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    DYNC2I1 dynein 2 intermediate chain 1 [ Homo sapiens (human) ]

    Gene ID: 55112, updated on 3-Apr-2024

    Summary

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    Official Symbol
    DYNC2I1provided by HGNC
    Official Full Name
    dynein 2 intermediate chain 1provided by HGNC
    Primary source
    HGNC:HGNC:21862
    See related
    Ensembl:ENSG00000126870 MIM:615462; AllianceGenome:HGNC:21862
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    DIC6; SRPS6; SRTD8; WDR60; FAP163; CFAP163
    Summary
    This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD) and may facilitate the formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes including cell cycle progression, signal transduction, apoptosis, and gene regulation. The encoded protein contains four WD repeats and may play a role in the formation of cilia. Mutations in this gene have been associated with short-rib polydactyly and Jeune syndromes. [provided by RefSeq, Mar 2014]
    Expression
    Broad expression in testis (RPKM 15.3), fat (RPKM 3.5) and 21 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    7q36.3
    Exon count:
    35
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (158839245..158958698)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (160062945..160186808)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (158631936..158738880)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:158526538-158527737 Neighboring gene ribosomal protein L21 pseudogene 76 Neighboring gene extended synaptotagmin 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158589571-158590070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158593246-158593746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158593747-158594247 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:158596845-158597436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:158604138-158604712 Neighboring gene Sharpr-MPRA regulatory region 8416 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26931 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26932 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18869 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18870 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18873 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18871 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18872 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26933 Neighboring gene uncharacterized LOC124901796 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158650125-158650666 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158654251-158654750 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:158670703-158671380 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:158671381-158672057 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:158702850-158704049 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:158735855-158736701 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158749944-158750515 Neighboring gene uncharacterized LOC124901794 Neighboring gene uncharacterized LOC124901795 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:158768653-158769393 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26936

    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. Expanding the phenotype associated with biallelic WDR60 mutations: Siblings with retinal degeneration and polydactyly lacking other features of short rib thoracic dystrophies. Kakar N, et al. Am J Med Genet A, 2018 Feb. PMID 29271569
    2. Dynein-2 intermediate chains play crucial but distinct roles in primary cilia formation and function. Vuolo L, et al. Elife, 2018 Oct 16. PMID 30320547, Free PMC Article
    3. New mutations in DYNC2H1 and WDR60 genes revealed by whole-exome sequencing in two unrelated Sardinian families with Jeune asphyxiating thoracic dystrophy. Cossu C, et al. Clin Chim Acta, 2016 Apr 1. PMID 26874042
    4. Short-rib polydactyly and Jeune syndromes are caused by mutations in WDR60. McInerney-Leo AM, et al. Am J Hum Genet, 2013 Sep 5. PMID 23910462, Free PMC Article
    5. Structure of the dynein-2 complex and its assembly with intraflagellar transport trains. Toropova K, et al. Nat Struct Mol Biol, 2019 Sep. PMID 31451806, Free PMC Article

    See all (42) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. WDR60 plays a major role and TCTEX1D2 plays an auxiliary role in the dynein-2 complex to mediate retrograde ciliary protein trafficking.
      Title: Interaction of WDR60 intermediate chain with TCTEX1D2 light chain of the dynein-2 complex is crucial for ciliary protein trafficking.
    2. loss of function of dynein-2 WDR34 and WDR60 subunits leads to defects in transition zone architecture, as well as intraflagellar transport.
      Title: Dynein-2 intermediate chains play crucial but distinct roles in primary cilia formation and function.
    3. Our finding broadens the spectrum of WDR60-related phenotypes and shows the utility of broad multigene panels during the genetic work-up of patients with ciliopathies.
      Title: Expanding the phenotype associated with biallelic WDR60 mutations: Siblings with retinal degeneration and polydactyly lacking other features of short rib thoracic dystrophies.
    4. exome analysis allowed to identify mutations not previously reported in the DYNC2H1 (MIM 603297) and WDR60 (MIM 615462) genes, both codifying for ciliary intraflagellar transport components whose mutations are known to cause Jeune syndrome
      Title: New mutations in DYNC2H1 and WDR60 genes revealed by whole-exome sequencing in two unrelated Sardinian families with Jeune asphyxiating thoracic dystrophy.
    5. These findings show that WDR60 mutations can cause skeletal ciliopathies and suggest a role for WDR60 in ciliogenesis.
      Title: Short-rib polydactyly and Jeune syndromes are caused by mutations in WDR60.
    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
    Short-rib thoracic dysplasia 8 with or without polydactyly
    MedGen: C3809691 OMIM: 615503 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Identification of ten loci associated with height highlights new biological pathways in human growth.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    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

