RNF13 p.Asp353=
c.1059T>C · rs199606748 · VCV1539072
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00666%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.077 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -3.8 |
| Overall | ||
| CADD | 0.167 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00666%
African / African-American · 5/75,064 alleles
Filtering AF
0.00255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00161%
Overall
0.000434%
7/1,614,214 alleles · very rare
exomes 4/1,461,860 · genomes 3/152,354 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00666% | 15,013 |
| European (non-Finnish) | 0.000169% | 590,009 |
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.Asp353=
- Coding
- c.1059T>C
- MANE Select
- NM_183381
- dbSNP
- rs199606748
- Type
- single nucleotide variant
- Location
- chr3:149961017 (GRCh38)
- Gene constraint
- LOEUF 0.813 · pLI 0.59 (gnomAD)
- Structure
- AlphaFold pLDDT 74.65 · 2 PDB
- Residue 353
- a UniProt-annotated variant site (found in a tumor sample; uncertain significance; abolished ability to regulate protein trafficking and localization); the 'disordered' region
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-asp353 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown