Genetic testing plays a critical role in diagnosing hereditary conditions, guiding treatment decisions, and predicting disease risks. As technology advances, medical billing and coding must keep pace. The 2025 CPT code updates introduce several new genetic testing codes, impacting medical practices, laboratories, and insurance reimbursement.
If you handle medical coding, billing, or revenue cycle management, understanding these updates is crucial for accurate claims submission and compliance. This guide covers new 2025 CPT codes for genetic testing, billing guidelines, and reimbursement strategies.
## Overview of 2025 CPT Code Changes for Genetic Testing
Current Procedural Terminology (CPT) codes are used in medical billing to report diagnostic procedures, including genetic tests. The genetic testing CPT codes are divided into three main categories:
**Tier 1 Molecular Pathology Codes**– Standardized tests for commonly analyzed genes, such as BRCA1/BRCA2. **Tier 2 Molecular Pathology CPT Codes**– Used for less common genetic markers and panel-based tests. **Proprietary Laboratory Analyses (PLA) Codes**– Lab-specific genetic tests used by individual providers. **Genomic Sequencing Procedure (GSP) Codes**– Codes assigned to next-generation sequencing (NGS) and panel-based genomic testing.
Each year, the CPT code set is updated to reflect advancements in medical services. The 2025 CPT code update includes new codes for genetic and molecular testing, particularly in:
– Proprietary Laboratory Analyses (PLA) Codes
– Molecular Diagnostics
– Hereditary Testing
These updates help healthcare providers bill correctly for genetic testing services, ensuring faster reimbursements and fewer claim denials.
Scenario:
Handling Genetic Test Claim Denials
A clinic submits a genetic test claim using an outdated CPT code, leading to a denial from the payer. The billing team reviews the updated 2025 CPT codes, resubmits the claim with proper documentation, and successfully secures reimbursement. Lesson: Always verify new CPT codes before submitting claims to avoid revenue loss.
## 2025 Optimized CPT Coding Guide for Molecular Pathology
The American Medical Association (AMA) has introduced 420 updates to the CPT code set, including 270 new codes, 112 deletions, and 38 revisions. Notably, 37% of the new codes pertain to proprietary laboratory analyses, primarily focusing on novel genetic testing.
|Code|Description|
|–|–|
|81105|HPA-1 genotyping|
|81106|HPA-2 genotyping|
|81107|HPA-3 genotyping|
|81108|HPA-4 genotyping|
|81109|HPA-5 genotyping|
|81110|HPA-6 genotyping|
|81111|HPA-9 genotyping|
|81112|HPA-15 genotyping|
|81120|IDH1 common variants|
|81121|IDH2 common variants|
|81161|DMD duplication/deletion analysis|
|81162|BRCA1 & BRCA2 full sequencing and del/dup analysis|
|81163|BRCA1 & BRCA2 full sequencing analysis|
|81164|BRCA1 & BRCA2 full del/dup analysis|
|81165|BRCA1 full sequencing analysis|
|81166|BRCA1 full del/dup analysis|
|81167|BRCA2 full del/dup analysis|
|81168|CCND1/IGH translocation analysis|
|81170|ABL1 gene analysis|
|81171|AFF2 gene analysis for abnormal alleles|
|81172|AFF2 gene analysis for allele characterization|
|81173|AR gene full sequencing|
|81174|AR gene known familial variant analysis|
|81175|ASXL1 full gene sequencing|
|81176|ASXL1 targeted sequencing analysis|
|81177|ATN1 gene analysis for abnormal alleles|
|81178|ATXN1 gene analysis for abnormal alleles|
|81179|ATXN2 gene analysis for abnormal alleles|
|81180|ATXN3 gene analysis for abnormal alleles|
|81181|ATXN7 gene analysis for abnormal alleles|
|81182|ATXN8OS gene analysis for abnormal alleles|
|81183|ATXN10 gene analysis for abnormal alleles|
|81184|CACNA1A gene analysis for abnormal alleles|
|81185|CACNA1A full gene sequencing|
|81186|CACNA1A gene known familial variant analysis|
|81187|CNBP gene analysis for abnormal alleles|
|81188|CSTB gene analysis for abnormal alleles|
|81189|CSTB full gene sequencing|
|81190|CSTB known familial variant analysis|
|81191|NTRK1 translocation analysis|
|81192|NTRK2 translocation analysis|
|81193|NTRK3 translocation analysis|