    • FLJ10300, FLJ23575

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables dynein heavy chain binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables dynein light chain binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cilium assembly IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in embryonic skeletal system morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in intraciliary retrograde transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    colocalizes_with centrosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    colocalizes_with ciliary base IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in ciliary base IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in ciliary tip TAS
    Traceable Author Statement
    more info
    		  
    located_in cilium TAS
    Traceable Author Statement
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of cytoplasmic dynein complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular space HDA PubMed 
    colocalizes_with interphase microtubule organizing center IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in pericentriolar material IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    colocalizes_with spindle pole IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    cytoplasmic dynein 2 intermediate chain 1
    Names
    WD repeat domain 60
    WD repeat-containing protein 60
    testicular secretory protein Li 66

    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.

    Genomic

    1. NG_034051.2 RefSeqGene

      Range
      22314..111945
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001350914.2 → NP_001337843.1  cytoplasmic dynein 2 intermediate chain 1 isoform b

      Status: REVIEWED

      Source sequence(s)
      AC004863, AC124833
      Conserved Domains (3) summary
      COG2319
      Location:581 → 971
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:599 → 627
      7WD40; WD40 repeat [structural motif]
      cl26511
      Location:5 → 289
      Neuromodulin_N; Gap junction protein N-terminal region

    2. NM_001350915.2 → NP_001337844.1  cytoplasmic dynein 2 intermediate chain 1 isoform c

      Status: REVIEWED

      Source sequence(s)
      AC004863, AC124833
      Conserved Domains (2) summary
      COG2319
      Location:436 → 826
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:454 → 482
      7WD40; WD40 repeat [structural motif]

    3. NM_001350916.2 → NP_001337845.1  cytoplasmic dynein 2 intermediate chain 1 isoform d

      Status: REVIEWED

      Source sequence(s)
      AC004863, AC124833
      UniProtKB/TrEMBL
      A4D230
      Conserved Domains (2) summary
      COG2319
      Location:140 → 530
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:426 → 462
      7WD40; WD40 repeat [structural motif]

    4. NM_001350917.2 → NP_001337846.1  cytoplasmic dynein 2 intermediate chain 1 isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5), as well as variant 6, encodes isoform e.
      Source sequence(s)
      AC004863, AC124833
      UniProtKB/TrEMBL
      A4D230
      Conserved Domains (2) summary
      COG2319
      Location:211 → 601
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:497 → 533
      7WD40; WD40 repeat [structural motif]

    5. NM_001350918.2 → NP_001337847.1  cytoplasmic dynein 2 intermediate chain 1 isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6), as well as variant 5, encodes isoform e.
      Source sequence(s)
      AC004863, AC124833
      UniProtKB/TrEMBL
      A4D230
      Conserved Domains (2) summary
      COG2319
      Location:211 → 601
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:497 → 533
      7WD40; WD40 repeat [structural motif]

    6. NM_018051.5 → NP_060521.4  cytoplasmic dynein 2 intermediate chain 1 isoform a

      See identical proteins and their annotated locations for NP_060521.4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AC124833, AL137660, BC014491, BM718580, DB072968
      Consensus CDS
      CCDS47757.1
      UniProtKB/Swiss-Prot
      Q8WVS4, Q9NW58
      UniProtKB/TrEMBL
      A0A140VK66
      Related
      ENSP00000384290.3, ENST00000407559.8
      Conserved Domains (3) summary
      PTZ00121
      Location:5 → 453
      PTZ00121; MAEBL; Provisional
      COG2319
      Location:627 → 1017
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:645 → 673
      7WD40; WD40 repeat [structural motif]

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    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
      158839245..158958698
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047420560.1 → XP_047276516.1  cytoplasmic dynein 2 intermediate chain 1 isoform X1

    2. XM_006716041.3 → XP_006716104.1  cytoplasmic dynein 2 intermediate chain 1 isoform X3

      Conserved Domains (3) summary
      COG2319
      Location:630 → 1020
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:648 → 676
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:915 → 987
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    3. XM_017012382.2 → XP_016867871.1  cytoplasmic dynein 2 intermediate chain 1 isoform X8

