Is CD3E p.Ala108Val (c.323C>T) pathogenic?

CD3E p.Ala108Val (c.323C>T) is classified Benign in CD3E (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-22). AlphaMissense: likely benign (0.1664); Low-frequency (popmax 1.34%, afr); Associated with immunodeficiency 18.

What condition is associated with CD3E p.Ala108Val (c.323C>T)?

CD3E p.Ala108Val (c.323C>T) is associated with immunodeficiency 18 (ClinVar).

How common is CD3E p.Ala108Val (c.323C>T) in the general population?

CD3E p.Ala108Val (c.323C>T) is low-frequency (popmax 1.34%, afr) (gnomAD).

What do computational predictors say about CD3E p.Ala108Val (c.323C>T)?

AlphaMissense predicts likely benign (score 0.1664) — an in-silico prediction, not a clinical call.

CD3E p.Ala108Val

Q: How is T-B+ severe combined immunodeficiency due to CD3delta/CD3epsilon/CD3zeta inherited?

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

c.323C>T · rs35299792 · VCV474802

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

AlphaMissense

likely benign

0.1664 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.34%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

immunodeficiency 18

Computational evidence

Protein change
AlphaMissense	0.1664	likely benign
REVEL	0.032	moderately benign-leaning
SaProt	LLR -7.74	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 -2.3	GERP -2.1
Regional constraint	o/e 0.88	unconstrained · MANE · 11 kb · p 0.052 · regional, not allelic
Overall
CADD	1.135	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 1.34% African / African-American · 1,006/74,990 alleles

Filtering AF 1.27% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.25%

Overall 0.0741% 1,196/1,614,098 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.34%	75
Remaining individualsnot grpmax-eligible	0.118%	845
Admixed American	0.095%	1,053
Middle Eastern	0.0495%	2,021
South Asian	0.0132%	7,590
East Asian	0.00668%	14,963
European (non-Finnish)	0.00339%	29,501
Finnishnot grpmax-eligible	0.00156%	64,008

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.Ala108Val
Coding: c.323C>T
MANE Select: NM_000733
dbSNP: rs35299792
Type: single nucleotide variant
Location: chr11:118312837 (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 108: the ig-like domain

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

Disease context

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

For T-B+ severe combined immunodeficiency due to CD3delta/CD3epsilon/CD3zeta (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy

Similar variants

CD3E p.Ala108Glu Uncertain significance ★ ⚠ same residue
CD3E p.Ala108= Likely benign ★ 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

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-ala108val (accessed [today's date]).

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