Is IFT80 p.Glu304= (c.912G>A) pathogenic?

IFT80 p.Glu304= (c.912G>A) is classified Conflicting classifications of pathogenicity in IFT80 (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2026-01-07). Very rare (popmax 0.00297%, nfe); Associated with Jeune syndrome.

What condition is associated with IFT80 p.Glu304= (c.912G>A)?

IFT80 p.Glu304= (c.912G>A) is associated with Jeune syndrome, asphyxiating thoracic dystrophy 2 (ClinVar).

How common is IFT80 p.Glu304= (c.912G>A) in the general population?

IFT80 p.Glu304= (c.912G>A) is very rare (popmax 0.00297%, nfe) (gnomAD).

IFT80 p.Glu304=

c.912G>A · rs199575501 · VCV697279

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00297%, nfe)

Conditions

Jeune syndrome

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -0.27	GERP -2, phastCons 0.18
Overall
CADD	6.439	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00297% European (non-Finnish) · 35/1,179,280 alleles

Filtering AF 0.00215% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00191%

Overall 0.0135% 217/1,612,944 alleles · very rare exomes 194/1,461,006 · genomes 23/151,938 · joint denominator

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.514%	194
Remaining individualsnot grpmax-eligible	0.048%	2,082
European (non-Finnish)grpmax	0.00297%	33,694

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Glu304=
Coding: c.912G>A
MANE Select: NM_020800
dbSNP: rs199575501
Type: single nucleotide variant
Location: chr3:160319805 (GRCh38)

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

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-glu304 (accessed [today's date]).

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