Is IFT80 p.Ala467= (c.1401T>C) pathogenic?

IFT80 p.Ala467= (c.1401T>C) is classified Uncertain significance in IFT80 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). No allele count reported in gnomAD v4.1 (AN 1,587,410); Associated with asphyxiating thoracic dystrophy 2.

What condition is associated with IFT80 p.Ala467= (c.1401T>C)?

IFT80 p.Ala467= (c.1401T>C) is associated with asphyxiating thoracic dystrophy 2 (ClinVar).

How common is IFT80 p.Ala467= (c.1401T>C) in the general population?

IFT80 p.Ala467= (c.1401T>C) is no allele count reported in gnomAD v4.1 (AN 1,587,410) (gnomAD).

IFT80 p.Ala467=

c.1401T>C · rs1714770364 · VCV902943

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,587,410)

Conditions

asphyxiating thoracic dystrophy 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 4	GERP 1.9, phastCons 1
Overall
CADD	9.378	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,587,410). 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.Ala467=
Coding: c.1401T>C
MANE Select: NM_020800
dbSNP: rs1714770364
Type: single nucleotide variant
Location: chr3:160282593 (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

asphyxiating thoracic dystrophy 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

IFT80 p.Arg495Ter 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.Ala236Val Uncertain significance ★★ ⚠ same condition
IFT80 p.Arg220Cys Uncertain significance ★★ ⚠ same condition
IFT80 p.Arg220His 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-ala467 (accessed [today's date]).

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