CD3D c.55+20G>C
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
immunodeficiency 19
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +20 | near-intronic (+20 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.3 | GERP 0.72 |
| Non-coding constraint | Z 1.86 | 1 kb window · o/e 0.87 · regional · uncalibrated |
| Overall | ||
| CADD | 12.27 | 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
- CD3D
- Coding
- c.55+20G>C
- MANE Select
- NM_000732
- dbSNP
- rs2496877631
- Type
- single nucleotide variant
- Location
- chr11:118342533 (GRCh38)
- Gene constraint
- LOEUF 1.325 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 77.57 · 31 PDB
Disease context
immunodeficiency 19 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor T-B+ severe combined immunodeficiency due to CD3delta/CD3epsilon/CD3zeta (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy
Similar variants
- CD3D c.274+5G>A Pathogenic/Likely pathogenic ★★ same condition
- CD3D c.407-2A>G Likely pathogenic ★★ same condition
- CD3D p.Arg68Ter Pathogenic ★★ same condition
- CD3D p.Cys93Ter Pathogenic ★★ same condition
- CD3D c.274+4C>T Uncertain significance ★★ same condition
- CD3D c.450+6C>T Uncertain significance ★★ same condition
- CD3D p.Ala119Asp Uncertain significance ★★ ⚠ same condition
- CD3D p.Arg169Gln 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/cd3d-c-55-plus-20g-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown