IFT43 p.Cys58=
c.174C>T · rs768619837 · VCV2800472
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00401%, 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 -1.3 | GERP -0.54 |
| Overall | ||
| CADD | 1.014 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00401%
African / African-American · 3/74,850 alleles
Filtering AF
0.00106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000495%
Overall
0.00031%
5/1,612,966 alleles · very rare
exomes 3/1,460,856 · genomes 2/152,110 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00401% | 24,950 |
| South Asian | 0.0022% | 45,521 |
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.Cys58=
- Coding
- c.174C>T
- MANE Select
- NM_001102564
- dbSNP
- rs768619837
- Type
- single nucleotide variant
- Location
- chr14:76022353 (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 58
- the 'disordered' region
Similar variants
- IFT43 p.Cys58_Arg59delinsTer Pathogenic ★ 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-cys58 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown