RNF13 p.Ser89=
c.267A>G · rs2108442188 · VCV1598524
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00145%, nfe)
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 -0.6 | GERP -4.6 |
| Overall | ||
| CADD | 4.748 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00145%
European (non-Finnish) · 17/1,172,948 alleles
Filtering AF
0.000883%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000722%
Overall
0.00112%
18/1,603,376 alleles · very rare
exomes 18/1,451,030 · genomes 0/152,346 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00145% | 68,997 |
| South Asian | 0.00111% | 89,954 |
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.Ser89=
- Coding
- c.267A>G
- MANE Select
- NM_183381
- dbSNP
- rs2108442188
- Type
- single nucleotide variant
- Location
- chr3:149872100 (GRCh38)
- Gene constraint
- LOEUF 0.813 · pLI 0.59 (gnomAD)
- Structure
- AlphaFold pLDDT 74.65 · 2 PDB
- Residue 89
- 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-ser89 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown