Is DGKA p.Pro210Ala (c.628C>G) pathogenic?

DGKA p.Pro210Ala (c.628C>G) is classified Uncertain significance in DGKA (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-26). AlphaMissense: likely benign (0.0897); Absent from gnomAD v4.1.

How common is DGKA p.Pro210Ala (c.628C>G) in the general population?

DGKA p.Pro210Ala (c.628C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DGKA p.Pro210Ala (c.628C>G)?

AlphaMissense predicts likely benign (score 0.0897) — an in-silico prediction, not a clinical call.

DGKA p.Pro210Ala

c.628C>G · VCV4659729

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0897 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.0897	likely benign
REVEL	0.362	indeterminate
SaProt	LLR -6.72	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.2	GERP 1.4, phastCons 1
Regional constraint	o/e 0.74	unconstrained · MANE · 16 kb · p 1.1e-11 · regional, not allelic
Overall
CADD	21.0	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.

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: DGKA
Protein: p.Pro210Ala
Coding: c.628C>G
MANE Select: NM_001345
Type: single nucleotide variant
Location: chr12:55939448 (GRCh38)
Gene constraint: LOEUF 0.419 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 82.51 · 2 PDB

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

Similar variants

DGKA p.Asn347Lys Benign ★★ same type
DGKA p.Asp202= Benign ★★ same type
DGKA p.Arg110Gln Uncertain significance ★ ⚠ same type
DGKA p.Arg290Gly Uncertain significance ★ ⚠ same type
DGKA p.Arg404Gln Uncertain significance ★ ⚠ same type
DGKA p.Arg428Gln Uncertain significance ★ ⚠ same type
DGKA p.Arg499Gln Uncertain significance ★ ⚠ same type
DGKA p.Arg677Cys 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/dgka-p-pro210ala (accessed [today's date]).

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