IFT43 p.Ala31=
c.93G>A · rs760349984 · VCV1646378
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00878%, sas)
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 -0.94 | GERP -3.1 |
| Overall | ||
| CADD | 5.79 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00878%
South Asian · 8/91,066 alleles
Filtering AF
0.00437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00312%
Overall
0.000929%
15/1,613,854 alleles · very rare
exomes 13/1,461,746 · genomes 2/152,108 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00878% | 11,383 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,803 |
| European (non-Finnish) | 0.000424% | 236,002 |
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.Ala31=
- Coding
- c.93G>A
- MANE Select
- NM_001102564
- dbSNP
- rs760349984
- Type
- single nucleotide variant
- Location
- chr14:75988923 (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 31
- the 'disordered' region
Similar variants
- IFT43 p.Ala31Pro Uncertain significance ★★ ⚠ same residue
- IFT43 p.Ala31Val 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
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-ala31 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown