Is RNF13 p.Val286= (c.858T>C) pathogenic?

RNF13 p.Val286= (c.858T>C) is classified Likely benign in RNF13 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-02). Absent from gnomAD v4.1.

How common is RNF13 p.Val286= (c.858T>C) in the general population?

RNF13 p.Val286= (c.858T>C) is absent from gnomAD v4.1 (gnomAD).

RNF13 p.Val286=

c.858T>C · rs2473635120 · VCV2759550

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.079	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.47	GERP 0.61, phastCons 1
Overall
CADD	7.748	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: RNF13
Protein: p.Val286=
Coding: c.858T>C
MANE Select: NM_183381
dbSNP: rs2473635120
Type: single nucleotide variant
Location: chr3:149960816 (GRCh38)
Gene constraint: LOEUF 0.813 · pLI 0.59 (gnomAD)
Structure: AlphaFold pLDDT 74.65 · 2 PDB
Residue 286: a UniProt-annotated variant site (found in a tumor sample; uncertain significance; abolished ability to regulate protein trafficking and localization); a β-strand; the 'disordered' region

Full RNF13 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

RNF13 p.Val286Ala Uncertain significance ★ ⚠ same residue
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

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-val286 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown