IFT80

intraflagellar transport 80, the group of WD repeat domain containing|IFT-B2 complex

Basic information

Region (hg38): 3:160256986-160399880

Previous symbols: [ "WDR56" ]

Links

ENSG00000068885 ∙ NCBI:57560 ∙ OMIM:611177 ∙ HGNC:29262 ∙ Uniprot:Q9P2H3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• asphyxiating thoracic dystrophy 2 (Definitive), mode of inheritance: AR
• asphyxiating thoracic dystrophy 2 (Moderate), mode of inheritance: AR
• Jeune syndrome (Supportive), mode of inheritance: AR
• Beemer-Langer syndrome (Supportive), mode of inheritance: AR
• short rib-polydactyly syndrome, Verma-Naumoff type (Supportive), mode of inheritance: AR
• asphyxiating thoracic dystrophy 2 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Craniofacial; Musculoskeletal; Neurologic; Renal	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal	17468754; 19610081; 19648123; 30767363

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IFT80 gene.

• Jeune thoracic dystrophy (25 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFT80 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			3	82	4	89
missense			238	4	2	244
nonsense	12	1	1			14
start loss						0
frameshift	12	1	1			14
inframe indel		1	2			3
splice donor/acceptor (+/-2bp)	1	9	2			12
splice region			11	29	4	44
non coding			42	80	28	150
Total	25	12	289	166	34

Highest pathogenic variant AF is 0.0000263

Variants in IFT80

This is a list of pathogenic ClinVar variants found in the IFT80 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-160257160-G-C		Asphyxiating thoracic dystrophy 2	Uncertain significance (Jan 12, 2018)
3-160257271-G-A		Asphyxiating thoracic dystrophy 2	Uncertain significance (Jan 13, 2018)
3-160257301-G-GTA		Jeune thoracic dystrophy	Uncertain significance (Jun 14, 2016)
3-160257303-A-G		Asphyxiating thoracic dystrophy 2	Uncertain significance (Jan 12, 2018)
3-160257321-C-T		Asphyxiating thoracic dystrophy 2	Benign (Jan 13, 2018)
3-160257404-A-G		Asphyxiating thoracic dystrophy 2	Uncertain significance (Jan 12, 2018)
3-160257415-T-C		Asphyxiating thoracic dystrophy 2	Uncertain significance (Apr 27, 2017)
3-160257436-A-G		Asphyxiating thoracic dystrophy 2	Likely benign (Jan 13, 2018)
3-160257581-T-C		Asphyxiating thoracic dystrophy 2	Uncertain significance (Jan 13, 2018)
3-160257588-T-A		Asphyxiating thoracic dystrophy 2	Uncertain significance (Jan 13, 2018)
3-160257638-A-G		Asphyxiating thoracic dystrophy 2	Uncertain significance (Jan 13, 2018)
3-160257681-C-A		Asphyxiating thoracic dystrophy 2	Uncertain significance (Jan 13, 2018)
3-160257728-T-G		Asphyxiating thoracic dystrophy 2	Uncertain significance (Jan 13, 2018)
3-160257733-A-C		Asphyxiating thoracic dystrophy 2	Uncertain significance (Jan 12, 2018)
3-160257758-C-G		Asphyxiating thoracic dystrophy 2	Uncertain significance (Jan 13, 2018)
3-160257785-C-A		Asphyxiating thoracic dystrophy 2	Uncertain significance (Jan 12, 2018)
3-160257848-T-C		Asphyxiating thoracic dystrophy 2	Uncertain significance (Jan 13, 2018)
3-160257866-G-C		Asphyxiating thoracic dystrophy 2	Uncertain significance (Jan 13, 2018)
3-160257974-T-C		Asphyxiating thoracic dystrophy 2	Uncertain significance (Jan 13, 2018)
3-160257985-T-C		Asphyxiating thoracic dystrophy 2	Uncertain significance (Jan 12, 2018)
3-160258108-T-C		Asphyxiating thoracic dystrophy 2	Uncertain significance (Jan 13, 2018)
3-160258128-T-C		Asphyxiating thoracic dystrophy 2	Uncertain significance (Jan 13, 2018)
3-160258206-C-T		Asphyxiating thoracic dystrophy 2	Uncertain significance (Jan 12, 2018)
3-160258207-G-A		Asphyxiating thoracic dystrophy 2	Uncertain significance (Jan 15, 2018)
3-160258395-C-G		Asphyxiating thoracic dystrophy 2	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFT80	protein_coding	protein_coding	ENST00000326448	19	142895

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.41e-19	0.244	125653	0	95	125748	0.000378

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	320	406	0.789	0.0000198	5104
Missense in Polyphen		80	96.032	0.83306		1207
Synonymous	-0.276	141	137	1.03	0.00000696	1419
Loss of Function	1.60	36	48.0	0.750	0.00000246	565

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00109	0.00108
Ashkenazi Jewish	0.00	0.00
East Asian	0.00115	0.00114
Finnish	0.0000534	0.0000462
European (Non-Finnish)	0.000301	0.000299
Middle Eastern	0.00115	0.00114
South Asian	0.000401	0.000392
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the intraflagellar transport (IFT) complex B, which is essential for the development and maintenance of motile and sensory cilia. {ECO:0000269|PubMed:17468754}.
• Pathway: Intraflagellar transport;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.568
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.47

Haploinsufficiency Scores

• pHI: 0.326
• hipred: N
• hipred_score: 0.221
• ghis: 0.600

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.252

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ift80
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); skeleton phenotype; limbs/digits/tail phenotype; growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; craniofacial phenotype

Zebrafish Information Network

• Gene name: ift80
• Affected structure: photoreceptor cell
• Phenotype tag: abnormal
• Phenotype quality: degeneration

Gene ontology

• Biological process: osteoblast differentiation;chondrocyte differentiation;smoothened signaling pathway;intraciliary transport involved in cilium assembly;positive regulation of smoothened signaling pathway;negative regulation of epithelial cell proliferation;bone morphogenesis;non-motile cilium assembly;negative regulation of non-canonical Wnt signaling pathway
• Cellular component: cytoplasm;centrosome;cilium;intraciliary transport particle B;ciliary tip