IFT56

intraflagellar transport 56, the group of IFT-B1 complex|Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 7:139133744-139191986

Previous symbols: [ "TTC26" ]

Links

ENSG00000105948 ∙ NCBI:79989 ∙ OMIM:617453 ∙ HGNC:21882 ∙ Uniprot:A0AVF1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• biliary, renal, neurologic, and skeletal syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Biliary, renal, neurologic, and skeletal syndrome	AR	Cardiovascular; Endocrine; Gastrointestinal; Renal	The condition can include cardiovascular and renal anomalies, and awareness may enable early diagnosis and medical or surgical management; The condition can include pituitary insufficiency, and awareness may allow early diagnosis and management; The condition can involve hepatic dysfunction, and medical management as well as hepatic transplant may be beneficial	Cardiovascular; Craniofacial; Endocrine; Gastrointestinal; Genitourinary; Musculoskeletal; Neurologic; Renal	31595528; 32617964; 34177428
Cardiovascular

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IFT56 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFT56 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				5	2	7
missense		1	30	4	3	38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		2				2
splice region				1		1
non coding				5	3	8
Total	0	3	30	14	8

Variants in IFT56

This is a list of pathogenic ClinVar variants found in the IFT56 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-139134654-G-C		Biliary, renal, neurologic, and skeletal syndrome • Hydrocephalus	Pathogenic/Likely pathogenic (Mar 14, 2024)
7-139134688-G-A		not specified	Uncertain significance (Nov 03, 2022)
7-139134689-G-A		not specified	Likely benign (Apr 22, 2024)
7-139134699-C-T			Benign (Oct 20, 2022)
7-139137853-C-T			Benign (Feb 08, 2022)
7-139137927-G-A			Likely benign (Oct 23, 2022)
7-139139890-G-A		not specified	Uncertain significance (Dec 03, 2021)
7-139139898-A-C			Uncertain significance (Jun 13, 2022)
7-139139965-C-T		not specified	Uncertain significance (Jan 26, 2023)
7-139147221-C-T		Biliary, renal, neurologic, and skeletal syndrome	Uncertain significance (Sep 08, 2023)
7-139147264-A-G		not specified	Uncertain significance (Jun 21, 2023)
7-139147277-C-A		not specified	Uncertain significance (Feb 07, 2025)
7-139148190-T-C			Benign (Nov 01, 2022)
7-139148219-C-T		not specified	Uncertain significance (May 31, 2024)
7-139148230-T-C			Likely benign (Feb 03, 2022)
7-139148252-T-C			Benign (May 20, 2022)
7-139148370-C-T		not specified	Uncertain significance (May 10, 2022)
7-139160958-A-G		not specified	Uncertain significance (Nov 06, 2023)
7-139160972-A-G		not specified	Uncertain significance (Oct 09, 2024)
7-139161018-A-G		Caroli disease • Biliary, renal, neurologic, and skeletal syndrome	Likely pathogenic (Mar 17, 2024)
7-139165116-A-T			Likely benign (Jun 12, 2021)
7-139165117-T-A			Likely benign (Aug 24, 2022)
7-139165228-C-T			Benign (Jul 05, 2022)
7-139165254-G-C			Likely benign (Oct 13, 2022)
7-139166843-A-G		not specified	Uncertain significance (May 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFT56	protein_coding	protein_coding	ENST00000464848	18	58243

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.43e-8	0.999	125705	0	43	125748	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.34	226	290	0.779	0.0000143	3675
Missense in Polyphen		49	79.451	0.61673		1028
Synonymous	0.482	93	99.1	0.938	0.00000478	978
Loss of Function	2.91	19	38.5	0.494	0.00000203	456

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000635	0.000635
Ashkenazi Jewish	0.00	0.00
East Asian	0.000435	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000435	0.000435
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the intraflagellar transport (IFT) complex B required for transport of proteins in the motile cilium. Required for transport of specific ciliary cargo proteins related to motility, while it is neither required for IFT complex B assembly or motion nor for cilium assembly. Required for efficient coupling between the accumulation of GLI2 and GLI3 at the ciliary tips and their dissociation from the negative regulator SUFU. Plays a key role in maintaining the integrity of the IFT complex B and the proper ciliary localization of the IFT complex B components. Not required for IFT complex A ciliary localization or function. Essential for maintaining proper microtubule organization within the ciliary axoneme. {ECO:0000250|UniProtKB:Q8BS45}.
• Pathway: Intraflagellar transport;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.856
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.54

Haploinsufficiency Scores

• pHI: 0.149
• hipred: Y
• hipred_score: 0.558
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.256

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttc26
• Phenotype: cellular phenotype; craniofacial phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; embryo phenotype; skeleton phenotype; vision/eye phenotype; limbs/digits/tail phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); reproductive system 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: ttc26
• Affected structure: pronephric tubule
• Phenotype tag: abnormal
• Phenotype quality: distended

Gene ontology

• Biological process: smoothened signaling pathway;axoneme assembly;intraciliary anterograde transport;intraciliary transport involved in cilium assembly;intraciliary transport;cilium assembly;protein localization to cilium;manchette assembly
• Cellular component: centrosome;cilium;intraciliary transport particle B;motile cilium;ciliary basal body;ciliary tip;ciliary base
• Molecular function: intraciliary transport particle B binding