Sugi Variant
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DUSP4/p.Glu153Lys

DUSP4 p.Glu153Lys

c.457G>A · rs763712883 · VCV3086334

Uncertain significance Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
ambiguous
0.413 · ACMG-weighted
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, amr)
Missense predictors
0/2 damaging
REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense0.413ambiguous
REVEL0.103moderately benign-leaning
SaProtLLR -8.28tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI—not assessed · no allele here is in the release
Constraint at this position
ConservationphyloP 4.8GERP 0.69, phastCons 1
Regional constrainto/e 0.88unconstrained · MANE · 13 kb · p 0.014 · regional, not allelic
Overall
CADD24.7PHRED · 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
Grpmax group 0.0134% Admixed American · 8/59,792 alleles
Filtering AF 0.00664% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00484%
Overall 0.00174% 28/1,612,266 alleles · ultra-rare exomes 22/1,460,218 · genomes 6/152,048 · joint denominator
Ancestry group Frequency 1 in
Ashkenazi Jewishnot grpmax-eligible 0.0271% 3,687
Admixed Americangrpmax 0.0134% 7,474
Remaining individualsnot grpmax-eligible 0.0016% 62,412
African / African-American 0.00134% 74,788
South Asian 0.0011% 90,828
European (non-Finnish) 0.000763% 131,030

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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
DUSP4
Protein
p.Glu153Lys
Coding
c.457G>A
MANE Select
NM_001394
dbSNP
rs763712883
Type
single nucleotide variant
Location
chr8:29340220 (GRCh38)
Gene constraint
LOEUF 0.808 · pLI 0.02 (gnomAD)
Structure
AlphaFold pLDDT 78.78 · 1 PDB
Residue 153
the rhodanese domain
Full DUSP4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

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/dusp4-p-glu153lys (accessed [today's date]).

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