IFT80 p.Gln681=
c.2043G>A · rs2473099506 · VCV2884158
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
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 0.81 | GERP -2.1, phastCons 1 |
| Overall | ||
| CADD | 6.298 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,876 alleles
Overall
6.2e-05%
1/1,613,670 alleles · very rare
exomes 1/1,461,414 · genomes 0/152,256 · 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
- IFT80
- Protein
- p.Gln681=
- Coding
- c.2043G>A
- MANE Select
- NM_020800
- dbSNP
- rs2473099506
- Type
- single nucleotide variant
- Location
- chr3:160277362 (GRCh38)
- Gene constraint
- LOEUF 0.739 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.50
Similar variants
- 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
- IFT80 p.Arg220Cys 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-gln681 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown