IFT52

intraflagellar transport 52, the group of IFT-B1 complex

Basic information

Region (hg38): 20:43590936-43647299

Previous symbols: [ "C20orf9" ]

Links

ENSG00000101052 ∙ NCBI:51098 ∙ OMIM:617094 ∙ HGNC:15901 ∙ Uniprot:Q9Y366 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• short-rib thoracic dysplasia 16 with or without polydactyly (Limited), mode of inheritance: AR
• cranioectodermal dysplasia (Supportive), mode of inheritance: AR
• short-rib thoracic dysplasia 16 with or without polydactyly (Strong), mode of inheritance: AR
• short-rib thoracic dysplasia 16 with or without polydactyly (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Short-rib thoracic dysplasia 16 with or without polydactyly	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	Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	26880018; 27522498

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IFT52 gene.

• not provided (139 variants)
• Inborn genetic diseases (11 variants)
• Short-rib thoracic dysplasia 16 with or without polydactyly (4 variants)
• not specified (1 variants)
• Jeune thoracic dystrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFT52 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				28	4	32
missense			49	4	1	54
nonsense	2					2
start loss						0
frameshift			4			4
inframe indel			1			1
splice donor/acceptor (+/-2bp)			1			1
splice region			4	9	5	18
non coding			1	19	19	39
Total	2	0	56	51	24

Highest pathogenic variant AF is 0.0000197

Variants in IFT52

This is a list of pathogenic ClinVar variants found in the IFT52 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-43594710-G-A			Likely benign (Jun 05, 2022)
20-43594710-G-C			Uncertain significance (Jan 17, 2024)
20-43594740-C-T			Likely benign (Jan 03, 2019)
20-43594761-C-G			Likely benign (Jul 27, 2022)
20-43594763-A-C			Uncertain significance (Oct 25, 2022)
20-43594795-C-T		not specified	Uncertain significance (Feb 13, 2024)
20-43594802-A-G			Uncertain significance (Jul 07, 2023)
20-43594822-C-T		IFT52-related disorder	Likely benign (Jan 06, 2024)
20-43594828-A-G			Likely benign (Nov 07, 2022)
20-43594828-A-T			Likely benign (Oct 05, 2023)
20-43594832-A-G			Likely benign (Apr 23, 2023)
20-43594837-G-A			Likely benign (Apr 25, 2023)
20-43595049-C-G			Benign (May 13, 2021)
20-43596425-G-A			Likely benign (Nov 23, 2023)
20-43596430-T-C			Likely benign (Sep 06, 2022)
20-43596435-C-G			Uncertain significance (May 19, 2022)
20-43596436-T-C			Likely benign (Nov 14, 2017)
20-43596450-C-T			Likely benign (Jul 12, 2022)
20-43596459-G-T		not specified	Uncertain significance (Jul 25, 2023)
20-43596472-G-A		Short-rib thoracic dysplasia 16 with or without polydactyly	Uncertain significance (Sep 13, 2022)
20-43596474-G-A		Short-rib thoracic dysplasia 16 with or without polydactyly	Benign (Jan 31, 2024)
20-43596474-GA-AG			Uncertain significance (Apr 06, 2022)
20-43596503-A-G		not specified	Uncertain significance (Oct 02, 2023)
20-43596511-A-G		not specified	Uncertain significance (Jan 27, 2022)
20-43596516-A-G			Likely benign (Jun 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFT52	protein_coding	protein_coding	ENST00000373030	13	56366

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000201	0.974	125695	0	53	125748	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.44	173	235	0.735	0.0000120	2911
Missense in Polyphen		41	59.489	0.6892		751
Synonymous	0.203	84	86.4	0.972	0.00000457	805
Loss of Function	2.06	13	23.9	0.545	0.00000116	295

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000725	0.000725
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000654	0.000653
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.000654	0.000653
South Asian	0.000231	0.000229
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in ciliogenesis as part of a complex involved in intraflagellar transport (IFT), the bi-directional movement of particles required for the assembly, maintenance and functioning of primary cilia (PubMed:27466190). Required for the anterograde transport of IFT88 (PubMed:27466190). {ECO:0000269|PubMed:27466190}.
• Disease: DISEASE: Short-rib thoracic dysplasia 16 with or without polydactyly (SRTD16) [MIM:617102]: A form of short-rib thoracic dysplasia, a group of autosomal recessive ciliopathies that are characterized by a constricted thoracic cage, short ribs, shortened tubular bones, and a 'trident' appearance of the acetabular roof. Polydactyly is variably present. Non-skeletal involvement can include cleft lip/palate as well as anomalies of major organs such as the brain, eye, heart, kidneys, liver, pancreas, intestines, and genitalia. Some forms of the disease are lethal in the neonatal period due to respiratory insufficiency secondary to a severely restricted thoracic cage, whereas others are compatible with life. Disease spectrum encompasses Ellis-van Creveld syndrome, asphyxiating thoracic dystrophy (Jeune syndrome), Mainzer-Saldino syndrome, and short rib-polydactyly syndrome. {ECO:0000269|PubMed:26880018, ECO:0000269|PubMed:27466190}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Intraflagellar transport;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.262
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.54

Haploinsufficiency Scores

• pHI: 0.356
• hipred: N
• hipred_score: 0.322
• ghis: 0.619

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.288

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ift52
• 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)

Gene ontology

• Biological process: neural tube formation;heart looping;smoothened signaling pathway;dorsal/ventral pattern formation;intraciliary anterograde transport;intraciliary transport involved in cilium assembly;intraciliary transport;embryonic digit morphogenesis;negative regulation of epithelial cell proliferation;cilium assembly;regulation of protein processing;non-motile cilium assembly
• Cellular component: centrosome;centriole;cilium;intraciliary transport particle B;motile cilium;photoreceptor connecting cilium;dendrite terminus;ciliary tip;ciliary base
• Molecular function: protein C-terminus binding