IFT43 p.Pro104=
c.312G>A · rs144732564 · VCV1133877
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0601%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.30 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -7.9 | GERP -4.5 |
| Overall | ||
| CADD | 13.75 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0601%
East Asian · 27/44,894 alleles
Filtering AF
0.0424%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0365%
Overall
0.0243%
392/1,613,990 alleles · ultra-rare
exomes 379/1,461,676 · genomes 13/152,314 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0601% | 1,663 |
| Admixed American | 0.0433% | 2,309 |
| South Asian | 0.0264% | 3,795 |
| European (non-Finnish) | 0.0257% | 3,894 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,250 |
| African / African-American | 0.00267% | 37,522 |
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.Pro104=
- Coding
- c.312G>A
- MANE Select
- NM_001102564
- dbSNP
- rs144732564
- Type
- single nucleotide variant
- Location
- chr14:76082311 (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.Pro104Leu 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
- IFT43 c.444+5G>A Uncertain significance ★★ same type
- IFT43 p.Ala162Thr Uncertain significance ★★ ⚠ same type
- IFT43 p.Ala162Val 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-pro104 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown