPT 81209 for BLM;
  • CPT 81220 until CPT 81224 for CFTR;
  • CPT 81242 for FANCC;
  • CPT 81250 for G6PC;
  • CPT 81251 for GBA;
  • CPT 81361 until CPT 81364 for HBB;
  • CPT 81255 for HEXA;
  • CPT 81260 for IKBKAP, and
  • CPT 81290 for MCOLN1.

You can also use the Tier 2 molecular pathology codes for ACADM, ARSA, ATP7B, BCKDHA, BCKDHB, DHCR7, GAA, GALT, and PAH.

CPT Code 81443 describes the entire panel, and you should not separately report the individual codes in addition to this code.

You can report CPT code 81412 for tests performed for Ashkenazi Jewish-associated disorders.

You can not bill CPT code 81443 together with CPT 81412.

Report CPT code 81257 for hemoglobin A testing if the test is performed separately.

You can use CPT code 81243 for FMR1 testing (if performed separately).

(If hemoglobin A testing is performed separately, use)

23. CPT Code 81445

CPT 81445 can be reported when a sequence analysis panel is performed by a lab analyst for the evaluation of at least five or a maximum of 50 genes that are related to solid organ cancers.

23.1 Description

The 81445 CPT code is officially defined by CPT and is described in the book as: “Targeted genomic sequence analysis panel, solid organ neoplasm, DNA analysis, and RNA analysis when performed, 5-50 genes (e.g., ALK, BRAF, CDKN2A, EGFR, ERBB2, KIT, KRAS, NRAS, MET, PDGFRA, PDGFRB, PGR, PIK3CA, PTEN, RET), interrogation for sequence variants and copy number variants or rearrangements, if performed.”

23.2 Procedure

The CPT 81445 procedure starts with a lab analyst taking a specimen from a patient (cells or tumor tissue), so he or she can perform a genomic sequence panel for 5-50 genes for analysis of tumor cells for common variations.

Then, the lab analyst uses a next-generation gene sequencer to determine the nucleotides in the DNA of the patient.

Although not limited to testing for a specific condition, clinicians may order CPT code 81445 as part of genetic counseling and evaluation of patients for susceptibility to certain severe, heritable conditions.

These conditions are common in people of Ashkenazi (German or Eastern European) Jewish descent, such as;

  • Cystic fibrosis is characterized by thick, sticky mucus that blocks pancreatic ducts and clogs the lungs; and
  • the conditions described by the CPT code 81443 procedure.

23.3 Billing Guidelines

Report CPT 81406 with CPT 81445 for copy number assessment by microarray.

CPT provides various other molecular pathology codes for tests involving several of the genes listed as examples in CPT code 81445.

You should not additionally report a code for a test that evaluates a single gene if the panel test includes that gene. For example:

  • CPT 81210 for BRAF;
  • CPT 81235 for EGFR, or
  • CPT 81275 for KRAS.

24. CPT Code 81448

CPT 81448 is another genomic sequence analysis panel CPT code that describes a test where a lab analyst evaluates the specimen of a patient of five or more peripheral–neuropathy–related genes.

24.1 Description

The 81448 CPT code procedure is officially defined by CPT as: “Hereditary peripheral neuropathies (e.g., Charcot-Marie-Tooth, spastic paraplegia), genomic sequence analysis panel, must include sequencing of at least five peripheral neuropathy-related genes (e.g., BSCL2, GJB1, MFN2, MPZ, REEP1, SPAST, SPG11, SPTLC1).”

24.2 Procedure

This procedure can be billed when a lab analyst uses the blood of a patient for genomic sequence analysis of five or more peripheral–neuropathy–related genes with a next-generation gene sequencer.

Although not limited to testing for a specific condition, clinicians may order the CPT code 81448 test to aid in the diagnosis of inherited peripheral neuropathies such as;

  • hereditary spastic paraplegia (HSP); or
  • Charcot–Marie–Tooth (CMT) [known as hereditary motor and sensory neuropathy (HMSN)].

Because mutations in the peripheral myelin protein 22 (PMP22) gene may commonly cause some of these conditions, clinicians may first order PMP22 testing and order CPT code 81448 testing only as a second–tier test.

Because symptoms of various forms of hereditary peripheral neuropathies overlap and because a broad range of genetic mutations may contribute to these conditions, a comprehensive genetic panel such as CPT code 81448 may help establish the diagnosis and genetic cause of the condition.

24.3 Billing Guidelines

CPT provides multiple other codes that describe individual gene sequence analyses that might be part of this panel, such as;

  • CPT 81403 for GJB1;
  • CPT 81405 for MPZ, REEP1;
  • CPT 81406 for BSCL2, MFN2, SPAST;
  • CPT 81407 for SPG11; and
  • CPT 81324 until CPT 81326 for PMP22.

CPT code 81488 describes the entire panel, and you should not separately report the individual codes in addition to this code.

