CYFIP1 p.Ala1055=
c.3165C>T · rs150653373 · VCV744883
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0663%, mid)
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 -0.31 | GERP -2.7, phastCons 0.008 |
| Overall | ||
| CADD | 2.975 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0663%
Middle Eastern · 4/6,034 alleles
Filtering AF
0.0226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0136%
Overall
0.00983%
158/1,607,000 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0663% | 1,509 |
| Admixed American | 0.0171% | 5,836 |
| Remaining individualsnot grpmax-eligible | 0.0129% | 7,771 |
| European (non-Finnish) | 0.0106% | 9,419 |
| South Asian | 0.01% | 9,982 |
| African / African-American | 0.00268% | 37,282 |
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
- CYFIP1
- Protein
- p.Ala1055=
- Coding
- c.3165C>T
- MANE Select
- NM_014608
- dbSNP
- rs150653373
- Type
- single nucleotide variant
- Location
- chr15:22874595 (GRCh38)
- Gene constraint
- LOEUF 0.44 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 90.24 · 5 PDB
- Residue 1055
- an α-helix
Similar variants
- CYFIP1 p.Phe600Leu Uncertain significance ★★ ⚠ same type
- CYFIP1 c.3043-4C>G Benign/Likely benign ★★ same type
- CYFIP1 p.Ala1003Val Benign ★★ ⚠ same type
- CYFIP1 p.Ala385Thr Benign ★★ ⚠ same type
- CYFIP1 p.Glu347= Benign ★★ same type
- CYFIP1 p.Gly903Ser Benign/Likely benign ★★ same type
- CYFIP1 p.Ile795Val Benign ★★ same type
- CYFIP1 p.Leu1201= Benign ★★ 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/cyfip1-p-ala1055 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown