Is DUSP11 p.Ala306Thr (c.916G>A) pathogenic?

DUSP11 p.Ala306Thr (c.916G>A) is classified Uncertain significance in DUSP11 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-29). AlphaMissense: likely benign (0.0723); Absent from gnomAD v4.1.

How common is DUSP11 p.Ala306Thr (c.916G>A) in the general population?

DUSP11 p.Ala306Thr (c.916G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DUSP11 p.Ala306Thr (c.916G>A)?

AlphaMissense predicts likely benign (score 0.0723) — an in-silico prediction, not a clinical call.

DUSP11 p.Ala306Thr

c.916G>A · VCV3842883

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0723 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Computational evidence

Protein change
AlphaMissense	0.0723	likely benign
REVEL	0.027	moderately 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 -1.5	GERP -4.1
Regional constraint	o/e 1.01	unconstrained · MANE · 17 kb · p 0.86 · regional, not allelic
Overall
CADD	0.054	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM A353T vs ClinVar A306T) — verify the residue.

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: DUSP11
Protein: p.Ala306Thr
Coding: c.916G>A
MANE Select: NM_003584
Type: single nucleotide variant
Location: chr2:73762738 (GRCh38)
Gene constraint: LOEUF 1.286 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 69.34 · 3 PDB

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-ala306thr (accessed [today's date]).

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