Is DRC3 p.Arg142Trp (c.424C>T) pathogenic?

DRC3 p.Arg142Trp (c.424C>T) is classified Uncertain significance in DRC3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-08). AlphaMissense: likely benign (0.0941); Very rare (popmax 0.00933%, afr).

How common is DRC3 p.Arg142Trp (c.424C>T) in the general population?

DRC3 p.Arg142Trp (c.424C>T) is very rare (popmax 0.00933%, afr) (gnomAD).

What do computational predictors say about DRC3 p.Arg142Trp (c.424C>T)?

AlphaMissense predicts likely benign (score 0.0941) — an in-silico prediction, not a clinical call.

DRC3 p.Arg142Trp

c.424C>T · VCV4662105

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0941 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00933%, afr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0941	likely benign
REVEL	0.075	moderately benign-leaning
SaProt	LLR -12.63	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Pangolin	Δ0.21	gain · loss 0.00 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP 0.25	GERP 0.058
Overall
CADD	22.6	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00933% African / African-American · 7/75,032 alleles

Filtering AF 0.00437% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00308%

Overall 0.00353% 57/1,613,806 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00933%	10,719
Remaining individualsnot grpmax-eligible	0.0048%	20,827
European (non-Finnish)	0.00381%	26,219
South Asian	0.0022%	45,530

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: DRC3
Protein: p.Arg142Trp
Coding: c.424C>T
MANE Select: NM_133180 · reported on NM_031294
Type: single nucleotide variant
Location: chr17:17988078 (GRCh38)
Structure: AlphaFold pLDDT 75.86 · 2 PDB
Residue 142: the ptb domain

Full DRC3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DRC3 p.Ala201Val Uncertain significance ★ ⚠ same type
DRC3 p.Ala221Thr Uncertain significance ★ ⚠ same type
DRC3 p.Ala228Val Uncertain significance ★ ⚠ same type
DRC3 p.Ala239Thr Uncertain significance ★ ⚠ same type
DRC3 p.Arg120Gln Uncertain significance ★ ⚠ same type
DRC3 p.Arg191Gln Uncertain significance ★ ⚠ same type
DRC3 p.Arg192Cys Uncertain significance ★ ⚠ same type
DRC3 p.Arg192His 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/drc3-p-arg142trp (accessed [today's date]).

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