CFAP65 p.Pro973=
c.2919C>T · rs139797387 · VCV783209
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.903%, 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 -1.5 | GERP -3.9 |
| Overall | ||
| CADD | 3.315 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.903%
African / African-American · 677/74,984 alleles
Filtering AF
0.846%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.824%
Overall
0.056%
900/1,606,524 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.903% | 111 |
| Middle Eastern | 0.0991% | 1,009 |
| Admixed American | 0.0814% | 1,229 |
| Remaining individualsnot grpmax-eligible | 0.0627% | 1,596 |
| European (non-Finnish) | 0.0105% | 9,567 |
| East Asian | 0.00895% | 11,170 |
| South Asian | 0.00335% | 29,836 |
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
- CFAP65
- Protein
- p.Pro973=
- Coding
- c.2919C>T
- MANE Select
- NM_194302
- dbSNP
- rs139797387
- Type
- single nucleotide variant
- Location
- chr2:219022231 (GRCh38)
- Gene constraint
- LOEUF 0.85 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.03
- Residue 973
- a UniProt-annotated variant site (in spgf40); the msp domain
Similar variants
- CFAP65 p.Arg1231= Benign ★★ same type
- CFAP65 p.Arg1545Gln Benign ★★ same type
- CFAP65 p.Arg760Gln Benign ★★ same type
- CFAP65 p.Asp1313= Likely benign ★★ same type
- CFAP65 p.Leu1127= Benign/Likely benign ★★ same type
- CFAP65 p.Leu1523= Benign/Likely benign ★★ same type
- CFAP65 p.Leu1906= Benign/Likely benign ★★ same type
- CFAP65 p.Lys1805= Likely 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/cfap65-p-pro973 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown