IFT80

Chr 3AR

intraflagellar transport 80

Also known as: ATD2, CFAP167, FAP167, SRTD2, WDR56

NCBI Gene: 57560 ENSG00000068885 UniProt: Q9P2H3 OMIM: 611177

The protein encoded by this gene is part of the intraflagellar transport complex B and is necessary for the function of motile and sensory cilia. Defects in this gene are a cause of asphyxiating thoracic dystrophy 2 (ATD2). Three transcript variants encoding two different isoforms have been found for this gene.[provided by RefSeq, Jun 2010]

OMIM Research

OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Short-rib thoracic dysplasia 2 with or without polydactylyMIM #611263

Clinical highlights

Gene–disease validity (ClinGen)

Definitive · asphyxiating thoracic dystrophy 2 · AR · ClinGen 2024

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.99

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.99LOEUF

pLI 0.000

Z-score 1.60

OE 0.75 (0.57–0.99)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

1.51Z-score

OE missense 0.79 (0.72–0.86)

320 obs / 405.7 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.75 (0.57–0.99)

0≤0.351.4

Missense OE?0.79 (0.72–0.86)

0≤0.61.4

Synonymous OE?1.03

0≤1.21.6

LoF obs/exp: 36 / 48.0Missense obs/exp: 320 / 405.7Syn Z: -0.28

Background carrier burden — how many people carry a rare variant somewhere in IFT80?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 81

853 rare PASS variants

Rare truncating (LoF)

1 in 470

174 rare PASS variants

Rare synonymous (reference)

1 in 140

314 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for IFT80. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 110	1 in 1,100
South Asian	~43k	1 in 72	1 in 710
Remaining (unassigned)	~30k	1 in 51	1 in 440
European (Finnish)	~27k	1 in 250	≈ 1 in 27,000
Admixed American	~22k	1 in 66	1 in 820
African / African American	~21k	1 in 120	1 in 720
East Asian	~20k	1 in 87	1 in 210
Ashkenazi Jewish	~13k	1 in 280	none seen
Middle Eastern	~2,884	1 in 45	1 in 360

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 14 of 19 coding exons well covered in gnomAD exomes; exons 2, 4, 7, 10, 14 marginal. Genomes: all 19.? see exons ↓