Is DUSP28 p.Tyr117Phe (c.350A>T) pathogenic?

DUSP28 p.Tyr117Phe (c.350A>T) is classified Uncertain significance in DUSP28 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-21). AlphaMissense: likely benign (0.1398); Absent from gnomAD v4.1.

How common is DUSP28 p.Tyr117Phe (c.350A>T) in the general population?

DUSP28 p.Tyr117Phe (c.350A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DUSP28 p.Tyr117Phe (c.350A>T)?

AlphaMissense predicts likely benign (score 0.1398) — an in-silico prediction, not a clinical call.

DUSP28 p.Tyr117Phe

c.350A>T · VCV4245558

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1398 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1398	likely benign
REVEL	0.71	pathogenic-leaning
SaProt	LLR -7.25	tolerated
⇒ REVEL calls this damaging; AlphaMissense and SaProt do not.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 5.4	GERP 0.31, phastCons 1
Regional constraint	o/e 1.38	unconstrained · MANE · 779 bp · p 4.4e-10 · regional, not allelic
Overall
CADD	22.3	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

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: DUSP28
Protein: p.Tyr117Phe
Coding: c.350A>T
MANE Select: NM_001282771 · reported on NM_001370465
Type: single nucleotide variant
Location: chr2:240561034 (GRCh38)

Full DUSP28 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/dusp28-p-tyr117phe (accessed [today's date]).

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