Is DDB2 p.Arg313Gln (c.938G>A) pathogenic?

DDB2 p.Arg313Gln (c.938G>A) is classified Uncertain significance in DDB2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-23). AlphaMissense: likely benign (0.267); Very rare (popmax 0.00891%, eas); Associated with Inborn genetic diseases.

What condition is associated with DDB2 p.Arg313Gln (c.938G>A)?

DDB2 p.Arg313Gln (c.938G>A) is associated with Inborn genetic diseases (ClinVar).

How common is DDB2 p.Arg313Gln (c.938G>A) in the general population?

DDB2 p.Arg313Gln (c.938G>A) is very rare (popmax 0.00891%, eas) (gnomAD).

What do computational predictors say about DDB2 p.Arg313Gln (c.938G>A)?

AlphaMissense predicts likely benign (score 0.267) — an in-silico prediction, not a clinical call.

DDB2 p.Arg313Gln

c.938G>A · rs1022769202 · VCV2465177

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.267 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00891%, eas)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.267	likely benign
REVEL	0.532	indeterminate
SaProt	LLR -10.54	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.8	GERP 0.97, phastCons 1
Regional constraint	o/e 0.78	unconstrained · MANE · 24 kb · p 1.9e-07 · regional, not allelic
Overall
CADD	28.9	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 0.00891% East Asian · 4/44,896 alleles

Filtering AF 0.00298% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0026%

Overall 0.00322% 52/1,614,054 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00891%	11,224
European (non-Finnish)	0.00381%	26,223
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,608
African / African-American	0.00267%	37,466

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: DDB2
Protein: p.Arg313Gln
Coding: c.938G>A
MANE Select: NM_000107
dbSNP: rs1022769202
Type: single nucleotide variant
Location: chr11:47235327 (GRCh38)
Gene constraint: LOEUF 0.719 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 83.69 · 10 PDB
Residue 313: a β-strand

Full DDB2 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

DDB2 p.Arg313Ter Pathogenic ★ same residue
DDB2 p.Glu178Ala Uncertain significance ★★ ⚠ same condition
DDB2 p.Phe94Cys Uncertain significance ★★ ⚠ same condition
DDB2 p.Pro27Thr Uncertain significance ★★ ⚠ same condition
DDB2 p.Ser85Cys Uncertain significance ★★ ⚠ same condition
DDB2 p.Ser85Tyr Uncertain significance ★★ ⚠ same condition
DDB2 p.Thr406Met Uncertain significance ★★ ⚠ same condition
DDB2 p.Ala301Val 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/ddb2-p-arg313gln (accessed [today's date]).

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