CFAP43 p.Phe1310=
c.3930T>C · rs550124982 · VCV3042624
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.532%, sas)
Conditions
1
CFAP43-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.064 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.3 | GERP -0.68, phastCons 1 |
| Overall | ||
| CADD | 7.428 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.532%
South Asian · 474/89,142 alleles
Filtering AF
0.492%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.477%
Overall
0.0341%
545/1,596,308 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.532% | 188 |
| Remaining individualsnot grpmax-eligible | 0.0422% | 2,371 |
| Middle Eastern | 0.0342% | 2,921 |
| European (non-Finnish) | 0.00351% | 28,468 |
| East Asian | 0.00224% | 44,550 |
| African / African-American | 0.00134% | 74,864 |
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
- CFAP43
- Protein
- p.Phe1310=
- Coding
- c.3930T>C
- MANE Select
- NM_025145
- dbSNP
- rs550124982
- Type
- single nucleotide variant
- Location
- chr10:104145490 (GRCh38)
- Gene constraint
- LOEUF 0.78 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.27 · 1 PDB
- Residue 1310
- a UniProt-annotated variant site (in spgf19)
Disease context
CFAP43-related disorder
Similar variants
- CFAP43 p.Cys1591Arg Uncertain significance ⚠ same condition
- CFAP43 p.Ala738Thr Likely benign same condition
- CFAP43 p.Arg1378= Likely benign same condition
- CFAP43 p.Asp203= Likely benign same condition
- CFAP43 p.Gln1413= Likely benign same condition
- CFAP43 p.Gln1433= Benign same condition
- CFAP43 p.Ile343= Likely benign same condition
- CFAP43 p.Ile393Thr Benign same condition
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/cfap43-p-phe1310 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown