Summary & Overview
CPT 0213U: Whole Genome and Mitochondrial Comparator Analysis
CPT code 0213U is a Proprietary Laboratory Analyses (PLA) code for Variantyx Inc.’s Genomic Unity® Whole Genome Analysis – Comparator, a specialized laboratory test that sequences the whole genome and mitochondrial DNA of a relative to create a reference genome for comparison with a proband. This test supports evaluation of rare constitutional and genetic disorders by enabling analysts to distinguish inherited variation and improve interpretation of proband variants. Nationally, PLA codes like 0213U matter because they identify manufacturer- or lab-specific assays that can influence coverage determinations, claim adjudication, and genomic medicine workflows.
Key payers discussed include Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, and Medicare. Readers will find an overview of clinical context for using a comparator relative’s genome, typical sites of service, and the implications of PLA status for billing and payer review. The publication outlines benchmarks for utilization and payment where available, summarizes relevant policy considerations for payer coverage of proprietary genomic tests, and provides clinical context on how comparator sequencing can affect diagnostic yield in rare genetic disease evaluation. Data not available in the input will be noted where applicable.
Billing Code Overview
CPT code 0213U is a Proprietary Laboratory Analyses (PLA) code for the Genomic Unity® Whole Genome Analysis – Comparator offered by Variantyx Inc. The test performs whole genome sequencing including mitochondrial DNA analysis on a relative of a proband patient to create a reference genome sequence that can be compared to the proband’s genome to evaluate rare constitutional or genetic disorders.
Service Type: Whole genome and mitochondrial DNA comparative analysis (laboratory diagnostic test)
Typical Site of Service: Clinical diagnostic laboratory or specialized genomic testing laboratory; specimen collected in an outpatient clinic or medical office and analyzed at the performing laboratory
Clinical & Coding Specifications
Clinical Context
A proband (index) patient presents to a genetics clinic for evaluation of a suspected rare constitutional or genetic disorder after clinical features (developmental delay, congenital anomalies, unexplained multisystem disease, or a family history of a genetic condition) prompt comprehensive genomic testing. The genetics team orders a whole genome analysis for the proband and requests a comparative reference genome derived from an unaffected or affected relative to improve variant interpretation accuracy. A blood or saliva specimen is collected from the relative and sent to Variantyx Inc. for the Genomic Unity® Whole Genome Analysis – Comparator (0213U). The laboratory performs whole genome sequencing and mitochondrial DNA analysis on the relative to create a reference genome sequence. Bioinformatic comparison between the relative’s reference genome and the proband’s genome enables the lab analyst and clinical geneticist to refine variant calls, distinguish inherited from de novo variants, and improve diagnostic yield. Typical workflow steps include: ordering and consent, specimen collection from both proband and relative, sample accessioning at the originating lab, sequencing and analysis at Variantyx using the proprietary assay, reporting of comparator-informed variant interpretations, and return of results to the ordering genetics provider for clinical correlation and counseling.
Coding Specifications
| Modifier | Description | When to Use |
|---|---|---|
00 | Default/No modifier | Use when no specific modifier applies |
22 | Increased procedural services | Use when additional work beyond typical PLA reporting is documented and justified
26 | Professional component | Use when billing only the professional interpretation component separate from technical services
52 | Reduced services | Use when the test or analysis is partially completed and a reduced service is reported
53 | Discontinued procedure | Use when testing is started but halted for documented clinical reasons
62 | Two surgeons | Rarely used for lab procedures; applicable if two qualified laboratorians are required and policy allows
78 | Return to operating/procedure room for related procedure by same physician | Generally not applicable but included in PLA modifier list for institutional workflows
80 | Assistant surgeon | Not typically applicable to laboratory PLA testing; used if an assistant provider is reported for professional component where payer allows
82 | Assistant surgeon (when qualified resident not available) | Similar limited applicability to professional component reporting
TC | Technical component | Use when billing only the technical component (sequencing, data generation) separate from interpretation
QK | Qualified nonphysician lab interpretation (payment adjustment) | Use when a qualified nonphysician (e.g., PhD laboratory director) performs the interpretation and payor recognizes the modifier
QX | Advanced practice clinician billing with modifier QK | Use when both an APN/PA and a qualified nonphysician are involved and payor policy requires both modifiers
QY | Clinical laboratory services furnished by a Federal qualified health center (FQHC) | Use when applicable to payer policy for FQHCs
SH | Diagnostic service and technical component only | Use when only the technical component is provided by the reporting lab
| Taxonomy Code | Specialty | Notes |
|---|---|---|
207Q00000X | Clinical Molecular Genetics Laboratory | Labs performing whole genome and mitochondrial DNA analysis |
207L00000X | Clinical Laboratory | General laboratory specialty performing sequencing and technical testing
208000000X | Clinical Geneticist | Ordering and interpreting clinician tying comparator results to clinical diagnosis
363A00000X | Molecular Pathology | Expertise in genomic variant interpretation and reporting
207R00000X | Diagnostic Radiology (not typical) | Data not typical; included only if institutional workflows require radiology involvement
Related Diagnoses
| ICD-10 Code | Description | Clinical Relevance |
|---|---|---|
Q87.8 | Other specified congenital malformation syndromes affecting multiple systems | Used when congenital anomalies suggest a syndromic genetic disorder requiring whole genome comparator analysis |
R62.0 | Delayed milestone in childhood | Developmental delay in pediatrics prompting comprehensive genomic evaluation
G40.9 | Epilepsy, unspecified | Genetic epilepsies often require genome analysis and family comparator testing for variant interpretation
F84.0 | Autistic disorder | Autism spectrum disorders with suspected genetic etiology where familial reference genomes can aid interpretation
Z14.8 | Genetic carrier and genetic susceptibility to other diseases | Used when assessing familial variants and carrier status with comparator sequencing
Related CPT Codes
| CPT Code | Description | Relationship to This Procedure |
|---|---|---|
81275 | Exome sequencing, interpretation and report (proband) | Performed when trio or proband exome sequencing is ordered; may precede or accompany whole genome comparator analysis |
81415 | Exome sequencing, clinical (interpretation) | Alternative comprehensive sequencing code used in clinical genomic workflows when exome rather than genome is performed
88291 | Microdissection for molecular testing | May be used when tumor or tissue enrichment is required prior to genomic sequencing (if applicable)
81599 | Unlisted molecular pathology procedure | Used rarely for novel or proprietary assays prior to PLA assignment; historical relevance
0106U | (Example PLA) — other proprietary genomic assays | Other PLA-level proprietary genomic test codes may be billed alongside or in parallel for complementary analyses