Is IFT80 p.Arg495Ter (c.1483C>T) pathogenic?

IFT80 p.Arg495Ter (c.1483C>T) is classified Pathogenic/Likely pathogenic in IFT80 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-02-15). Very rare (popmax 0.00537%, afr); Associated with Jeune syndrome.

What condition is associated with IFT80 p.Arg495Ter (c.1483C>T)?

IFT80 p.Arg495Ter (c.1483C>T) is associated with Jeune syndrome, asphyxiating thoracic dystrophy 2 (ClinVar).

How common is IFT80 p.Arg495Ter (c.1483C>T) in the general population?

IFT80 p.Arg495Ter (c.1483C>T) is very rare (popmax 0.00537%, afr) (gnomAD).

IFT80 p.Arg495Ter

c.1483C>T · rs369779153 · VCV2181200

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00537%, afr)

Conditions

Jeune syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 14 of 20
Splicing
SpliceAI	Δ0.49	donor loss, 33 bp away · masked 0 · deltas
Pangolin	Δ0.40	loss · gain 0.01 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 6.5	GERP 1.1, phastCons 1
Overall
CADD	38.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00537% African / African-American · 4/74,420 alleles

Filtering AF 0.00175% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0011%

Overall 0.00188% 30/1,596,160 alleles · very rare exomes 26/1,444,200 · genomes 4/151,960 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00537%	18,605
South Asian	0.00225%	44,390
European (non-Finnish)	0.00197%	50,787
Remaining individualsnot grpmax-eligible	0.00162%	61,808

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.Arg495Ter
Coding: c.1483C>T
MANE Select: NM_020800
dbSNP: rs369779153
Type: single nucleotide variant
Location: chr3:160282511 (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

Also linked: asphyxiating thoracic dystrophy 2

Similar variants

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
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-arg495ter (accessed [today's date]).

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