CFAP65 p.Pro1705=
c.5115G>A · VCV3388077
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0692%, sas)
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 -0.23 | GERP -3.2, phastCons 0.004 |
| Overall | ||
| CADD | 10.62 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0692%
South Asian · 63/91,062 alleles
Filtering AF
0.0554%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0505%
Overall
0.00551%
89/1,613,994 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0692% | 1,445 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,500 |
| East Asian | 0.00446% | 22,440 |
| African / African-American | 0.00267% | 37,516 |
| European (non-Finnish) | 0.00144% | 69,410 |
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.Pro1705=
- Coding
- c.5115G>A
- MANE Select
- NM_194302
- Type
- single nucleotide variant
- Location
- chr2:219004392 (GRCh38)
- Gene constraint
- LOEUF 0.85 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.03
- Residue 1705
- a UniProt-annotated variant site (in spgf40)
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-pro1705 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown