IFT80 p.Pro450=
c.1350G>A · rs201146135 · VCV695215
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.266%, eas)
Conditions
1
Jeune syndrome
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 -0.28 | GERP -3.5, phastCons 0.1 |
| Overall | ||
| CADD | 8.285 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.266%
East Asian · 119/44,666 alleles
Filtering AF
0.228%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.213%
Overall
0.0212%
342/1,610,100 alleles · rare
exomes 319/1,458,160 · genomes 23/151,940 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.266% | 375 |
| Admixed American | 0.124% | 809 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,924 |
| European (non-Finnish) | 0.0109% | 9,197 |
| South Asian | 0.00771% | 12,971 |
| African / African-American | 0.00535% | 18,702 |
| Finnishnot grpmax-eligible | 0.00157% | 63,878 |
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
- IFT80
- Protein
- p.Pro450=
- Coding
- c.1350G>A
- MANE Select
- NM_020800
- dbSNP
- rs201146135
- Type
- single nucleotide variant
- Location
- chr3:160285834 (GRCh38)
- Gene constraint
- LOEUF 0.739 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.50
Similar variants
- IFT80 p.Pro450Leu Uncertain significance ★★ ⚠ same residue
- IFT80 p.Arg495Ter Pathogenic/Likely pathogenic ★★ same condition
- IFT80 p.Trp155Ter Pathogenic/Likely pathogenic ★★ same condition
- IFT80 c.1076+6C>A Uncertain significance ★★ same condition
- IFT80 c.1836+5T>C Uncertain significance ★★ same condition
- IFT80 c.370+6T>C Uncertain significance ★★ same condition
- IFT80 p.Ala154Val Uncertain significance ★★ ⚠ same condition
- IFT80 p.Ala236Val Uncertain significance ★★ ⚠ 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/ift80-p-pro450 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown