Is CD3E p.Thr43fs (c.128_129del) pathogenic?

CD3E p.Thr43fs (c.128129del) is classified Pathogenic in CD3E (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-01-10). Absent from gnomAD; Associated with Immunodeficiency 18, severe combined immunodeficiency variant.

What condition is associated with CD3E p.Thr43fs (c.128_129del)?

CD3E p.Thr43fs (c.128_129del) is associated with Immunodeficiency 18, severe combined immunodeficiency variant (ClinVar).

How common is CD3E p.Thr43fs (c.128_129del) in the general population?

CD3E p.Thr43fs (c.128_129del) is absent from gnomAD (gnomAD).

CD3E p.Thr43fs

c.128_129del · rs483352929 · VCV12746

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Immunodeficiency 18, severe combined immunodeficiency variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 6 of 9
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7	GERP 1.8, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CD3E
Protein: p.Thr43fs
Coding: c.128_129del
MANE Select: NM_000733
dbSNP: rs483352929
Type: Deletion
Location: chr11:118312642 (GRCh38)
Gene constraint: LOEUF 0.659 · pLI 0.47 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 73.56 · 44 PDB
Residue 43: the ig-like domain

Full CD3E gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Immunodeficiency 18, severe combined immunodeficiency variant — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CD3E p.Leu58fs Pathogenic ★★ same type
CD3E p.Gly143fs Pathogenic ★ same type
CD3E p.Ser88fs Pathogenic ★ same type
CD3E c.567+65_567+66del Uncertain significance ★ same type
CD3E c.70+4del Uncertain significance ★ same type
CD3E p.Gly68_Gly76del Uncertain significance ★ same type
CD3E p.Lys177fs Uncertain significance ★ same type
CD3E c.353-5del Benign ★ 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/cd3e-p-thr43fs (accessed [today's date]).

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