CYFIP2 p.Thr373=
c.1119G>A · rs776039764 · VCV1299008
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00801%, afr)
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 -3.7 | GERP -4.6 |
| Overall | ||
| CADD | 3.166 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00801%
African / African-American · 6/74,888 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00229%
Overall
0.00198%
32/1,613,470 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00801% | 12,481 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,612 |
| South Asian | 0.0033% | 30,343 |
| European (non-Finnish) | 0.00161% | 62,091 |
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.Thr373=
- Coding
- c.1119G>A
- MANE Select
- NM_001037333
- dbSNP
- rs776039764
- Type
- single nucleotide variant
- Location
- chr5:157314352 (GRCh38)
- Gene constraint
- LOEUF 0.274 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 87.28
Similar variants
- CYFIP2 p.Thr373Met Uncertain significance ★ ⚠ same residue
- 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
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-thr373 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown