Is RFWD3 p.Pro262= (c.786C>T) pathogenic?

RFWD3 p.Pro262= (c.786C>T) is classified Likely benign in RFWD3 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-29). Absent from gnomAD v4.1.

How common is RFWD3 p.Pro262= (c.786C>T) in the general population?

RFWD3 p.Pro262= (c.786C>T) is absent from gnomAD v4.1 (gnomAD).

RFWD3 p.Pro262=

c.786C>T · rs1960391385 · VCV2020312

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.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.11
Overall
CADD	4.824	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: RFWD3
Protein: p.Pro262=
Coding: c.786C>T
MANE Select: NM_018124
dbSNP: rs1960391385
Type: single nucleotide variant
Location: chr16:74649138 (GRCh38)
Gene constraint: LOEUF 0.931 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 70.95 · 1 PDB
Residue 262: the 'disordered' region

Full RFWD3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

RFWD3 p.Pro262His Uncertain significance ★ ⚠ same residue
RFWD3 p.Ala22Pro Uncertain significance ★★ ⚠ same type
RFWD3 p.Ala231Pro Uncertain significance ★★ ⚠ same type
RFWD3 p.Ala244Val Uncertain significance ★★ ⚠ same type
RFWD3 p.Ala24Val Uncertain significance ★★ ⚠ same type
RFWD3 p.Ala372Thr Uncertain significance ★★ ⚠ same type
RFWD3 p.Ala447Gly Uncertain significance ★★ ⚠ same type
RFWD3 p.Ala581Gly 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/rfwd3-p-pro262 (accessed [today's date]).

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