Is DUSP3 p.Asn61= (c.183C>T) pathogenic?

DUSP3 p.Asn61= (c.183C>T) is classified Likely benign in DUSP3 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-01). Rare (popmax 0.267%, nfe).

How common is DUSP3 p.Asn61= (c.183C>T) in the general population?

DUSP3 p.Asn61= (c.183C>T) is rare (popmax 0.267%, nfe) (gnomAD).

DUSP3 p.Asn61=

c.183C>T · rs148312361 · VCV2647815

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.267%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -8.7	GERP -3.4
Overall
CADD	1.382	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.267% European (non-Finnish) · 3,153/1,180,040 alleles

Filtering AF 0.259% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.256%

Overall 0.219% 3,528/1,614,198 alleles · rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.351%	285
European (non-Finnish)grpmax	0.267%	374
Remaining individualsnot grpmax-eligible	0.133%	753
Finnishnot grpmax-eligible	0.122%	821
Admixed American	0.0616%	1,623
South Asian	0.0571%	1,752
Middle Eastern	0.0495%	2,021
African / African-American	0.02%	5,003
East Asian	0.00668%	14,962

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: DUSP3
Protein: p.Asn61=
Coding: c.183C>T
MANE Select: NM_004090
dbSNP: rs148312361
Type: single nucleotide variant
Location: chr17:43774881 (GRCh38)
Gene constraint: LOEUF 1.062 · pLI 0.04 (gnomAD)
Structure: AlphaFold pLDDT 96.10 · 9 PDB
Residue 61: the tyrosine-protein phosphatase domain; a β-strand

Full DUSP3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DUSP3 p.Arg104Thr Uncertain significance ★ ⚠ same type
DUSP3 p.Arg119Gln Uncertain significance ★ ⚠ same type
DUSP3 p.Arg125Trp Uncertain significance ★ ⚠ same type
DUSP3 p.Arg158Cys Uncertain significance ★ ⚠ same type
DUSP3 p.Asn174Ser Uncertain significance ★ ⚠ same type
DUSP3 p.Asn74Ser Uncertain significance ★ ⚠ same type
DUSP3 p.Asp164Tyr Uncertain significance ★ ⚠ same type
DUSP3 p.Gln10Glu 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/dusp3-p-asn61 (accessed [today's date]).

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