CYFIP2 p.Ser361=
c.1083C>T · rs376982797 · VCV2421998
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00345%, amr)
Conditions
1
Inborn genetic diseases
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 -11 | GERP -4.6 |
| Overall | ||
| CADD | 4.304 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00345%
Admixed American · 2/57,930 alleles
Filtering AF
0.000767%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000608%
Overall
0.00137%
22/1,601,098 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00345% | 28,965 |
| African / African-American | 0.00268% | 37,331 |
| East Asian | 0.00226% | 44,330 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,088 |
| European (non-Finnish) | 0.00128% | 78,267 |
| South Asian | 0.00113% | 88,544 |
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
- CYFIP2
- Protein
- p.Ser361=
- Coding
- c.1083C>T
- MANE Select
- NM_001037333
- dbSNP
- rs376982797
- Type
- single nucleotide variant
- Location
- chr5:157311754 (GRCh38)
- Gene constraint
- LOEUF 0.274 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 87.28
Similar variants
- CYFIP2 p.Glu640Lys Pathogenic ★★ same condition
- CYFIP2 p.Ala1074Thr Uncertain significance ★★ ⚠ same condition
- CYFIP2 p.Arg1041His Uncertain significance ★★ ⚠ same condition
- CYFIP2 p.Arg1098His Uncertain significance ★★ ⚠ same condition
- CYFIP2 p.Arg1098Leu Uncertain significance ★★ ⚠ same condition
- CYFIP2 p.Arg1100Trp Uncertain significance ★★ ⚠ same condition
- CYFIP2 p.Arg1206Trp Uncertain significance ★★ ⚠ same condition
- CYFIP2 p.Arg1239His Uncertain significance ★★ ⚠ same condition
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/cyfip2-p-ser361 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown