CD2AP p.Ala92=
c.276T>C · rs138428273 · VCV1132146
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0171%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.057 | GERP -0.64, phastCons 0.87 |
| Overall | ||
| CADD | 9.275 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0171%
European (non-Finnish) · 202/1,180,014 alleles
Filtering AF
0.0152%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0144%
Overall
0.0134%
216/1,614,140 alleles · ultra-rare
exomes 192/1,461,806 · genomes 24/152,334 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0171% | 5,842 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,812 |
| Admixed American | 0.00833% | 12,005 |
| African / African-American | 0.00133% | 75,056 |
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.Ala92=
- Coding
- c.276T>C
- MANE Select
- NM_012120
- dbSNP
- rs138428273
- Type
- single nucleotide variant
- Location
- chr6:47533712 (GRCh38)
- Gene constraint
- LOEUF 0.815 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.04 · 12 PDB
- Residue 92
- the 'interaction with anln and localization to the midbody' region
Similar variants
- 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
- CD2AP c.*496A>G 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-ala92 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown