Is IFT80 p.Lys94= (c.282G>A) pathogenic?

IFT80 p.Lys94= (c.282G>A) is classified Benign/Likely benign in IFT80 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2025-11-13). Rare (popmax 0.619%, sas); Associated with connective tissue disorder.

What condition is associated with IFT80 p.Lys94= (c.282G>A)?

IFT80 p.Lys94= (c.282G>A) is associated with connective tissue disorder, asphyxiating thoracic dystrophy 2, Jeune syndrome (ClinVar).

How common is IFT80 p.Lys94= (c.282G>A) in the general population?

IFT80 p.Lys94= (c.282G>A) is rare (popmax 0.619%, sas) (gnomAD).

IFT80 p.Lys94=

c.282G>A · rs548358266 · VCV343982

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

rare (popmax 0.619%, sas)

Conditions

connective tissue disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.25	acceptor gain · deltas
Constraint at this position
Conservation	phyloP 1.7	GERP 0.76, phastCons 1
Overall
CADD	17.25	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.619% South Asian · 555/89,632 alleles

Filtering AF 0.577% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.56%

Overall 0.0371% 595/1,603,610 alleles · rare exomes 556/1,451,414 · genomes 39/152,196 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.619%	161
Remaining individualsnot grpmax-eligible	0.0547%	1,829
Middle Eastern	0.0166%	6,028
East Asian	0.00224%	44,724
African / African-American	0.00134%	74,684
European (non-Finnish)	0.000256%	390,949

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.Lys94=
Coding: c.282G>A
MANE Select: NM_020800
dbSNP: rs548358266
Type: single nucleotide variant
Location: chr3:160377518 (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

connective tissue disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: asphyxiating thoracic dystrophy 2 Jeune syndrome

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-lys94 (accessed [today's date]).

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