Is DQX1 p.Arg306Gln (c.917G>A) pathogenic?

DQX1 p.Arg306Gln (c.917G>A) is classified Likely benign in DQX1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-31). AlphaMissense: likely benign (0.0675); Ultra-rare (popmax 0.0133%, afr).

How common is DQX1 p.Arg306Gln (c.917G>A) in the general population?

DQX1 p.Arg306Gln (c.917G>A) is ultra-rare (popmax 0.0133%, afr) (gnomAD).

What do computational predictors say about DQX1 p.Arg306Gln (c.917G>A)?

AlphaMissense predicts likely benign (score 0.0675) — an in-silico prediction, not a clinical call.

DQX1 p.Arg306Gln

c.917G>A · VCV3842396

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0675 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0133%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0675	likely benign
REVEL	0.013	strongly benign-leaning
SaProt	LLR -4.57	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 -0.061	GERP -1.8, phastCons 0.001
Regional constraint	o/e 0.92	unconstrained · MANE · 7,280 bp · p 0.018 · regional, not allelic
Overall
CADD	9.524	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 0.0133% African / African-American · 10/74,912 alleles

Filtering AF 0.00723% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0055%

Overall 0.00229% 37/1,614,022 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0133%	7,491
Admixed American	0.005%	19,995
South Asian	0.00329%	30,363
East Asian	0.00223%	44,890
European (non-Finnish)	0.00161%	62,107
Remaining individualsnot grpmax-eligible	0.0016%	62,488

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: DQX1
Protein: p.Arg306Gln
Coding: c.917G>A
MANE Select: NM_133637
Type: single nucleotide variant
Location: chr2:74523437 (GRCh38)
Gene constraint: LOEUF 0.971 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.42
Residue 306: the helicase c-terminal domain

Full DQX1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

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DQX1 p.Ala248Thr Uncertain significance ★ ⚠ same type
DQX1 p.Ala251Thr Uncertain significance ★ ⚠ same type
DQX1 p.Ala310Asp Uncertain significance ★ ⚠ same type
DQX1 p.Ala327Val Uncertain significance ★ ⚠ same type
DQX1 p.Ala477Val Uncertain significance ★ ⚠ same type
DQX1 p.Ala555Thr Uncertain significance ★ ⚠ same type
DQX1 p.Ala707Gly 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/dqx1-p-arg306gln (accessed [today's date]).

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