CYFIP2 p.Phe390=
c.1170C>T · rs139943836 · VCV1166202
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.809%, 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 -4.4 | GERP -4.6 |
| Overall | ||
| CADD | 5.175 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.809%
Middle Eastern · 49/6,060 alleles
Filtering AF
0.628%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.564%
Overall
0.196%
3,168/1,613,872 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.809% | 124 |
| Ashkenazi Jewishnot grpmax-eligible | 0.493% | 203 |
| Remaining individualsnot grpmax-eligible | 0.213% | 470 |
| European (non-Finnish) | 0.213% | 470 |
| South Asian | 0.184% | 542 |
| Admixed American | 0.173% | 577 |
| Finnishnot grpmax-eligible | 0.0453% | 2,206 |
| African / African-American | 0.0373% | 2,680 |
| East Asian | 0.00223% | 44,888 |
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.Phe390=
- Coding
- c.1170C>T
- MANE Select
- NM_001037333
- dbSNP
- rs139943836
- Type
- single nucleotide variant
- Location
- chr5:157314403 (GRCh38)
- Gene constraint
- LOEUF 0.274 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 87.28
Similar variants
- CYFIP2 p.Arg87Cys Pathogenic/Likely pathogenic ★★ same type
- CYFIP2 p.Arg87Pro Pathogenic/Likely pathogenic ★★ same type
- CYFIP2 p.Glu640Lys Pathogenic ★★ same type
- CYFIP2 p.Tyr108His Likely pathogenic ★★ ⚠ same type
- CYFIP2 p.Ala1074Thr Uncertain significance ★★ ⚠ same type
- CYFIP2 p.Ala773Thr Uncertain significance ★★ ⚠ same type
- CYFIP2 p.Ala80Val Uncertain significance ★★ ⚠ same type
- CYFIP2 p.Arg1041His 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/cyfip2-p-phe390 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown