IFT80 p.Ile563=
c.1689T>A · rs1714508262 · VCV2911142
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00267%, afr)
Conditions
2
asphyxiating thoracic dystrophy 2
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 1.4 | GERP 0.65, phastCons 1 |
| Overall | ||
| CADD | 7.311 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/75,028 alleles
Filtering AF
0.000442%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000124%
2/1,613,504 alleles · very rare
exomes 2/1,461,192 · genomes 0/152,312 · 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.Ile563=
- Coding
- c.1689T>A
- MANE Select
- NM_020800
- dbSNP
- rs1714508262
- Type
- single nucleotide variant
- Location
- chr3:160279340 (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 c.*108A>G 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-ile563 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown