CFAP44 p.Lys1215=
c.3645G>A · rs761359904 · VCV796322
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00541%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.046 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.28 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 0.78 | GERP -3.9, phastCons 1 |
| Overall | ||
| CADD | 5.158 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00541%
European (non-Finnish) · 62/1,146,338 alleles
Filtering AF
0.00431%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00391%
Overall
0.00417%
64/1,535,314 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00541% | 18,489 |
| Remaining individualsnot grpmax-eligible | 0.00333% | 30,009 |
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
- CFAP44
- Protein
- p.Lys1215=
- Coding
- c.3645G>A
- MANE Select
- NM_001164496
- dbSNP
- rs761359904
- Type
- single nucleotide variant
- Location
- chr3:113330639 (GRCh38)
- Gene constraint
- LOEUF 0.697 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.87 · 1 PDB
- Residue 1215
- a UniProt-annotated variant site (in spgf20)
Similar variants
- CFAP44 p.Glu463Ter Pathogenic ★★ same type
- CFAP44 c.4759-3C>T Benign ★★ same type
- CFAP44 p.Ala157= Benign ★★ same type
- CFAP44 p.Ala486Val Likely benign ★★ ⚠ same type
- CFAP44 p.Arg1059Gln Benign ★★ same type
- CFAP44 p.Arg1495Trp Benign ★★ ⚠ same type
- CFAP44 p.Arg1651Trp Benign/Likely benign ★★ ⚠ same type
- CFAP44 p.Arg1806= Benign/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/cfap44-p-lys1215 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown