CFAP44 p.Leu425=
c.1275C>T · rs143438550 · VCV733428
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.46%, mid)
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 2.6 | GERP 0.15, phastCons 1 |
| Overall | ||
| CADD | 6.225 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.46%
Middle Eastern · 88/6,040 alleles
Filtering AF
1.21%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.12%
Overall
0.045%
726/1,613,506 alleles · low-frequency
exomes 657/1,461,242 · genomes 69/152,264 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.46% | 69 |
| Admixed American | 0.0968% | 1,034 |
| Remaining individualsnot grpmax-eligible | 0.056% | 1,785 |
| South Asian | 0.0472% | 2,117 |
| European (non-Finnish) | 0.0417% | 2,398 |
| African / African-American | 0.0107% | 9,375 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,582 |
| Finnishnot grpmax-eligible | 0.00156% | 63,988 |
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.Leu425=
- Coding
- c.1275C>T
- MANE Select
- NM_001164496
- dbSNP
- rs143438550
- Type
- single nucleotide variant
- Location
- chr3:113401635 (GRCh38)
- Gene constraint
- LOEUF 0.697 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.87 · 1 PDB
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-leu425 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown