CFAP65 p.Leu1127=
c.3381G>C · rs114688732 · VCV716839
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.1%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.057 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.47 | GERP -0.44, phastCons 0.029 |
| Overall | ||
| CADD | 6.025 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.1%
African / African-American · 827/75,070 alleles
Filtering AF
1.04%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.01%
Overall
0.0679%
1,096/1,613,850 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.1% | 91 |
| Middle Eastern | 0.165% | 605 |
| Admixed American | 0.117% | 858 |
| Remaining individualsnot grpmax-eligible | 0.11% | 906 |
| European (non-Finnish) | 0.01% | 10,000 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
| South Asian | 0.0011% | 91,086 |
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.Leu1127=
- Coding
- c.3381G>C
- MANE Select
- NM_194302
- dbSNP
- rs114688732
- Type
- single nucleotide variant
- Location
- chr2:219019598 (GRCh38)
- Gene constraint
- LOEUF 0.85 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.03
- Residue 1127
- 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.Leu1523= Benign/Likely benign ★★ same type
- CFAP65 p.Leu1906= Benign/Likely benign ★★ same type
- CFAP65 p.Lys1805= 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-leu1127 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown