REV1 p.Ser117=
c.351C>T · VCV4577181
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00111%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.2 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 19.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00111%
South Asian · 1/90,368 alleles
Filtering AF
0.000124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9e-05%
Overall
0.000372%
6/1,610,748 alleles · very rare
exomes 5/1,458,648 · genomes 1/152,100 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00111% | 90,368 |
| European (non-Finnish) | 0.000424% | 235,813 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- REV1
- Protein
- p.Ser117=
- Coding
- c.351C>T
- MANE Select
- NM_016316
- Type
- single nucleotide variant
- Location
- chr2:99442469 (GRCh38)
- Gene constraint
- LOEUF 0.361 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 67.20 · 17 PDB
- Residue 117
- the brct domain; an α-helix
Similar variants
- REV1 p.Leu1131His Benign ★★ same type
- REV1 p.Ala335Thr Uncertain significance ★ ⚠ same type
- REV1 p.Ala494Val Uncertain significance ★ ⚠ same type
- REV1 p.Ala581Gly Uncertain significance ★ ⚠ same type
- REV1 p.Ala789Thr Uncertain significance ★ ⚠ same type
- REV1 p.Ala907Asp Uncertain significance ★ ⚠ same type
- REV1 p.Arg219Ser Uncertain significance ★ ⚠ same type
- REV1 p.Arg290Gln Uncertain significance ★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/rev1-p-ser117 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown