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    IFT56 intraflagellar transport 56 [ Homo sapiens (human) ]

    Gene ID: 79989, updated on 27-Nov-2024

    Summary

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    Official Symbol
    IFT56provided by HGNC
    Official Full Name
    intraflagellar transport 56provided by HGNC
    Primary source
    HGNC:HGNC:21882
    See related
    Ensembl:ENSG00000105948 MIM:617453; AllianceGenome:HGNC:21882
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    BRENS; DYF13; TTC26; dyf-13
    Summary
    Predicted to enable intraciliary transport particle B binding activity. Involved in cilium assembly. Located in cilium. Part of intraciliary transport particle B. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in testis (RPKM 5.7), thyroid (RPKM 2.6) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See IFT56 in Genome Data Viewer
    Location:
    7q34
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (139133778..139191986)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (140447060..140505276)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (138818524..138876732)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene microRNA 10399 Neighboring gene zinc finger CCCH-type containing, antiviral 1 Neighboring gene ribosomal protein L17 pseudogene 28 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:138786521-138787092 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26746 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:138794119-138794622 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26749 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26750 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26751 Neighboring gene Sharpr-MPRA regulatory region 4033 Neighboring gene Sharpr-MPRA regulatory region 8039 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:138859395-138860231 Neighboring gene NANOG hESC enhancer GRCh37_chr7:138867531-138868130 Neighboring gene Sharpr-MPRA regulatory region 12471 Neighboring gene MSL3 pseudogene 2 Neighboring gene uncharacterized LOC124901756 Neighboring gene FCF1 pseudogene 11

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Pituitary stalk interruption syndrome broadens the clinical spectrum of the TTC26 ciliopathy. David O, et al. Clin Genet, 2020 Sep. PMID 32617964
    2. Biallelic Mutations in Tetratricopeptide Repeat Domain 26 (Intraflagellar Transport 56) Cause Severe Biliary Ciliopathy in Humans. Shaheen R, et al. Hepatology, 2020 Jun. PMID 31595528
    3. TTC26/DYF13 is an intraflagellar transport protein required for transport of motility-related proteins into flagella. Ishikawa H, et al. Elife, 2014 Jan 1. PMID 24596149, Free PMC Article
    4. Overall Architecture of the Intraflagellar Transport (IFT)-B Complex Containing Cluap1/IFT38 as an Essential Component of the IFT-B Peripheral Subcomplex. Katoh Y, et al. J Biol Chem, 2016 May 20. PMID 26980730, Free PMC Article
    5. Interactome of the Autoimmune Risk Protein ANKRD55. Ugidos N, et al. Front Immunol, 2019. PMID 31620119, Free PMC Article

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Pituitary stalk interruption syndrome broadens the clinical spectrum of the TTC26 ciliopathy.
      Title: Pituitary stalk interruption syndrome broadens the clinical spectrum of the TTC26 ciliopathy.
    2. Biallelic Mutations in Tetratricopeptide Repeat Domain 26 (Intraflagellar Transport 56) Cause Severe Biliary Ciliopathy in Humans.
      Title: Biallelic Mutations in Tetratricopeptide Repeat Domain 26 (Intraflagellar Transport 56) Cause Severe Biliary Ciliopathy in Humans.
    3. TTC26 is an intraflagellar transport protein required for transport of motility-related proteins into flagella.
      Title: TTC26/DYF13 is an intraflagellar transport protein required for transport of motility-related proteins into flagella.
    4. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Biliary, renal, neurologic, and skeletal syndrome
    MedGen: C5561990 OMIM: 619534 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ12571, MGC163211

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables intraciliary transport particle B binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in axoneme assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cilium assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in cilium assembly NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in intraciliary anterograde transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intraciliary anterograde transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in intraciliary transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in intraciliary transport involved in cilium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in manchette assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein localization to cilium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in smoothened signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in centrosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in ciliary basal body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in ciliary base IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in ciliary tip TAS
    Traceable Author Statement
    more info
    		  
    located_in cilium IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in cilium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cilium NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in cilium TAS
    Traceable Author Statement
    more info
    		  
    part_of intraciliary transport particle B IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of intraciliary transport particle B IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    part_of intraciliary transport particle B ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in neuron projection IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    intraflagellar transport protein 56
    Names
    TPR repeat protein 26
    tetratricopeptide repeat domain 26
    tetratricopeptide repeat protein 26

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001144920.3 → NP_001138392.1  intraflagellar transport protein 56 isoform 2

      See identical proteins and their annotated locations for NP_001138392.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks lacks an alternate exon that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC009220, BC144151, BP315162, CA450032
      Consensus CDS
      CCDS55172.1
      UniProtKB/Swiss-Prot
      A0AVF1
      Related
      ENSP00000410655.1, ENST00000430935.5
      Conserved Domains (2) summary
      sd00006
      Location:58 → 86
      TPR; TPR repeat [structural motif]
      cl26002
      Location:33 → 323
      TPR_11; TPR repeat

