CD96 p.Pro417=
c.1251C>A · rs76343124 · VCV342541
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.844%, afr)
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 1.3 | GERP -0.95, phastCons 1 |
| Overall | ||
| CADD | 8.328 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.844%
African / African-American · 632/74,838 alleles
Filtering AF
0.79%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.768%
Overall
0.0416%
668/1,605,106 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.844% | 118 |
| Remaining individualsnot grpmax-eligible | 0.0305% | 3,274 |
| Admixed American | 0.015% | 6,667 |
| South Asian | 0.0022% | 45,435 |
| European (non-Finnish) | 0.000512% | 195,315 |
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
- CD96
- Protein
- p.Pro417=
- Coding
- c.1251C>A
- MANE Select
- NM_005816
- dbSNP
- rs76343124
- Type
- single nucleotide variant
- Location
- chr3:111624334 (GRCh38)
- Gene constraint
- LOEUF 1.16 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.81 · 1 PDB
- Residue 417
- the 'disordered' region
Similar variants
- CD96 p.Pro417Ser Uncertain significance ★ ⚠ same residue
- CD96 c.1249+1G>A Uncertain significance ★★ same type
- CD96 c.544-1512C>T Uncertain significance ★★ ⚠ same type
- CD96 p.Asp205Gly Uncertain significance ★★ ⚠ same type
- CD96 p.Asp224Asn Uncertain significance ★★ ⚠ same type
- CD96 p.Ile151Thr Uncertain significance ★★ ⚠ same type
- CD96 p.Leu120Pro Uncertain significance ★★ ⚠ same type
- CD96 p.Lys500Arg 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/cd96-p-pro417 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown