Is DUSP13B p.Arg318Trp (c.952C>T) pathogenic?

DUSP13B p.Arg318Trp (c.952C>T) is classified Uncertain significance in DUSP13B (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-17). AlphaMissense: likely benign (0.1666); Ultra-rare (popmax 0.016%, afr).

How common is DUSP13B p.Arg318Trp (c.952C>T) in the general population?

DUSP13B p.Arg318Trp (c.952C>T) is ultra-rare (popmax 0.016%, afr) (gnomAD).

What do computational predictors say about DUSP13B p.Arg318Trp (c.952C>T)?

AlphaMissense predicts likely benign (score 0.1666) — an in-silico prediction, not a clinical call.

DUSP13B p.Arg318Trp

c.952C>T · rs374552296 · VCV2204198

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1666 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.016%, afr)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.1666	likely benign
REVEL	0.632	indeterminate
SaProt	LLR -11.75	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.3	GERP -3.2, phastCons 1
Regional constraint	o/e 1.08	unconstrained · MANE · 937 bp · p 0.38 · regional, not allelic
Overall
CADD	29.6	PHRED · no single calibrated threshold — expert panels disagree

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM R182W vs ClinVar R318W) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.016% African / African-American · 12/75,038 alleles

Filtering AF 0.0092% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00721%

Overall 0.00149% 24/1,614,148 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.016%	6,253
South Asian	0.00329%	30,361
East Asian	0.00223%	44,866
Admixed American	0.00167%	60,028
European (non-Finnish)	0.000593%	168,576

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: DUSP13B
Protein: p.Arg318Trp
Coding: c.952C>T
MANE Select: NM_001363514
dbSNP: rs374552296
Type: single nucleotide variant
Location: chr10:75094729 (GRCh38)
Structure: AlphaFold pLDDT 90.56 · 2 PDB

Full DUSP13B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DUSP13B p.Arg318Gln Uncertain significance ★ ⚠ same residue
DUSP13B p.Pro161Gln Uncertain significance ★★ ⚠ same type
DUSP13B c.582-1G>T Uncertain significance ★ same type
DUSP13B p.Ala165Thr Uncertain significance ★ ⚠ same type
DUSP13B p.Ala256Asp Uncertain significance ★ ⚠ same type
DUSP13B p.Ala262Gly Uncertain significance ★ ⚠ same type
DUSP13B p.Ala287Asp Uncertain significance ★ ⚠ same type
DUSP13B p.Arg146Gln 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/dusp13b-p-arg318trp (accessed [today's date]).

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