    2. NM_001144923.3 → NP_001138395.1  intraflagellar transport protein 56 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.
      Source sequence(s)
      AC009220, AK299132, BP315162, CA450032
      Consensus CDS
      CCDS55173.1
      UniProtKB/Swiss-Prot
      A0AVF1
      Related
      ENSP00000339135.4, ENST00000343187.8
      Conserved Domains (2) summary
      TIGR02917
      Location:33 → 286
      PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein
      sd00006
      Location:124 → 148
      TPR; TPR repeat [structural motif]

    3. NM_001287512.2 → NP_001274441.1  intraflagellar transport protein 56 isoform 4

      See identical proteins and their annotated locations for NP_001274441.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks three alternate exons that result in the loss of an in-frame segment in the 5' coding region, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
      Source sequence(s)
      AC009220, AK295092, CA450032
      Consensus CDS
      CCDS75665.1
      UniProtKB/TrEMBL
      B7Z2T3, B7Z6R6
      Related
      ENSP00000418788.1, ENST00000495038.5
      Conserved Domains (3) summary
      sd00006
      Location:58 → 86
      TPR; TPR repeat [structural motif]
      pfam10345
      Location:14 → 190
      Cohesin_load; Cohesin loading factor
      pfam12895
      Location:35 → 113
      ANAPC3; Anaphase-promoting complex, cyclosome, subunit 3

    4. NM_001287513.2 → NP_001274442.1  intraflagellar transport protein 56 isoform 5

      See identical proteins and their annotated locations for NP_001274442.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in its 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (5) is shorter at the N-terminus, compared to isoform 1.
      Source sequence(s)
      AC009220, AK293444, BP315162, CA450032
      UniProtKB/TrEMBL
      B7Z1H0
      Conserved Domains (2) summary
      TIGR02917
      Location:53 → 218
      PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein
      sd00006
      Location:50 → 74
      TPR; TPR repeat [structural motif]

    5. NM_001318333.2 → NP_001305262.1  intraflagellar transport protein 56 isoform 6

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) uses an alternate splice site in its 5' UTR and a downstream in-frame start codon, compared to variant 1. The encoded isoform (6) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC009220, BC013912, BC034466, BP315162, CA450032
      UniProtKB/TrEMBL
      Q96CU4
      Conserved Domains (2) summary
      TIGR02917
      Location:18 → 206
      PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein
      sd00006
      Location:15 → 39
      TPR; TPR repeat [structural motif]

    6. NM_001321740.2 → NP_001308669.1  intraflagellar transport protein 56 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC009220, BC013912, BC034466, CA450032
      UniProtKB/TrEMBL
      Q96CU4
      Conserved Domains (2) summary
      sd00006
      Location:58 → 86
      TPR; TPR repeat [structural motif]
      pfam13414
      Location:64 → 113
      TPR_11; TPR repeat

    7. NM_001321741.2 → NP_001308670.1  intraflagellar transport protein 56 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AC009220, BC013912, BC034466, BP315162, CA450032
      UniProtKB/TrEMBL
      B7Z6R6
      Related
      ENSP00000419178.2, ENST00000478836.6
      Conserved Domains (2) summary
      sd00006
      Location:58 → 86
      TPR; TPR repeat [structural motif]
      pfam12895
      Location:35 → 113
      ANAPC3; Anaphase-promoting complex, cyclosome, subunit 3

    8. NM_001321742.2 → NP_001308671.1  intraflagellar transport protein 56 isoform 9

      Status: VALIDATED

      Source sequence(s)
      AC009220, BC013912
      Consensus CDS
      CCDS83230.1
      UniProtKB/TrEMBL
      Q96CU4
      Related
      ENSP00000443253.1, ENST00000474035.6
      Conserved Domains (2) summary
      sd00006
      Location:56 → 86
      TPR; TPR repeat [structural motif]
      cl26002
      Location:33 → 252
      TPR_11; TPR repeat

    9. NM_024926.4 → NP_079202.2  intraflagellar transport protein 56 isoform 1

      See identical proteins and their annotated locations for NP_079202.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC009220, BC126331, BP315162, CA450032
      Consensus CDS
      CCDS5852.1
      UniProtKB/Swiss-Prot
      A0AVF1, A4D1S3, B7Z5M0, C9J2N7, F8W724, Q9H9S8, Q9NTC0
      UniProtKB/TrEMBL
      B7Z6R6
      Related
      ENSP00000419279.1, ENST00000464848.5
      Conserved Domains (2) summary
      sd00006
      Location:58 → 86
      TPR; TPR repeat [structural motif]
      pfam13414
      Location:64 → 113
      TPR_11; TPR repeat

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      139133778..139191986
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      140447060..140505276
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A0AVF1.1 GenPept UniProtKB/Swiss-Prot:A0AVF1

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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