    4. XM_047420556.1 → XP_047276512.1  cytoplasmic dynein 2 intermediate chain 1 isoform X2

    5. XM_047420555.1 → XP_047276511.1  cytoplasmic dynein 2 intermediate chain 1 isoform X1

    6. XM_047420558.1 → XP_047276514.1  cytoplasmic dynein 2 intermediate chain 1 isoform X6

    7. XM_047420559.1 → XP_047276515.1  cytoplasmic dynein 2 intermediate chain 1 isoform X7

    8. XM_011516369.3 → XP_011514671.1  cytoplasmic dynein 2 intermediate chain 1 isoform X1

      Conserved Domains (3) summary
      COG2319
      Location:584 → 974
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:602 → 630
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:869 → 941
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    9. XM_011516367.3 → XP_011514669.1  cytoplasmic dynein 2 intermediate chain 1 isoform X4

      Conserved Domains (3) summary
      COG2319
      Location:630 → 1020
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:648 → 676
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:915 → 987
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    10. XM_047420557.1 → XP_047276513.1  cytoplasmic dynein 2 intermediate chain 1 isoform X5

    11. XM_017012381.3 → XP_016867870.1  cytoplasmic dynein 2 intermediate chain 1 isoform X1

      Conserved Domains (3) summary
      COG2319
      Location:584 → 974
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:602 → 630
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:869 → 941
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    12. XM_047420561.1 → XP_047276517.1  cytoplasmic dynein 2 intermediate chain 1 isoform X9

    13. XM_047420563.1 → XP_047276519.1  cytoplasmic dynein 2 intermediate chain 1 isoform X10

    14. XM_047420562.1 → XP_047276518.1  cytoplasmic dynein 2 intermediate chain 1 isoform X11

    15. XM_017012388.2 → XP_016867877.1  cytoplasmic dynein 2 intermediate chain 1 isoform X10

      UniProtKB/TrEMBL
      A4D230
      Conserved Domains (2) summary
      COG2319
      Location:140 → 530
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:426 → 462
      7WD40; WD40 repeat [structural motif]

    RNA

    1. XR_007060058.1 RNA Sequence

    2. XR_007060061.1 RNA Sequence

    3. XR_007060060.1 RNA Sequence

    4. XR_007060057.1 RNA Sequence

    5. XR_007060062.1 RNA Sequence

    6. XR_007060059.1 RNA Sequence

    7. XR_007060063.1 RNA Sequence

    8. XR_007060064.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      160062945..160186808
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054358564.1 → XP_054214539.1  cytoplasmic dynein 2 intermediate chain 1 isoform X1

    2. XM_054358557.1 → XP_054214532.1  cytoplasmic dynein 2 intermediate chain 1 isoform X3

    3. XM_054358565.1 → XP_054214540.1  cytoplasmic dynein 2 intermediate chain 1 isoform X8

    4. XM_054358556.1 → XP_054214531.1  cytoplasmic dynein 2 intermediate chain 1 isoform X2

    5. XM_054358555.1 → XP_054214530.1  cytoplasmic dynein 2 intermediate chain 1 isoform X1

    6. XM_054358560.1 → XP_054214535.1  cytoplasmic dynein 2 intermediate chain 1 isoform X6

    7. XM_054358561.1 → XP_054214536.1  cytoplasmic dynein 2 intermediate chain 1 isoform X7

    8. XM_054358558.1 → XP_054214533.1  cytoplasmic dynein 2 intermediate chain 1 isoform X4

    9. XM_054358559.1 → XP_054214534.1  cytoplasmic dynein 2 intermediate chain 1 isoform X5

    10. XM_054358563.1 → XP_054214538.1  cytoplasmic dynein 2 intermediate chain 1 isoform X1

    11. XM_054358562.1 → XP_054214537.1  cytoplasmic dynein 2 intermediate chain 1 isoform X1

    12. XM_054358566.1 → XP_054214541.1  cytoplasmic dynein 2 intermediate chain 1 isoform X9

    13. XM_054358567.1 → XP_054214542.1  cytoplasmic dynein 2 intermediate chain 1 isoform X10

    14. XM_054358568.1 → XP_054214543.1  cytoplasmic dynein 2 intermediate chain 1 isoform X10

    RNA

    1. XR_008487646.1 RNA Sequence

    2. XR_008487648.1 RNA Sequence

    3. XR_008487647.1 RNA Sequence

    4. XR_008487645.1 RNA Sequence

    5. XR_008487650.1 RNA Sequence

    6. XR_008487649.1 RNA Sequence

    7. XR_008487651.1 RNA Sequence

    8. XR_008487652.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WVS4.3 GenPept UniProtKB/Swiss-Prot:Q8WVS4

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