25. CPT Code 81450

CPT 81450 can be used to report when a genomic sequence analysis panel is performed of at least five and with a maximum of 50 genes that are related to lymph or blood cancers. They are also known as hematolymphoid neoplasms.

25.1 Description

The 81450 CPT code’s descriptor is defined in the CPT book as: “Targeted genomic sequence analysis panel, hematolymphoid neoplasm or disorder, DNA analysis, and RNA analysis when performed, 5-50 genes (e.g., BRAF, CEBPA, DNMT3A, EZH2, FLT3, IDH1, IDH2, JAK2, KRAS, KIT, MLL, NRAS, NPM1, NOTCH1), interrogation for sequence variants, and copy number variants or rearrangements, or isoform expression or mRNA expression levels, if performed.”

25.2 Procedure

The lab analyst takes the patient’s specimen (for example, bone marrow aspirate) and performs a panel to analyze the patient’s DNA for common variants known to cause lymph and blood cancer.

The lab analyst uses a next-generation gene sequencer to look at the order of nucleotides in the patient’s DNA.

If performed, this procedure also includes RNA analysis. Suppose the lab test can evaluate different forms of RNA or protein and evaluate any of the genes in this test for sequence variants or copy number variants. The additional evaluation is also included in CPT 81450.

Although not limited to testing for a specific condition, clinicians may order this test to help evaluate hematolymphoid cancers to characterize the genetic mutation involved in the disease and help the clinician determine the appropriate treatment.

25.3 Billing Guidelines

CPT provides various other molecular pathology codes for tests involving several of the genes listed as examples in the 81450 CPT code panel.

You should not additionally report a code for a test that evaluates a single gene, such as;

  • CPT 81210 for BRAF;
  • CPT 81270 for JAK2;
  • CPT 81275 for KRAS, or
  • CPT 81245 for FLT3.

Bill CPT 81406 for copy number assessments by microarray.

26. CPT Code 81455

CPT 81455 may be used when 51 genes or more are evaluated by a genomic sequence analysis panel. The genes are related to solid organ cancers or to lymph or blood cancer and are also known as hematolymphoid neoplasms.

26.1 Description

The CPT book defines CPT code 81455 as: “Targeted genomic sequence analysis panel, solid organ or hematolymphoid neoplasm, DNA analysis, and RNA analysis when performed, 51 or greater genes (e.g., ALK, BRAF, CDKN2A, CEBPA, DNMT3A, EGFR, ERBB2, EZH2, FLT3, IDH1, IDH2, JAK2, KIT, KRAS, MLL, NPM1, NRAS, MET, NOTCH1, PDGFRA, PDGFRB, PGR, PIK3CA, PTEN, RET), interrogation for sequence variants and copy number variants or rearrangements if performed.”

26.2 Procedure

A genomic sequence analysis panel is performed by a lab analyst to analyze possible RNA or DNA specimens that are the cause of cancer.

The panel is done with next generation gene sequencer to look into the order of nucleotides in the DNA of a patient.

It is possible that the lab analyst tests different forms of RNA or protein for sequence or copy number variants.

CPT 81455 can help to evaluate hematolymphoid cancer or solid tissue tumors by characterizing the genetic mutation that is involved in the disease in order to choose the proper treatment.

26.3 Billing Guidelines

CPT provides various other molecular pathology codes for tests involving several of the genes listed as examples in the CPT code 81455 panel.

You should not additionally report a code for a test that evaluates a single gene, such as;

  • CPT 81210 for BRAF;
  • CPT 81235 for EGFR;
  • CPT 81270 for JAK2;
  • CPT 81275 for KRAS, or
  • CPT 81245 for FLT3.

27. CPT Code 81460

CPT 81460 can be billed when a lab analyst does a genomic sequence panel for the evaluation of genetic sequences of the complete mitochondrial genome.

The genes are related to muscle or nerve pathologies and are listed in the official description. Heteroplasmy detection is included in this procedure.

27.1 Description

The CPT book defines the descriptor of CPT code 81460 as: “Whole mitochondrial genome (e.g., Leigh syndrome, mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes [MELAS], myoclonic epilepsy with ragged-red fibers [MERFF], neuropathy, ataxia, and retinitis pigmentosa [NARP], Leber hereditary optic neuropathy [LHON]), genomic sequence, must include sequence analysis of entire mitochondrial genome with heteroplasmy detection.”

27.2 Procedure

This test also involves a genomic sequence panel by a lab analyst. He or she uses the blood of a patient for the panel of the mitochondrial genome and looks for heteroplasmy.

27.3 Billing Guidelines

CPT code 81460 describes gene sequencing of the entire mitochondrial DNA. For a test to evaluate whole mitochondrial genome duplication and deletion analysis, select CPT 81465 instead.

For gene analysis of nuclear-encoded mitochondrial DNA, select an appropriate code, such as CPT code 81440.

28. CPT Code 81465

Report CPT 81465 when a lab analyst performed a genomic sequence analysis panel for the evaluation of the whole mitochondrial genome to look for large deletions related to muscle or nerve pathologies. Heteroplasmy detection is included.

28.1 Description

The CPT book describes the 81465 CPT code as follows: “Whole mitochondrial genome large deletion analysis panel (e.g., Kearns-Sayre syndrome, chronic progressive external ophthalmoplegia), including heteroplasmy detection, if performed.”

28.2 Procedure

The 81465 CPT code procedure starts with a lab analyst taking blood from a patient. He or she uses that for a deletion analysis panel for the patient’s entire mitochondrial genome.

It is possible to detect the differences in mitochondrial DNA. This harbors mutations in certain mitochondria and is also called heteroplasmy.

This procedure can include an MLPA method (Multiplex Ligation dependent Probe Amplification) to help detect deletions and duplications in nucleotide sequences.

28.3 Billing Guidelines

CPT code 81465 describes a large deletion panel that evaluates the entire mitochondrial DNA. For a full genome sequencing of mitochondrial DNA, use CPT code 81460.

For gene analysis of nuclear-encoded mitochondrial DNA, select an appropriate code, such as CPT code 81440.

29. CPT Code 81470

CPT 81470 can be billed when a genomic sequence panel is used by a lab analyst for the evaluation of the specimen of the patient.

He or she evaluates the genetic sequences of 60 genes or more. The genes in the official description below are included and may relate to XLID (X–linked intellectual disability disorders).

29.1 Description

The manual from CPT describes CPT code 81470 as follows: “X-linked intellectual disability (XLID) (e.g., syndromic and non-syndromic XLID); genomic sequence analysis panel, must include sequencing of at least 60 genes, including ARX, ATRX, CDKL5, FGD1, FMR1, HUWE1, IL1RAPL, KDM5C, L1CAM, MECP2, MED12, MID1, OCRL, RPS6KA3, and SLC16A2.”

29.2 Procedure

This procedure is described by CPT 81470 and starts with a lab analyst taking a specimen (blood, for example) from a patient to perform a genomic sequence analysis of 60 genes or more with a next-generation gene sequencer.

Clinicians may order the 81470 CPT code test for genetic counseling and to aid in the diagnosis of certain hereditary intellectual disabilities linked to the X chromosome. The analysis may help distinguish between various genetic disorders, such as syndromic and non-syndromic XLID. 

29.3 Billing Guidelines

CPT code 81470 is similar to CPT code81471. Make sure that you distinguish these codes and the proper one, or report both if the lab analyst performs both procedures. 

30. CPT Code 81471

CPT 81471 may be used when a genomic sequence panel is performed for the evaluation of 60 genes or more. These genes are included in the official code descriptor and may be related to XLID (X–linked intellectual disability disorders).

30.1 Description

The official descriptor of CPT code 81471 can be found in the book of CPT and is as follows: “X-linked intellectual disability (XLID) (e.g., syndromic and non-syndromic XLID); duplication/deletion gene analysis, must include analysis of at least 60 genes, including ARX, ATRX, CDKL5, FGD1, FMR1, HUWE1, IL1RAPL, KDM5C, L1CAM, MECP2, MED12, MID1, OCRL, RPS6KA3, and SLC16A2.”

30.2 Procedure

The 81471 CPT code procedure also starts with a lab analyst using the blood (or other specimens) of a patient to perform deletion and duplication analysis of 60 genes or more.

The lab analyst might use the MLPA method for the detection of deletions and duplications in nucleotide sequences.

30.3 Billing Guidelines

CPT 81471 is often used for patients with a suspected X–linked intellectual disability disorder who have tested negative for mutations using the full gene sequencing test (CPT 81470).

Although most mutations associated with X–linked intellectual disability disorders will show up on the full gene sequence analysis, some patients have duplication or deletion mutations that normal sequencing methods don’t detect. 

CPT code 81470 is similar to CPT 81471. Distinguish them first to choose the right one or report both if both procedures are performed.

31. CPT Code 81479

CPT 81479 is the last genomic sequencing code and can be reported for molecular pathology procedures that are not specified by another code.

You can find the complete billing guide for the 81479 CPT code here.

References

https://www.cms.gov/medicare-coverage-database/view/article.aspx?articleId=57332

https://tuftshealthplan.com/documents/providers/guidelines/medical-necessity-guidelines/whole-genome-comm

https://www.blueshieldca.com/bsca/bsc/public/common/PortalComponents/provider/StreamDocumentServlet?fileName=PRV_GeneticCncrPnls.pdf

https://www.anthem.com/dam/medpolicies/abc/active/policies/pw_e000224.html

https://www.uhcprovider.com/content/dam/provider/docs/public/policies/medicaid-comm-plan/genetic-testing-cardiac-disease-cs.pdf

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