Is CD3G p.Glu67Lys (c.199G>A) pathogenic?

CD3G p.Glu67Lys (c.199G>A) is classified Uncertain significance in CD3G (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-19). AlphaMissense: likely benign (0.0748); Very rare (popmax 6.84e-05%).

How common is CD3G p.Glu67Lys (c.199G>A) in the general population?

CD3G p.Glu67Lys (c.199G>A) is very rare (popmax 6.84e-05%) (gnomAD).

What do computational predictors say about CD3G p.Glu67Lys (c.199G>A)?

AlphaMissense predicts likely benign (score 0.0748) — an in-silico prediction, not a clinical call.

CD3G p.Glu67Lys

c.199G>A · rs767070467 · VCV2612612

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0748 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 6.84e-05%)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0748	likely benign
REVEL	0.087	moderately benign-leaning
SaProt	LLR -6.18	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 -0.58	GERP -3.3
Regional constraint	o/e 1.00	unconstrained · MANE · 8,042 bp · p 0.94 · regional, not allelic
Overall
CADD	0.024	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 6.84e-05%

Overall 6.84e-05% 1/1,461,834 alleles · very rare

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: CD3G
Protein: p.Glu67Lys
Coding: c.199G>A
MANE Select: NM_000073
dbSNP: rs767070467
Type: single nucleotide variant
Location: chr11:118349862 (GRCh38)
Gene constraint: LOEUF 1.191 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 75.05 · 38 PDB
Residue 67: a disulfide bond; a β-strand; the ig-like domain

Full CD3G gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD3G c.55+1G>T Likely pathogenic ★★ same type
CD3G c.56-1G>A Likely pathogenic ★★ same type
CD3G p.Lys69Ter Pathogenic ★★ same type
CD3G p.Met1Val Pathogenic/Likely pathogenic ★★ same type
CD3G c.*308G>A Uncertain significance ★★ same type
CD3G p.Arg146Thr Uncertain significance ★★ ⚠ same type
CD3G p.Arg166Gln Uncertain significance ★★ ⚠ same type
CD3G p.Asn156Ser 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/cd3g-p-glu67lys (accessed [today's date]).

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