Is IFT80 p.Arg113= (c.339A>G) pathogenic?

IFT80 p.Arg113= (c.339A>G) is classified Uncertain significance in IFT80 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-25). Very rare (popmax 0.00671%, eas); Associated with asphyxiating thoracic dystrophy 2.

What condition is associated with IFT80 p.Arg113= (c.339A>G)?

IFT80 p.Arg113= (c.339A>G) is associated with asphyxiating thoracic dystrophy 2 (ClinVar).

How common is IFT80 p.Arg113= (c.339A>G) in the general population?

IFT80 p.Arg113= (c.339A>G) is very rare (popmax 0.00671%, eas) (gnomAD).

IFT80 p.Arg113=

c.339A>G · VCV3588744

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00671%, eas)

Conditions

asphyxiating thoracic dystrophy 2

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 0.15	GERP -1.5, phastCons 0.99
Overall
CADD	10.97	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00671% East Asian · 3/44,734 alleles

Filtering AF 0.00178% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000893%

Overall 0.000373% 6/1,608,126 alleles · very rare exomes 6/1,455,804 · genomes 0/152,322 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00671%	14,911
Ashkenazi Jewishnot grpmax-eligible	0.00339%	29,520
Remaining individualsnot grpmax-eligible	0.00161%	62,276
South Asian	0.0011%	90,866

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.Arg113=
Coding: c.339A>G
MANE Select: NM_020800
Type: single nucleotide variant
Location: chr3:160377461 (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-arg113 (accessed [today's date]).

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