RNF13 p.Ala111=
c.333A>G · rs1400786437 · VCV2787910
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00468%, 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 -0.09 | GERP -3.5, phastCons 0.009 |
| Overall | ||
| CADD | 8.228 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00468%
South Asian · 4/85,540 alleles
Filtering AF
0.00159%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000936%
Overall
0.000315%
5/1,585,452 alleles · very rare
exomes 5/1,435,290 · genomes 0/150,162 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00468% | 21,385 |
| European (non-Finnish) | 8.57e-05% | 1,166,608 |
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
- RNF13
- Protein
- p.Ala111=
- Coding
- c.333A>G
- MANE Select
- NM_183381
- dbSNP
- rs1400786437
- Type
- single nucleotide variant
- Location
- chr3:149895484 (GRCh38)
- Gene constraint
- LOEUF 0.813 · pLI 0.59 (gnomAD)
- Structure
- AlphaFold pLDDT 74.65 · 2 PDB
- Residue 111
- the pa domain
Similar variants
- RNF13 p.Ala378Val Uncertain significance ★★ ⚠ same type
- RNF13 p.Arg212Thr Uncertain significance ★★ ⚠ same type
- RNF13 p.Arg215Lys Uncertain significance ★★ ⚠ same type
- RNF13 p.Arg219His Uncertain significance ★★ ⚠ same type
- RNF13 p.Arg98Gly Uncertain significance ★★ ⚠ same type
- RNF13 p.Asn346Ser Uncertain significance ★★ ⚠ same type
- RNF13 p.Glu181Gln Uncertain significance ★★ ⚠ same type
- RNF13 p.Ile137Val 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/rnf13-p-ala111 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown