Is RNF10 p.Phe111= (c.333T>C) pathogenic?

RNF10 p.Phe111= (c.333T>C) is classified Likely benign in RNF10 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-07-16). Very rare (popmax 0.00502%, amr).

How common is RNF10 p.Phe111= (c.333T>C) in the general population?

RNF10 p.Phe111= (c.333T>C) is very rare (popmax 0.00502%, amr) (gnomAD).

RNF10 p.Phe111=

c.333T>C · rs1368935610 · VCV727629

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00502%, amr)

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 2.3	GERP -0.49, phastCons 1
Overall
CADD	8.758	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00502% Admixed American · 3/59,728 alleles

Filtering AF 0.00133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00067%

Overall 0.000186% 3/1,613,444 alleles · very rare exomes 3/1,461,140 · genomes 0/152,304 · 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: RNF10
Protein: p.Phe111=
Coding: c.333T>C
MANE Select: NM_014868
dbSNP: rs1368935610
Type: single nucleotide variant
Location: chr12:120546580 (GRCh38)
Gene constraint: LOEUF 0.519 · pLI 0.76 (gnomAD)
Structure: AlphaFold pLDDT 65.67
Residue 111: the 'disordered' region; the 'interaction with meox2' region

Full RNF10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

RNF10 p.Gly387Arg Benign ★★ same type
RNF10 p.Ala130Thr Uncertain significance ★ ⚠ same type
RNF10 p.Ala409Val Uncertain significance ★ ⚠ same type
RNF10 p.Ala723Thr Uncertain significance ★ ⚠ same type
RNF10 p.Ala771Pro Uncertain significance ★ ⚠ same type
RNF10 p.Arg378Trp Uncertain significance ★ ⚠ same type
RNF10 p.Arg499Cys Uncertain significance ★ ⚠ same type
RNF10 p.Arg525His 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/rnf10-p-phe111 (accessed [today's date]).

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