Is CD3E p.Gly30Ser (c.88G>A) pathogenic?

CD3E p.Gly30Ser (c.88G>A) is classified Conflicting classifications of pathogenicity in CD3E (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2023-07-30). AlphaMissense: likely benign (0.0679); Ultra-rare (popmax 0.0535%, afr); Associated with Inborn genetic diseases.

What condition is associated with CD3E p.Gly30Ser (c.88G>A)?

CD3E p.Gly30Ser (c.88G>A) is associated with Inborn genetic diseases, immunodeficiency 18 (ClinVar).

How common is CD3E p.Gly30Ser (c.88G>A) in the general population?

CD3E p.Gly30Ser (c.88G>A) is ultra-rare (popmax 0.0535%, afr) (gnomAD).

What do computational predictors say about CD3E p.Gly30Ser (c.88G>A)?

AlphaMissense predicts likely benign (score 0.0679) — an in-silico prediction, not a clinical call.

CD3E p.Gly30Ser

c.88G>A · rs773135734 · VCV1414672

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.0679 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0535%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0679	likely benign
REVEL	0.062	moderately benign-leaning
SaProt	LLR -5.32	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	Δ0.56	donor loss, 15 bp away · masked 0 · deltas
Pangolin	Δ0.38	loss · gain 0.02 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP -0.33	GERP -3.9
Regional constraint	o/e 0.88	unconstrained · MANE · 11 kb · p 0.052 · regional, not allelic
Overall
CADD	1.014	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 0.0535% African / African-American · 40/74,824 alleles

Filtering AF 0.0403% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0357%

Overall 0.00261% 42/1,611,528 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0535%	1,871
European (non-Finnish)	0.00017%	588,932

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: CD3E
Protein: p.Gly30Ser
Coding: c.88G>A
MANE Select: NM_000733
dbSNP: rs773135734
Type: single nucleotide variant
Location: chr11:118312155 (GRCh38)
Gene constraint: LOEUF 0.659 · pLI 0.47 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 73.56 · 44 PDB

Full CD3E 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

Also linked: immunodeficiency 18

Similar variants

CD3E p.Gly30Ala Uncertain significance ★ ⚠ same residue
CD3E c.103+1G>A Likely pathogenic ★★ same condition
CD3E c.49+1G>C Pathogenic ★★ same condition
CD3E p.Tyr96Ter Pathogenic/Likely pathogenic ★★ same condition
CD3E c.520+5G>A Uncertain significance ★★ same condition
CD3E p.Arg192Gln Uncertain significance ★★ ⚠ same condition
CD3E p.Arg206His Uncertain significance ★★ ⚠ same condition
CD3E p.Asn25Asp 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/cd3e-p-gly30ser (accessed [today's date]).

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