Is DGKB p.Asp423Glu (c.1269T>A) pathogenic?

DGKB p.Asp423Glu (c.1269T>A) is classified Uncertain significance in DGKB (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-15). AlphaMissense: likely benign (0.3187); Absent from gnomAD v4.1.

How common is DGKB p.Asp423Glu (c.1269T>A) in the general population?

DGKB p.Asp423Glu (c.1269T>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DGKB p.Asp423Glu (c.1269T>A)?

AlphaMissense predicts likely benign (score 0.3187) — an in-silico prediction, not a clinical call.

DGKB p.Asp423Glu

c.1269T>A · VCV3271709

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3187 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.3187	likely benign
REVEL	0.224	benign-leaning
SaProt	LLR -6.33	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 0.093	GERP -2.8, phastCons 0.097
Regional constraint	o/e 0.95	unconstrained · MANE · 663 kb · p 0.15 · regional, not allelic
Overall
CADD	17.58	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM D424E vs ClinVar D423E) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: DGKB
Protein: p.Asp423Glu
Coding: c.1269T>A
MANE Select: NM_001350709
Type: single nucleotide variant
Location: chr7:14621393 (GRCh38)
Gene constraint: LOEUF 0.755 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.02

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

Similar variants

DGKB p.Ala115Thr Uncertain significance ★ ⚠ same type
DGKB p.Ala417Thr Uncertain significance ★ ⚠ same type
DGKB p.Arg110Ile Uncertain significance ★ ⚠ same type
DGKB p.Arg120Gln Uncertain significance ★ ⚠ same type
DGKB p.Arg530Gly Uncertain significance ★ ⚠ same type
DGKB p.Asn412Asp Uncertain significance ★ ⚠ same type
DGKB p.Asp59Gly Uncertain significance ★ ⚠ same type
DGKB p.Asp78Gly 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/dgkb-p-asp423glu (accessed [today's date]).

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