Is DUSP11 p.Val173Met (c.517G>A) pathogenic?

DUSP11 p.Val173Met (c.517G>A) is classified Likely benign in DUSP11 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-06). AlphaMissense: likely benign (0.0531); Rare (popmax 0.105%, afr).

How common is DUSP11 p.Val173Met (c.517G>A) in the general population?

DUSP11 p.Val173Met (c.517G>A) is rare (popmax 0.105%, afr) (gnomAD).

What do computational predictors say about DUSP11 p.Val173Met (c.517G>A)?

AlphaMissense predicts likely benign (score 0.0531) — an in-silico prediction, not a clinical call.

DUSP11 p.Val173Met

c.517G>A · rs144123904 · VCV3086256

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0531 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.105%, afr)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Computational evidence

Protein change
AlphaMissense	0.0531	likely benign
REVEL	0.208	benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.9	GERP 0.93, phastCons 1
Regional constraint	o/e 1.01	unconstrained · MANE · 17 kb · p 0.86 · regional, not allelic
Overall
CADD	17.52	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 V220M vs ClinVar V173M) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.105% African / African-American · 79/74,968 alleles

Filtering AF 0.0866% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0797%

Overall 0.00639% 103/1,612,462 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.105%	949
Remaining individualsnot grpmax-eligible	0.00641%	15,606
Admixed American	0.00501%	19,953
South Asian	0.0044%	22,705
European (non-Finnish)	0.0011%	90,693

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: DUSP11
Protein: p.Val173Met
Coding: c.517G>A
MANE Select: NM_003584
dbSNP: rs144123904
Type: single nucleotide variant
Location: chr2:73767185 (GRCh38)
Gene constraint: LOEUF 1.286 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 69.34 · 3 PDB
Residue 173: the tyrosine-protein phosphatase domain

Full DUSP11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DUSP11 c.178-7G>C Benign ★★ same type
DUSP11 c.794+5C>G Benign ★★ same type
DUSP11 c.-118G>A Benign ★★ same type
DUSP11 c.-104G>T Uncertain significance ★ ⚠ same type
DUSP11 c.-108G>T Uncertain significance ★ ⚠ same type
DUSP11 c.-116G>A Uncertain significance ★ ⚠ same type
DUSP11 c.-117C>G Uncertain significance ★ ⚠ same type
DUSP11 c.-117C>T 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/dusp11-p-val173met (accessed [today's date]).

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