CD8A p.Ser116=
c.348G>A · rs758030009 · VCV3054302
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00134%, afr)
Conditions
1
CD8A-related disorder
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 -6.3 | GERP -3 |
| Overall | ||
| CADD | 1.275 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00134%
African / African-American · 1/74,904 alleles
Overall
0.000124%
2/1,613,946 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00134% | 74,904 |
| European (non-Finnish) | 8.47e-05% | 1,180,018 |
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
- CD8A
- Protein
- p.Ser116=
- Coding
- c.348G>A
- MANE Select
- NM_001768
- dbSNP
- rs758030009
- Type
- single nucleotide variant
- Location
- chr2:86790383 (GRCh38)
- Gene constraint
- LOEUF 1.496 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 79.03 · 8 PDB
- Residue 116
- a β-strand; the ig-like v-type domain
Disease context
CD8A-related disorder
Similar variants
- CD8A c.403+4C>G Uncertain significance ★★ same type
- CD8A c.626-2A>T Uncertain significance ★★ same type
- CD8A p.Arg165Leu Uncertain significance ★★ ⚠ same type
- CD8A p.Arg165Pro Uncertain significance ★★ ⚠ same type
- CD8A p.His127Tyr Uncertain significance ★★ ⚠ same type
- CD8A p.His208Leu Uncertain significance ★★ ⚠ same type
- CD8A p.Leu10Arg Uncertain significance ★★ ⚠ same type
- CD8A p.Pro130Arg Uncertain significance ★★ ⚠ 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/cd8a-p-ser116 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown