CCNH p.Phe87=
c.261C>T · rs191853622 · VCV733117
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.895%, amr)
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 |
|---|---|---|
| Pangolin | Δ0.28 | loss · gain 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 6.7 | GERP 2.7, phastCons 1 |
| Overall | ||
| CADD | 13.45 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.895%
Admixed American · 512/57,176 alleles
Filtering AF
0.831%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.806%
Overall
0.035%
545/1,559,074 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.895% | 112 |
| Remaining individualsnot grpmax-eligible | 0.0248% | 4,039 |
| African / African-American | 0.00949% | 10,533 |
| East Asian | 0.00457% | 21,898 |
| South Asian | 0.00113% | 88,862 |
| European (non-Finnish) | 0.000704% | 142,098 |
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
- CCNH
- Protein
- p.Phe87=
- Coding
- c.261C>T
- MANE Select
- NM_001239
- dbSNP
- rs191853622
- Type
- single nucleotide variant
- Location
- chr5:87409343 (GRCh38)
- Gene constraint
- LOEUF 1.05 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.26 · 49 PDB
- Residue 87
- an α-helix
Similar variants
- RASA1 c.1698+1G>A Pathogenic/Likely pathogenic ★★ same type
- RASA1 c.2012-2A>G Pathogenic/Likely pathogenic ★★ same type
- RASA1 c.2603+1G>A Pathogenic ★★ same type
- RASA1 c.2691-1G>T Pathogenic/Likely pathogenic ★★ same type
- RASA1 c.2925+1G>T Pathogenic ★★ same type
- RASA1 c.899+1G>T Likely pathogenic ★★ same type
- RASA1 p.Arg1010Ter Pathogenic ★★ same type
- RASA1 p.Arg285Ter Pathogenic ★★ 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/ccnh-p-phe87 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown