Top 20 molecular pathology procedure codes

Targeted molecular pathology testing is becoming more accessible to patients. There are over 220 Current Procedural Terminology (CPT) codes for these types of panels that guide the diagnosis and treatments for specific health conditions. Such testing is a proactive, rather than reactive, approach to healthcare.

How many molecular pathology tests are done each year?

Analysis of data from the Definitive Healthcare ClaimsMx product, breaks down molecular pathology medical procedure codes for the last two years. Between 2019 and 2020, the total number of molecular pathology claims decreased from nearly 450,000 to 371,000, potentially due to delays of care during the COVID-19 pandemic. The table below lists the molecular pathology procedure codes with the highest number of claims in 2020.

Molecular pathology procedure codes with most claims in 2020

Rank CPT code CPT code description Total procedures 2020 Total procedures 2019
1 81220 CFTR (cystic fibrosis transmembrane conductance regulator) (eg, cystic fibrosis) gene analysis; common variants (eg, ACMG/ACOG guidelines) 32,931 38,981
2 81241 F5 (coagulation factor V) (eg, hereditary hypercoagulability) gene analysis, Leiden variant 21,663 27,939
3 81240 F2 (prothrombin, coagulation factor II) (eg, hereditary hypercoagulability) gene analysis, 20210G>A variant 18,200 23,426
4 81206 BCR/ABL1 (t(9;22)) (eg, chronic myelogenous leukemia) translocation analysis; major breakpoint, qualitative or quantitative 18,118 21,531
5 81270 JAK2 (Janus kinase 2) (eg, myeloproliferative disorder) gene analysis, p.Val617Phe (V617F) variant 14,845 18,283
6 81329 SMN1 (Survival of motor neuron 1, telomeric) (eg, spinal muscular atrophy) gene analysis; doage/deletion analysis (eg, carrier testing), includes SMN2 (Survival of motor neuron 2, centromeric) analysis, if performed 13,320 9,632
7 81243 FMR1 (fragile X mental retardation 1) (eg, fragile X mental retardation) gene analysis; evaluation to detect abnormal (eg, expanded) alleles 10,707 13,462
8 81373 HLA Class I typing, low resolution (eg, antigen equivalents); one locus (eg, HLA-A, -B, or -C), each 9,788 3,161
9 81207 BCR/ABL1 (t(9;22)) (eg, chronic myelogenous leukemia) translocation analysis; minor breakpoint, qualitative or quantitative 9,304 10,665
10 81400 Molecular pathology procedure, Level 1 9,120 5,055
11 81268 Chimerism (engraftment) analysis, post transplantation specimen (eg, hematopoietic stem cell), includes comparison to previously performed baseline analyses; with cell selection (eg, CD3, CD33), each cell type 8,756 8,367
12 81267 Chimerism (engraftment) analysis, post transplantation specimen (eg, hematopoietic stem cell), includes comparison to previously performed baseline analyses; without cell selection 8,162 8,433
13 81371 HLA Class I and II typing, low resolution (eg, antigen equivalents); HLA-A, -B, and -DRB1 (eg, verification typing) 8,034 1,410
14 81256 HFE (hemochromatosis) (eg, hereditary hemochromatosis) gene analysis, common variants (eg, C282Y, H63D) 7,989 9,724
15 81382 HLA Class II typing, high resolution (ie, alleles or allele groups); one locus (eg, HLA-DRB1, -DRB3/4/5, -DQB1, -DQA1, -DPB1, or -DPA1), each 7,904 8,929
16 81379 HLA Class I typing, high resolution (ie, alleles or allele groups); complete (ie, HLA-A, -B, and -C) 7,868 1,681
17 81229 Cytogenomic (genome-wide) analysis for constitutional chromosomal abnormalities; interrogation of genomic regions for copy number and single nucleotide polymorphism (SNP) variants, comparative genomic variants, comparative genomic hybridization (CGH) microarray analysis 7,435 9,615
18 81210 BRAF (B-Raf proto-oncogene, serine/threonine kinase) (eg, colon cancer, melanoma), gene analysis, V600 variant(s) 5,051 6,891
19 81291 MTHFR (5,10-methylenetetrahydrofolate reductase) (eg, hereditary hypercoagulability) gene analysis, common variants (eg, 677T, 1298C) 5,046 7,790
20 81402 Molecular pathology procedure, Level 3 4,697 3,782

Fig. 1 Data from the Definitive Healthcare ClaimsMx product for calendar year 2019 and 2020. Commercial claims data is sourced from multiple medical claims clearinghouses in the United States and updated monthly. Data accurate as of October 2021.


Which molecular pathology tests have the highest number of claims?

Common uses for molecular pathology testing are for evaluating inherited conditions and oncology. Tests for cystic fibrosis (81220), hereditary hypercoagulability (81241 and 81240), chronic myelogenous leukemia (81206) and myeloproliferative disorder (81270) are the most performed molecular pathology tests. While many of the top molecular pathology procedures codes had fewer overall claims in 2020 compared to 2019, the same codes appear in the same top five rank in both years.

In addition to diagnosing types of and risk factors for certain types of cancer, molecular pathology plays a role in cancer treatment. Three HLA typing codes (81373: HLA Class I typing, low resolution, 81371: HLA Class I and II typing, low resolution and 81379: HLA Class I typing, high resolution) each had over 6,000 additional claims in 2020 compared to 2019. These codes relate to stem cell and bone marrow transplants and testing for treating patients with cancer.

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