IFT43 p.Pro163=
c.489G>A · rs148085072 · VCV314471
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0693%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.6 | GERP -5 |
| Overall | ||
| CADD | 1.245 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0693%
African / African-American · 52/75,020 alleles
Filtering AF
0.0542%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0489%
Overall
0.00874%
141/1,613,736 alleles · ultra-rare
exomes 113/1,461,472 · genomes 28/152,264 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0693% | 1,443 |
| South Asian | 0.0351% | 2,846 |
| Admixed American | 0.0233% | 4,287 |
| European (non-Finnish) | 0.00348% | 28,772 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,247 |
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.Pro163=
- Coding
- c.489G>A
- MANE Select
- NM_001102564
- dbSNP
- rs148085072
- Type
- single nucleotide variant
- Location
- chr14:76083271 (GRCh38)
- Gene constraint
- LOEUF 1.282 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 64.09 · 3 PDB
- Residue 163
- an α-helix
Similar variants
- IFT43 p.Pro163Gln Uncertain significance ★ same residue
- IFT43 p.Pro163Leu Benign ★ ⚠ 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
- IFT43 c.444+5G>A Uncertain significance ★★ same type
- IFT43 p.Ala162Thr 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-pro163 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown