--- title: "ABCA4 R2139W (c.6415C>T, rs61750653) | Dante Labs" description: "ClinVar classifies ABCA4 R2139W as Pathogenic (reviewed by expert panel). Where it sits in the genome, its predicted effect, and the Genome Test reports that look at it." url: "https://dantelabs.com/genes/abca4/variants/r2139w" --- 1. [Genes](https://dantelabs.com/genes) 2. [ABCA4](https://dantelabs.com/genes/abca4) 3. ABCA4 R2139W Variant # ABCA4 R2139W NM_000350.3(ABCA4):c.6415C>T (p.Arg2139Trp) Also known as - p.Arg2139Trp - p.R2139W - rs61750653 * ClinVar classification Pathogenic * Review status 3 stars out of 4 reviewed by expert panel * Last evaluated 5 December 2025 * Expert panel ClinGen ABCA4 Variant Curation Expert Panel, Clingen Data current to ClinVar release 2026-10-12 · Dante Labs data release 2026.10.16-c6eea6bf Facts last changed 16 October 2026 ## Summary R2139W is a missense variant in ABCA4: it changes a single amino acid in the protein the gene encodes. ClinVar classifies it as pathogenic for ABCA4-Related Retinopathy (reviewed by expert panel). ## ClinVar classifications | Condition | Classification | Review status | Submissions | Last evaluated | | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------- | ----------------------------------------- | ------------ | --------------- | | [ABCA4-Related Retinopathy](https://dantelabs.com/conditions/stargardt-disease) [ClinVar VCV000099458 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/clinvar/variation/99458/) | Pathogenic | 3 stars out of 4 reviewed by expert panel | 1 submission | 5 December 2025 | Classifications as ClinVar records them in release 2026-10-12. ClinVar updates them as evidence is reviewed. ## Where it lies in ABCA4 R2139W lies in exon 47 of the 50 in ABCA4's MANE Select transcript, NM_000350.3. [ABCA4 variants in exon 47 →](https://dantelabs.com/genes/abca4/variants?exon=47) [ABCA4's gene diagram →](https://dantelabs.com/genes/abca4#gene-structure) ## Molecular details | Gene | [ABCA4](https://dantelabs.com/genes/abca4) | | --------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------- | | Transcript | NM_000350.3 MANE Select | | Coding DNA change (HGVS c.) | c.6415C>T | | Protein change (HGVS p.) | p.Arg2139Trp p.R2139W | | Predicted consequence | Missense [missense_variant (opens in a new tab)](https://purl.obolibrary.org/obo/SO_0001583) | | Predicted impact | Moderate | | Position (GRCh38) | chr1:94000900 G>A | | Position (GRCh37) | chr1:94466456 G>A | | dbSNP ID | [rs61750653 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/snp/rs61750653) | | ClinVar Variation ID | [VCV000099458 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/clinvar/variation/99458/) | | ClinVar Allele ID | 105347 | | ClinGen Allele Registry ID | [CA227402 (opens in a new tab)](https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA227402) | | ClinVar name | NM_000350.3(ABCA4):c.6415C>T (p.Arg2139Trp) | ## ABCA4 R2139W in other databases - [ClinVar VCV000099458 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/clinvar/variation/99458/) - [dbSNP rs61750653 (opens in a new tab)](https://www.ncbi.nlm.nih.gov/snp/rs61750653) - [ClinGen Allele Registry CA227402 (opens in a new tab)](https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA227402) - [gnomAD 1-94000900-G-A (opens in a new tab)](https://gnomad.broadinstitute.org/variant/1-94000900-G-A?dataset=gnomad_r4) - [Ensembl rs61750653 (opens in a new tab)](https://www.ensembl.org/Homo_sapiens/Variation/Explore?v=rs61750653) ## Reports that look at this variant (1) These Genome Test condition reports include R2139W among the variants they look at. | Report | Conditions | Inheritance | | ----------------------------------------------------------------------- | ------------------------- | ------------------- | | [Stargardt Disease](https://dantelabs.com/conditions/stargardt-disease) | ABCA4-Related Retinopathy | Autosomal recessive | ## Other variants in ABCA4 - [A960Dfs\*17 Pathogenic 3 stars out of 4](https://dantelabs.com/genes/abca4/variants/a960dfs17) - [A967V Likely pathogenic 3 stars out of 4](https://dantelabs.com/genes/abca4/variants/a967v) - [A1773V Pathogenic 3 stars out of 4](https://dantelabs.com/genes/abca4/variants/a1773v) - [A1791Gfs\*9 Pathogenic 3 stars out of 4](https://dantelabs.com/genes/abca4/variants/a1791gfs9) - [c.1A>G Pathogenic 3 stars out of 4](https://dantelabs.com/genes/abca4/variants/c-1a-g) - [c.3G>T Pathogenic 3 stars out of 4](https://dantelabs.com/genes/abca4/variants/c-3g-t) - [c.1937+1G>A Pathogenic 3 stars out of 4](https://dantelabs.com/genes/abca4/variants/c-1937plus1g-a) - [c.3328+2T>A Pathogenic 3 stars out of 4](https://dantelabs.com/genes/abca4/variants/c-3328plus2t-a) - [c.3523-1G>A Pathogenic 3 stars out of 4](https://dantelabs.com/genes/abca4/variants/c-3523-1g-a) - [c.4253+43G>A Pathogenic 3 stars out of 4](https://dantelabs.com/genes/abca4/variants/c-4253plus43g-a) [All ABCA4 variants](https://dantelabs.com/genes/abca4/variants) ## Limitations This page describes publicly available information about a genetic variant. It is not a diagnosis, and it says nothing about whether you or anyone else carries this variant. Classifications come from ClinVar and change as new evidence is reviewed. A classification here may differ from the one in ClinVar today, or from the one a laboratory reports. Whole genome sequencing with short reads can miss or miscall some variants, particularly in repeated or highly similar stretches of DNA and in large insertions, deletions or rearrangements. If you have questions about a variant in your own results or in your family, talk to a genetic counsellor or your doctor. ## Sources & credits - Classifications from ClinVar (release 2026-10-12), National Center for Biotechnology Information. - Condition terms from the Mondo Disease Ontology (release 2026-10-06), used under CC BY 4.0. - Gene symbols and names from the HUGO Gene Nomenclature Committee (release 2026-10-16). - Allele identifiers from the ClinGen Allele Registry (release 2026-10-16-c4908f54). - Reference SNP identifiers from dbSNP (release b157), National Center for Biotechnology Information. - Gene–disease links from the Gene Curation Coalition, GenCC (release 2026-10-16). - Difficult regions from the Genome in a Bottle Consortium (release v3.6). - Transcripts from MANE (release v1.5), NCBI and EMBL-EBI. - Predicted consequences from mehari (release 0.11.0), with transcript models from cdot. - Built from Dante Labs data release 2026.10.16-c6eea6bf of 16 October 2026. ## Cite this page APA > Dante Labs. (16 October 2026). ABCA4 R2139W (c.6415C>T, rs61750653) (Version 2026.10.16-c6eea6bf). Retrieved 16 October 2026, from https\://dantelabs.com/genes/abca4/variants/r2139w Vancouver > Dante Labs. ABCA4 R2139W (c.6415C>T, rs61750653) \[Internet]. Version 2026.10.16-c6eea6bf. 16 October 2026 \[cited 16 October 2026]. Available from: https\://dantelabs.com/genes/abca4/variants/r2139w Download citation [RIS](https://dantelabs.com/genes/abca4/variants/r2139w/cite.ris) [BibTeX](https://dantelabs.com/genes/abca4/variants/r2139w/cite.bib) [CSL-JSON](https://dantelabs.com/genes/abca4/variants/r2139w/cite.json) ## Read your whole genome From $449 Free shipping · Results in 6–8 weeks [Explore the Genome Test](https://dantelabs.com/whole-genome-sequencing)