Is RNF13 p.Lys232= (c.696G>A) pathogenic?

RNF13 p.Lys232= (c.696G>A) is classified Likely benign in RNF13 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-06). Very rare (popmax 0.00265%, eas).

How common is RNF13 p.Lys232= (c.696G>A) in the general population?

RNF13 p.Lys232= (c.696G>A) is very rare (popmax 0.00265%, eas) (gnomAD).

RNF13 p.Lys232=

c.696G>A · VCV3680285

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00265%, eas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.156	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.1	GERP -0.16, phastCons 1
Overall
CADD	5.776	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00265% East Asian · 1/37,714 alleles

Overall 7.35e-05% 1/1,360,638 alleles · very rare exomes 1/1,208,452 · genomes 0/152,186 · joint denominator

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.Lys232=
Coding: c.696G>A
MANE Select: NM_183381
Type: single nucleotide variant
Location: chr3:149921223 (GRCh38)
Gene constraint: LOEUF 0.813 · pLI 0.59 (gnomAD)
Structure: AlphaFold pLDDT 74.65 · 2 PDB

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

Similar variants

RNF13 p.Lys232Asn Uncertain significance ★ ⚠ same residue
RNF13 p.Lys232Glu 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

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-lys232 (accessed [today's date]).

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