CFAP65 p.Lys1805=
c.5415G>A · rs73089095 · VCV2651903
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.72%, 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 -0.097 | GERP -0.68 |
| Overall | ||
| CADD | 1.587 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.72%
African / African-American · 540/74,996 alleles
Filtering AF
0.67%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.65%
Overall
0.0455%
735/1,613,932 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.72% | 139 |
| Admixed American | 0.1% | 1,000 |
| Remaining individualsnot grpmax-eligible | 0.0944% | 1,059 |
| Middle Eastern | 0.066% | 1,516 |
| Ashkenazi Jewishnot grpmax-eligible | 0.054% | 1,850 |
| European (non-Finnish) | 0.00475% | 21,072 |
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.Lys1805=
- Coding
- c.5415G>A
- MANE Select
- NM_194302
- dbSNP
- rs73089095
- Type
- single nucleotide variant
- Location
- chr2:219004092 (GRCh38)
- Gene constraint
- LOEUF 0.85 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.03
- Residue 1805
- a UniProt-annotated variant site (in spgf40); the 'disordered' region
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.Pro1921= 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-lys1805 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown