Is DNAJB11 p.Gln330Arg (c.989A>G) pathogenic?

DNAJB11 p.Gln330Arg (c.989A>G) is classified Likely benign in DNAJB11 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-03). AlphaMissense: likely benign (0.1368); Very rare (popmax 0.00362%, amr); Associated with Inborn genetic diseases.

What condition is associated with DNAJB11 p.Gln330Arg (c.989A>G)?

DNAJB11 p.Gln330Arg (c.989A>G) is associated with Inborn genetic diseases (ClinVar).

How common is DNAJB11 p.Gln330Arg (c.989A>G) in the general population?

DNAJB11 p.Gln330Arg (c.989A>G) is very rare (popmax 0.00362%, amr) (gnomAD).

What do computational predictors say about DNAJB11 p.Gln330Arg (c.989A>G)?

AlphaMissense predicts likely benign (score 0.1368) — an in-silico prediction, not a clinical call.

DNAJB11 p.Gln330Arg

c.989A>G · VCV4013500

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1368 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00362%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1368	likely benign
REVEL	0.229	benign-leaning
SaProt	LLR -6.91	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 11	GERP 2.3, phastCons 1
Regional constraint	o/e 0.81	unconstrained · MANE · 15 kb · p 7.3e-05 · regional, not allelic
Overall
CADD	22.6	PHRED · 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 0.00362% Admixed American · 2/55,234 alleles

Filtering AF 0.000601% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000225%

Overall 0.000189% 3/1,590,244 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00362%	27,617
European (non-Finnish)	8.53e-05%	1,171,917

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: DNAJB11
Protein: p.Gln330Arg
Coding: c.989A>G
MANE Select: NM_016306
Type: single nucleotide variant
Location: chr3:186584566 (GRCh38)
Gene constraint: LOEUF 0.933 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.34
Residue 330: a UniProt-annotated variant site (in pkd6)

Full DNAJB11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DNAJB11 p.Arg289Trp Uncertain significance ★★ ⚠ same condition
DNAJB11 p.Thr188Ser Uncertain significance ★★ ⚠ same condition
DNAJB11 p.Thr8Ile Uncertain significance ★★ ⚠ same condition
DNAJB11 p.Ala147Val Uncertain significance ★ ⚠ same condition
DNAJB11 p.Ala163Ser Uncertain significance ★ ⚠ same condition
DNAJB11 p.Ala19Val Uncertain significance ★ ⚠ same condition
DNAJB11 p.Arg167Gln Conflicting classifications of pathogenicity ★ ⚠ same condition
DNAJB11 p.Arg176Gln Uncertain significance ★ ⚠ same condition

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/dnajb11-p-gln330arg (accessed [today's date]).

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