Is DDRGK1 p.Arg306Gln (c.917G>A) pathogenic?

DDRGK1 p.Arg306Gln (c.917G>A) is classified Likely benign in DDRGK1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-09-17). AlphaMissense: likely benign (0.0573); Ultra-rare (popmax 0.0615%, sas); Associated with Inborn genetic diseases.

What condition is associated with DDRGK1 p.Arg306Gln (c.917G>A)?

DDRGK1 p.Arg306Gln (c.917G>A) is associated with Inborn genetic diseases (ClinVar).

How common is DDRGK1 p.Arg306Gln (c.917G>A) in the general population?

DDRGK1 p.Arg306Gln (c.917G>A) is ultra-rare (popmax 0.0615%, sas) (gnomAD).

What do computational predictors say about DDRGK1 p.Arg306Gln (c.917G>A)?

AlphaMissense predicts likely benign (score 0.0573) — an in-silico prediction, not a clinical call.

DDRGK1 p.Arg306Gln

c.917G>A · rs765906690 · VCV2399823

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0573 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0615%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0573	likely benign
REVEL	0.045	moderately benign-leaning
SaProt	LLR -4.56	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 -1	GERP -5.3
Regional constraint	o/e 0.96	unconstrained · MANE · 14 kb · p 0.41 · regional, not allelic
Overall
CADD	8.197	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 0.0615% South Asian · 56/91,058 alleles

Filtering AF 0.0486% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.044%

Overall 0.00508% 82/1,613,766 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0615%	1,626
Admixed American	0.0133%	7,500
Remaining individualsnot grpmax-eligible	0.0032%	31,238
African / African-American	0.00267%	37,452
European (non-Finnish)	0.00119%	84,282

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: DDRGK1
Protein: p.Arg306Gln
Coding: c.917G>A
MANE Select: NM_023935
dbSNP: rs765906690
Type: single nucleotide variant
Location: chr20:3190681 (GRCh38)
Gene constraint: LOEUF 1.213 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.52 · 8 PDB
Residue 306: the 'mediates interaction with ufl1' region

Full DDRGK1 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

DDRGK1 p.Ala29Val Uncertain significance ★★ ⚠ same condition
DDRGK1 p.Ala95Gly Uncertain significance ★★ ⚠ same condition
DDRGK1 p.Arg241His Uncertain significance ★★ ⚠ same condition
DDRGK1 p.Arg265Trp Uncertain significance ★★ ⚠ same condition
DDRGK1 p.Arg27Gln Uncertain significance ★★ ⚠ same condition
DDRGK1 p.Arg46Gln Uncertain significance ★★ ⚠ same condition
DDRGK1 p.Arg65Gln Uncertain significance ★★ ⚠ same condition
DDRGK1 p.Arg79Gly 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/ddrgk1-p-arg306gln (accessed [today's date]).

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