REV3L p.Ser142=
c.426C>T · rs761638789 · VCV3051042
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0105%, amr)
Conditions
1
REV3L-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.4 | GERP -1.1, phastCons 1 |
| Overall | ||
| CADD | 14.06 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0105%
Admixed American · 6/57,010 alleles
Filtering AF
0.00457%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00308%
Overall
0.00257%
41/1,596,704 alleles · ultra-rare
exomes 38/1,444,858 · genomes 3/151,846 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0105% | 9,502 |
| South Asian | 0.0035% | 28,600 |
| African / African-American | 0.00271% | 36,948 |
| European (non-Finnish) | 0.00238% | 41,933 |
| East Asian | 0.00227% | 44,066 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,826 |
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
- REV3L
- Protein
- p.Ser142=
- Coding
- c.426C>T
- MANE Select
- NM_001372078
- dbSNP
- rs761638789
- Type
- single nucleotide variant
- Location
- chr6:111405609 (GRCh38)
- Gene constraint
- LOEUF 0.261 · pLI 1.00 (gnomAD)
Disease context
REV3L-related disorder
Similar variants
- REV3L p.Ser532Thr Uncertain significance ⚠ same condition
- REV3L c.-4G>A Likely benign same condition
- REV3L p.Ala1143= Benign same condition
- REV3L p.Arg1970His Benign same condition
- REV3L p.Asp1812His Benign same condition
- REV3L p.Asp896= Likely benign same condition
- REV3L p.His193= Likely benign same condition
- REV3L p.His696Leu Likely benign same condition
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/rev3l-p-ser142 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown