Is RNF13 p.Ser157= (c.471T>C) pathogenic?

RNF13 p.Ser157= (c.471T>C) is classified Likely benign in RNF13 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-14). No allele count reported in gnomAD v4.1 (AN 1,529,032).

How common is RNF13 p.Ser157= (c.471T>C) in the general population?

RNF13 p.Ser157= (c.471T>C) is no allele count reported in gnomAD v4.1 (AN 1,529,032) (gnomAD).

RNF13 p.Ser157=

c.471T>C · rs924593862 · VCV2752400

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,529,032)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.21	GERP -2.5, phastCons 0.96
Overall
CADD	9.59	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,529,032). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: RNF13
Protein: p.Ser157=
Coding: c.471T>C
MANE Select: NM_183381
dbSNP: rs924593862
Type: single nucleotide variant
Location: chr3:149902133 (GRCh38)
Gene constraint: LOEUF 0.813 · pLI 0.59 (gnomAD)
Structure: AlphaFold pLDDT 74.65 · 2 PDB
Residue 157: the pa domain

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

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-ser157 (accessed [today's date]).

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