CFAP44 p.Ser239=
c.717C>T · rs144907390 · VCV730433
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.445%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.23 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -6.4 | GERP -4.8 |
| Overall | ||
| CADD | 0.127 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.445%
Middle Eastern · 27/6,062 alleles
Filtering AF
0.314%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.27%
Overall
0.205%
3,305/1,614,078 alleles · rare
exomes 3,046/1,461,808 · genomes 259/152,270 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.445% | 225 |
| Remaining individualsnot grpmax-eligible | 0.304% | 329 |
| European (non-Finnish) | 0.235% | 426 |
| Admixed American | 0.195% | 513 |
| South Asian | 0.17% | 588 |
| African / African-American | 0.0307% | 3,262 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0203% | 4,934 |
| Finnishnot grpmax-eligible | 0.0172% | 5,818 |
| East Asian | 0.0134% | 7,480 |
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.Ser239=
- Coding
- c.717C>T
- MANE Select
- NM_001164496
- dbSNP
- rs144907390
- Type
- single nucleotide variant
- Location
- chr3:113409279 (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-ser239 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown