Is DUSP13B p.Arg326Gln (c.977G>A) pathogenic?

DUSP13B p.Arg326Gln (c.977G>A) is classified Benign in DUSP13B (ClinVar, Single submitter, 1 submitter; last evaluated 2018-05-15). AlphaMissense: likely benign (0.0818); Low-frequency (popmax 1.15%, afr).

How common is DUSP13B p.Arg326Gln (c.977G>A) in the general population?

DUSP13B p.Arg326Gln (c.977G>A) is low-frequency (popmax 1.15%, afr) (gnomAD).

What do computational predictors say about DUSP13B p.Arg326Gln (c.977G>A)?

AlphaMissense predicts likely benign (score 0.0818) — an in-silico prediction, not a clinical call.

DUSP13B p.Arg326Gln

c.977G>A · rs61737441 · VCV734156

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0818 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.15%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0818	likely benign
REVEL	0.073	moderately benign-leaning
SaProt	LLR -6.72	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 2.7	GERP -1.4, phastCons 1
Regional constraint	o/e 1.08	unconstrained · MANE · 937 bp · p 0.38 · regional, not allelic
Overall
CADD	19.73	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM R190Q vs ClinVar R326Q) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.15% African / African-American · 865/75,056 alleles

Filtering AF 1.09% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.06%

Overall 0.0673% 1,087/1,614,106 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.15%	87
Middle Eastern	0.116%	865
Admixed American	0.103%	968
Remaining individualsnot grpmax-eligible	0.0976%	1,025
South Asian	0.011%	9,108
Ashkenazi Jewishnot grpmax-eligible	0.0101%	9,869
European (non-Finnish)	0.00661%	15,128
Finnishnot grpmax-eligible	0.00156%	63,974

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.Arg326Gln
Coding: c.977G>A
MANE Select: NM_001363514
dbSNP: rs61737441
Type: single nucleotide variant
Location: chr10:75094704 (GRCh38)
Structure: AlphaFold pLDDT 90.56 · 2 PDB

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

Similar variants

DUSP13B p.Arg326Gly Benign ★ ⚠ same residue
DUSP13B p.Pro161Gln Uncertain significance ★★ ⚠ same type
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

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-arg326gln (accessed [today's date]).

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