|81194|NTRK translocation analysis|
|81195|Cytogenomic genome-wide analysis for hematologic malignancies|
|81200|BCR/ABL1 translocation analysis|
|81201|BCR/ABL1 translocation analysis, minor breakpoint|
|81202|BCR/ABL1 translocation analysis, other breakpoint|
|81203|BRAF gene analysis, V600 variants|
|81204|EGFR gene analysis, common variants|
|81205|EGFR gene analysis, T790M variant|
|81206|EGFR gene analysis, resistance variants|
|81207|EGFR gene analysis, uncommon variants|
|81208|FLT3 gene analysis, common variants|
|81209|JAK2 gene analysis, V617F variant|
|81210|JAK2 gene analysis, other variants|
|81218|KRAS gene analysis, common variants|
|81219|KRAS gene analysis, other variants|
|81225|NPM1 gene analysis, common variants|
|81226|NRAS gene analysis, common variants|
|81230|RUNX1 gene full sequencing analysis|
|81231|RUNX1 gene targeted sequencing analysis|
|81235|TERT gene analysis|
|81240|TP53 gene full sequencing analysis|
|81241|TP53 gene known familial variant analysis|
|81250|UGT1A1 gene analysis|
|81255|VKORC1 gene analysis|
|81256|CYP2C19 gene analysis|
|81257|CYP2D6 gene analysis|
|81258|CYP2C9 gene analysis|
|81259|CYP2C cluster gene analysis|
|81265|HFE gene analysis for common variants|
|81266|HFE gene analysis for known familial variant|
|81267|HLA class I typing|
|81268|HLA class II typing|
|81270|HLA-B*5701 allele analysis|
|81272|HLA-DQB1 typing|
|81275|HLA-DRB1 typing|
|81280|CFTR gene analysis, common variants|
|81281|CFTR gene analysis, known familial variant|
|81282|CFTR gene full sequencing analysis|
|81283|CFTR gene del/dup analysis|
|81290|MGMT gene analysis|
|81291|MLH1 gene analysis, common variants|
|81292|MLH1 gene full sequencing|
|81293|MLH1 gene known familial variant|
|81294|MLH1 gene del/dup analysis|
|81295|MSH2 gene full sequencing|
|81296|MSH2 gene known familial variant|
|81297|MSH2 gene del/dup analysis|
|81298|MSH6 gene full sequencing|
|81299|MSH6 gene known familial variant|
|81300|MSH6 gene del/dup analysis|
|81301|PMS2 gene full sequencing|
|81302|PMS2 gene known familial variant|
|81303|PMS2 gene del/dup analysis|
|81310|NTRK fusion analysis|… ### Gene-Specific Code Selection
Code selection depends on the specific gene (s) being analyzed. Codes for gene variant testing use common variant names. While the listed variants are typically included in the test, this list is not exhaustive. Any additional variants of the same gene included in the analysis are part of the procedure and should not be reported separately.
Full gene sequencing should not be reported using variant-specific codes unless the CPT code explicitly includes “full gene sequence” in its description…. ### Tier 1 and Tier 2 Molecular Pathology Codes
**Tier 1 codes**apply to tests for a specific gene or Human Leukocyte Antigen (HLA) locus. **Tier 2 codes (81400-81408)**cover molecular pathology procedures not listed in Tier 1 and typically represent lower-volume or rare disease testing. These codes should be used only when necessary and as specified in coding and billing policies…. ### Genomic Sequencing Profiles (GSP)
When a genomic sequencing test includes genes listed under multiple code descriptors, the most specific code for the primary disorder should be reported. Submitting multiple codes for the same gene will result in claim rejection or denial…. ## Frequently Asked Questions
##
How many genes does CPT code 81408 test for?
CPT code 81408 pertains to molecular pathology procedures involving the analysis of specific genes associated with certain conditions. The exact number of genes tested under this code can vary, as it includes tests for rare genetic disorders. For precise information, it’s essential to consult the latest CPT code descriptions or relevant medical billing resources…. ##
What is CPT code 81479?
CPT code 81479 is designated for “Unlisted molecular pathology procedures.” It is used when a molecular pathology test doesn’t have a specific CPT code assigned. This code ensures that unique or less common genetic tests are appropriately billed, even in the absence of a designated code.