CFAP43 p.Ile343=
c.1029T>C · rs139423281 · VCV3040567
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Conditions
1
CFAP43-related disorder
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 0.55 | GERP -3.6, phastCons 0.9 |
| Overall | ||
| CADD | 4.869 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,078 alleles
Filtering AF
0.0128%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0122%
Overall
0.0115%
186/1,611,444 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,078 |
| European (non-Finnish) | 0.0147% | 6,814 |
| Admixed American | 0.01% | 9,956 |
| Remaining individualsnot grpmax-eligible | 0.00801% | 12,482 |
| African / African-American | 0.00134% | 74,892 |
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.Ile343=
- Coding
- c.1029T>C
- MANE Select
- NM_025145
- dbSNP
- rs139423281
- Type
- single nucleotide variant
- Location
- chr10:104203738 (GRCh38)
- Gene constraint
- LOEUF 0.78 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.27 · 1 PDB
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.Ile393Thr Benign ⚠ same condition
- CFAP43 p.Leu105= Likely 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-ile343 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown