IFT43 p.Leu7=
c.21G>A · rs193921095 · VCV314466
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.379%, 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 -0.28 | GERP -0.96, phastCons 0.006 |
| Overall | ||
| CADD | 4.064 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.379%
Middle Eastern · 23/6,062 alleles
Filtering AF
0.259%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.22%
Overall
0.0273%
440/1,614,210 alleles · rare
exomes 414/1,461,872 · genomes 26/152,338 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.379% | 264 |
| Admixed American | 0.0583% | 1,715 |
| Remaining individualsnot grpmax-eligible | 0.0544% | 1,838 |
| South Asian | 0.0395% | 2,530 |
| European (non-Finnish) | 0.0258% | 3,882 |
| African / African-American | 0.0107% | 9,382 |
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
- IFT43
- Protein
- p.Leu7=
- Coding
- c.21G>A
- MANE Select
- NM_001102564
- dbSNP
- rs193921095
- Type
- single nucleotide variant
- Location
- chr14:75985807 (GRCh38)
- Gene constraint
- LOEUF 1.282 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 64.09 · 3 PDB
Similar variants
- IFT43 p.Leu7Ser Uncertain significance ★★ ⚠ same residue
- IFT43 p.Leu7Ter Likely pathogenic ★ same residue
- IFT43 p.Leu7Met Uncertain significance ★ ⚠ same residue
- IFT43 p.Leu7Phe Uncertain significance ⚠ same residue
- IFT43 c.148-2A>C Likely pathogenic ★★ same type
- IFT43 c.296-5698C>T Likely pathogenic ★★ same type
- IFT43 c.296-5681A>G Uncertain significance ★★ same type
- IFT43 c.296-5697G>A Uncertain significance ★★ 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/ift43-p-leu7 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown