CD2AP p.Val326=
c.978C>T · rs202236302 · VCV2866285
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.263%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.20 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.8 | GERP -1, phastCons 1 |
| Overall | ||
| CADD | 13.31 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.263%
East Asian · 118/44,838 alleles
Filtering AF
0.225%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.21%
Overall
0.00777%
125/1,609,120 alleles · rare
exomes 110/1,457,006 · genomes 15/152,114 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.263% | 380 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,775 |
| African / African-American | 0.004% | 24,969 |
| South Asian | 0.0011% | 90,960 |
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
- CD2AP
- Protein
- p.Val326=
- Coding
- c.978C>T
- MANE Select
- NM_012120
- dbSNP
- rs202236302
- Type
- single nucleotide variant
- Location
- chr6:47579459 (GRCh38)
- Gene constraint
- LOEUF 0.815 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.04 · 12 PDB
- Residue 326
- the sh3 3 domain
Similar variants
- CD2AP p.Val326Ile Uncertain significance ★ ⚠ same residue
- CD2AP c.1274+3A>G Uncertain significance ★★ same type
- CD2AP c.1633-6T>A Uncertain significance ★★ same type
- CD2AP c.-130C>G Uncertain significance ★★ same type
- CD2AP c.-166A>G Uncertain significance ★★ same type
- CD2AP c.*319A>C Uncertain significance ★★ same type
- CD2AP c.*452C>G Uncertain significance ★★ same type
- CD2AP c.*494G>A 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/cd2ap-p-val326 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown