CFAP44 p.Leu1014=
c.3042C>T · rs776405406 · VCV761543
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00392%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.03 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.22 | donor loss, 23 bp away · masked 0 · deltas |
| Constraint at this position | ||
| Conservation | phyloP 0.81 | GERP -2.8, phastCons 0.97 |
| Overall | ||
| CADD | 6.788 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00392%
Admixed American · 2/50,986 alleles
Filtering AF
0.00202%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00173%
Overall
0.0026%
36/1,384,366 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00392% | 25,493 |
| European (non-Finnish) | 0.00279% | 35,827 |
| East Asian | 0.00245% | 40,872 |
| Remaining individualsnot grpmax-eligible | 0.00167% | 60,000 |
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.Leu1014=
- Coding
- c.3042C>T
- MANE Select
- NM_001164496
- dbSNP
- rs776405406
- Type
- single nucleotide variant
- Location
- chr3:113358768 (GRCh38)
- Gene constraint
- LOEUF 0.697 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.87 · 1 PDB
- Residue 1014
- 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-leu1014 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown