Is CD3G p.Ile11Met (c.33C>G) pathogenic?

CD3G p.Ile11Met (c.33C>G) is classified Conflicting classifications of pathogenicity in CD3G (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2025-05-06). AlphaMissense: likely benign (0.1169); Rare (popmax 0.171%, afr); Associated with combined immunodeficiency due to CD3gamma deficiency.

What condition is associated with CD3G p.Ile11Met (c.33C>G)?

CD3G p.Ile11Met (c.33C>G) is associated with combined immunodeficiency due to CD3gamma deficiency (ClinVar).

How common is CD3G p.Ile11Met (c.33C>G) in the general population?

CD3G p.Ile11Met (c.33C>G) is rare (popmax 0.171%, afr) (gnomAD).

What do computational predictors say about CD3G p.Ile11Met (c.33C>G)?

AlphaMissense predicts likely benign (score 0.1169) — an in-silico prediction, not a clinical call.

CD3G p.Ile11Met

Q: How is Combined immunodeficiency due to CD3gamma deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.33C>G · rs143990986 · VCV580921

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.1169 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.171%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

combined immunodeficiency due to CD3gamma deficiency

Computational evidence

Protein change
AlphaMissense	0.1169	likely benign
REVEL	0.211	benign-leaning
SaProt	LLR -7.09	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 0.21	GERP -2.8, phastCons 0.32
Regional constraint	o/e 1.00	unconstrained · MANE · 8,042 bp · p 0.94 · regional, not allelic
Overall
CADD	15.25	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 0.171% African / African-American · 127/74,402 alleles

Filtering AF 0.147% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.137%

Overall 0.0127% 200/1,571,206 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.171%	586
Admixed American	0.0471%	2,124
Remaining individualsnot grpmax-eligible	0.0295%	3,384
Middle Eastern	0.0167%	6,004
European (non-Finnish)	0.00251%	39,914

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.Ile11Met
Coding: c.33C>G
MANE Select: NM_000073
dbSNP: rs143990986
Type: single nucleotide variant
Location: chr11:118344456 (GRCh38)
Gene constraint: LOEUF 1.191 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 75.05 · 38 PDB

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

Disease context

combined immunodeficiency due to CD3gamma deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Combined immunodeficiency due to CD3gamma deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy

Similar variants

CD3G p.Ile11Thr Uncertain significance ★★ ⚠ same residue
CD3G c.55+1G>T Likely pathogenic ★★ same condition
CD3G c.56-1G>A Likely pathogenic ★★ same condition
CD3G p.Lys69Ter Pathogenic ★★ same condition
CD3G p.Met1Val Pathogenic/Likely pathogenic ★★ same condition
CD3G c.*308G>A Uncertain significance ★★ same condition
CD3G p.Arg146Thr Uncertain significance ★★ ⚠ same condition
CD3G p.Arg166Gln 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/cd3g-p-ile11met (accessed [today's date]).

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