Is DGKB p.Arg120Gln (c.359G>A) pathogenic?

DGKB p.Arg120Gln (c.359G>A) is classified Uncertain significance in DGKB (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-04). AlphaMissense: likely benign (0.0718); Very rare (popmax 0.00661%, sas).

How common is DGKB p.Arg120Gln (c.359G>A) in the general population?

DGKB p.Arg120Gln (c.359G>A) is very rare (popmax 0.00661%, sas) (gnomAD).

What do computational predictors say about DGKB p.Arg120Gln (c.359G>A)?

AlphaMissense predicts likely benign (score 0.0718) — an in-silico prediction, not a clinical call.

DGKB p.Arg120Gln

c.359G>A · rs749228389 · VCV2223917

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0718 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00661%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0718	likely benign
REVEL	0.048	moderately benign-leaning
SaProt	LLR -6.42	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 4.7	GERP 1.5, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 663 kb · p 0.15 · regional, not allelic
Overall
CADD	22.9	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

Grpmax group 0.00661% South Asian · 6/90,826 alleles

Filtering AF 0.00287% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00196%

Overall 0.00174% 28/1,611,240 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00661%	15,138
European (non-Finnish)	0.00178%	56,118
Remaining individualsnot grpmax-eligible	0.0016%	62,392

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: DGKB
Protein: p.Arg120Gln
Coding: c.359G>A
MANE Select: NM_001350709
dbSNP: rs749228389
Type: single nucleotide variant
Location: chr7:14718649 (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.Arg530Gly Uncertain significance ★ ⚠ same type
DGKB p.Asn412Asp Uncertain significance ★ ⚠ same type
DGKB p.Asp423Glu 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-arg120gln (accessed [today's date]).

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