IFT80 p.Lys612=
c.1836G>A · rs758317567 · VCV1040720
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Jeune syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.71 | donor loss at this position · masked 0 · deltas |
|---|---|---|
| Pangolin | Δ0.77 | loss · gain 0.05 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 5.9 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 21.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- IFT80
- Protein
- p.Lys612=
- Coding
- c.1836G>A
- MANE Select
- NM_020800
- dbSNP
- rs758317567
- Type
- single nucleotide variant
- Location
- chr3:160279193 (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-lys612 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown