IFT43 p.Ser51=
c.153C>G · VCV3649984
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
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 -2.9 | GERP -2.8 |
| Overall | ||
| CADD | 1.227 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,008 alleles
Overall
6.2e-05%
1/1,613,218 alleles · very rare
exomes 1/1,460,982 · genomes 0/152,236 · joint denominator
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.Ser51=
- Coding
- c.153C>G
- MANE Select
- NM_001102564
- Type
- single nucleotide variant
- Location
- chr14:76022332 (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 51
- the 'disordered' region
Similar variants
- 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
- IFT43 p.Ala202Val 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-ser51 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown