CD3G p.Lys150=
c.450G>A · VCV3605020
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
combined immunodeficiency due to CD3gamma deficiency
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.4 | GERP -1.3, phastCons 1 |
| Overall | ||
| CADD | 8.456 | PHRED · no single calibrated threshold — expert panels disagree |
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
- CD3G
- Protein
- p.Lys150=
- Coding
- c.450G>A
- MANE Select
- NM_000073
- Type
- single nucleotide variant
- Location
- chr11:118351638 (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 150
- the itam domain
Disease context
combined immunodeficiency due to CD3gamma deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Combined immunodeficiency due to CD3gamma deficiency (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy
Similar variants
- 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
- CD3G p.Asn156Ser 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-lys150 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown