CD2 p.Pro315=
c.945G>A · rs35591188 · VCV791111
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.39%, 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 -9.7 | GERP -4.2 |
| Overall | ||
| CADD | 1.571 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.39%
African / African-American · 1,790/74,978 alleles
Filtering AF
2.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.26%
Overall
0.142%
2,292/1,614,050 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.39% | 42 |
| Middle Eastern | 0.198% | 505 |
| Admixed American | 0.185% | 541 |
| Remaining individualsnot grpmax-eligible | 0.165% | 607 |
| European (non-Finnish) | 0.0225% | 4,453 |
| South Asian | 0.00769% | 13,009 |
| East Asian | 0.00669% | 14,957 |
| Finnishnot grpmax-eligible | 0.00156% | 64,018 |
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
- CD2
- Protein
- p.Pro315=
- Coding
- c.945G>A
- MANE Select
- NM_001767
- dbSNP
- rs35591188
- Type
- single nucleotide variant
- Location
- chr1:116768672 (GRCh38)
- Gene constraint
- LOEUF 1.143 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.25 · 7 PDB
- Residue 315
- the 'disordered' region
Similar variants
- CD2 p.Pro315Leu Uncertain significance ★ ⚠ same residue
- CD2 p.Ala270Thr Uncertain significance ★ ⚠ same type
- CD2 p.Ala292Ser Uncertain significance ★ ⚠ same type
- CD2 p.Ala342Thr Uncertain significance ★ ⚠ same type
- CD2 p.Arg129Lys Uncertain significance ★ ⚠ same type
- CD2 p.Arg129Trp Uncertain significance ★ ⚠ same type
- CD2 p.Arg243Gln Uncertain significance ★ ⚠ same type
- CD2 p.Arg243Leu 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/cd2-p-pro315 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown