Is DUSP13B p.Pro161Gln (c.482C>A) pathogenic?

DUSP13B p.Pro161Gln (c.482C>A) is classified Uncertain significance in DUSP13B (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-11-21). AlphaMissense: likely benign (0.1546); Ultra-rare (popmax 0.0483%, amr).

How common is DUSP13B p.Pro161Gln (c.482C>A) in the general population?

DUSP13B p.Pro161Gln (c.482C>A) is ultra-rare (popmax 0.0483%, amr) (gnomAD).

What do computational predictors say about DUSP13B p.Pro161Gln (c.482C>A)?

AlphaMissense predicts likely benign (score 0.1546) — an in-silico prediction, not a clinical call.

DUSP13B p.Pro161Gln

c.482C>A · rs148137334 · VCV2345348

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1546 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0483%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1546	likely benign
REVEL	0.104	moderately benign-leaning
SaProt	LLR -9.10	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.5, phastCons 1
Regional constraint	o/e 0.86	unconstrained · MANE · 3,780 bp · p 0.016 · regional, not allelic
Overall
CADD	21.7	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 P25Q vs ClinVar P161Q) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0483% Admixed American · 29/60,008 alleles

Filtering AF 0.0363% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0351%

Overall 0.0327% 527/1,613,888 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0483%	2,069
European (non-Finnish)	0.0392%	2,548
Ashkenazi Jewishnot grpmax-eligible	0.0338%	2,959
Remaining individualsnot grpmax-eligible	0.0272%	3,676
African / African-American	0.00933%	10,722
Finnishnot grpmax-eligible	0.00156%	64,032

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: DUSP13B
Protein: p.Pro161Gln
Coding: c.482C>A
MANE Select: NM_001363514
dbSNP: rs148137334
Type: single nucleotide variant
Location: chr10:75097811 (GRCh38)
Structure: AlphaFold pLDDT 90.56 · 2 PDB
Residue 161: the tyrosine-protein phosphatase domain; an α-helix

Full DUSP13B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DUSP13B p.Pro161Leu Uncertain significance ★ ⚠ same residue
DUSP13B c.582-1G>T Uncertain significance ★ same type
DUSP13B p.Ala165Thr Uncertain significance ★ ⚠ same type
DUSP13B p.Ala256Asp Uncertain significance ★ ⚠ same type
DUSP13B p.Ala262Gly Uncertain significance ★ ⚠ same type
DUSP13B p.Ala287Asp Uncertain significance ★ ⚠ same type
DUSP13B p.Arg146Gln Uncertain significance ★ ⚠ same type
DUSP13B p.Arg169His 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/dusp13b-p-pro161gln (accessed [today's date]).

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