Is IFT80 p.Val293= (c.879C>T) pathogenic?

IFT80 p.Val293= (c.879C>T) is classified Conflicting classifications of pathogenicity in IFT80 (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2025-12-08). Rare (popmax 0.303%, sas); Associated with Jeune syndrome.

What condition is associated with IFT80 p.Val293= (c.879C>T)?

IFT80 p.Val293= (c.879C>T) is associated with Jeune syndrome, connective tissue disorder, asphyxiating thoracic dystrophy 2 (ClinVar).

How common is IFT80 p.Val293= (c.879C>T) in the general population?

IFT80 p.Val293= (c.879C>T) is rare (popmax 0.303%, sas) (gnomAD).

IFT80 p.Val293=

c.879C>T · rs143660757 · VCV700235

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.303%, sas)

Conditions

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 -0.35	GERP -3.2, phastCons 0.001
Overall
CADD	8.122	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.303% South Asian · 276/91,034 alleles

Filtering AF 0.274% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.262%

Overall 0.0205% 331/1,612,760 alleles · rare exomes 300/1,460,906 · genomes 31/151,854 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.303%	330
African / African-American	0.0361%	2,773
Remaining individualsnot grpmax-eligible	0.0224%	4,462
East Asian	0.00669%	14,949
European (non-Finnish)	0.000933%	107,201

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.Val293=
Coding: c.879C>T
MANE Select: NM_020800
dbSNP: rs143660757
Type: single nucleotide variant
Location: chr3:160319838 (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: connective tissue disorder asphyxiating thoracic dystrophy 2

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-val293 (accessed [today's date]).

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