Is DUSP28 p.Arg122Cys (c.364C>T) pathogenic?

DUSP28 p.Arg122Cys (c.364C>T) is classified Uncertain significance in DUSP28 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-07). AlphaMissense: likely benign (0.3); Very rare (popmax 0.00226%, amr).

How common is DUSP28 p.Arg122Cys (c.364C>T) in the general population?

DUSP28 p.Arg122Cys (c.364C>T) is very rare (popmax 0.00226%, amr) (gnomAD).

What do computational predictors say about DUSP28 p.Arg122Cys (c.364C>T)?

AlphaMissense predicts likely benign (score 0.3) — an in-silico prediction, not a clinical call.

DUSP28 p.Arg122Cys

c.364C>T · VCV3274073

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00226%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
AlphaMissense	0.3	likely benign
REVEL	0.285	benign-leaning
SaProt	LLR -9.39	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 1.2	GERP 0.17, phastCons 1
Regional constraint	o/e 1.38	unconstrained · MANE · 779 bp · p 4.4e-10 · regional, not allelic
Overall
CADD	23.1	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.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00226% Admixed American · 1/44,300 alleles

Overall 0.000133% 2/1,508,994 alleles · very rare exomes 0/1,356,802 · genomes 2/152,192 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00226%	44,300
European (non-Finnish)	8.79e-05%	1,138,211

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: DUSP28
Protein: p.Arg122Cys
Coding: c.364C>T
MANE Select: NM_001370465
Type: single nucleotide variant
Location: chr2:240561048 (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-arg122cys (accessed [today's date]).

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