IFT172 p.Ala1583=
c.4749T>A · rs1160368460 · VCV1659716
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000254%, nfe)
Conditions
2
short-rib thoracic dysplasia 10 with or without polydactyly
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 0.29 | GERP -4, phastCons 0.48 |
| Overall | ||
| CADD | 5.072 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000254%
European (non-Finnish) · 3/1,179,980 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000186%
3/1,614,156 alleles · very rare
exomes 3/1,461,796 · genomes 0/152,360 · 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
- IFT172
- Protein
- p.Ala1583=
- Coding
- c.4749T>A
- MANE Select
- NM_015662
- dbSNP
- rs1160368460
- Type
- single nucleotide variant
- Location
- chr2:27446266 (GRCh38)
- Gene constraint
- LOEUF 0.745 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.98 · 1 PDB
- Residue 1583
- an α-helix
Similar variants
- IFT172 c.1411+2T>C Likely pathogenic ★★ same condition
- IFT172 c.1525-1G>A Pathogenic/Likely pathogenic ★★ same condition
- IFT172 c.184-2A>C Likely pathogenic ★★ same condition
- IFT172 c.2443-1G>C Likely pathogenic ★★ same condition
- IFT172 c.2976-2A>T Likely pathogenic ★★ same condition
- IFT172 c.3111+1G>T Likely pathogenic ★★ same condition
- IFT172 c.3821+1G>A Pathogenic/Likely pathogenic ★★ same condition
- IFT172 c.786-2A>G Likely pathogenic ★★ same condition
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/ift172-p-ala1583 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown