Is IFT80 p.Ile463fs (c.1388del) pathogenic?

IFT80 p.Ile463fs (c.1388del) is classified Pathogenic in IFT80 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-04-24). No gnomAD frequency available for this variant; Associated with Jeune syndrome.

What condition is associated with IFT80 p.Ile463fs (c.1388del)?

IFT80 p.Ile463fs (c.1388del) is associated with Jeune syndrome (ClinVar).

How common is IFT80 p.Ile463fs (c.1388del) in the general population?

IFT80 p.Ile463fs (c.1388del) is no gnomAD frequency available for this variant (gnomAD).

IFT80 p.Ile463fs

c.1388del · rs2108234807 · VCV1451633

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Jeune syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 14 of 20
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.7	GERP -2.4, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: IFT80
Protein: p.Ile463fs
Coding: c.1388del
MANE Select: NM_020800
dbSNP: rs2108234807
Type: Deletion
Location: chr3:160282606 (GRCh38)
Gene constraint: LOEUF 0.739 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.50

Full IFT80 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Jeune syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

IFT80 c.440-18del Benign/Likely benign ★★ same condition
IFT80 c.1380+2del Likely pathogenic ★ same condition
IFT80 c.639+1del Pathogenic ★ same condition
IFT80 p.Ala590fs Pathogenic ★ same condition
IFT80 p.Glu300fs Pathogenic ★ same condition
IFT80 p.Met318fs Pathogenic ★ same condition
IFT80 p.Ser101fs Pathogenic ★ same condition
IFT80 p.Tyr356fs 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/ift80-p-ile463fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown