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    DYNC2LI1 dynein cytoplasmic 2 light intermediate chain 1 [ Homo sapiens (human) ]

    Gene ID: 51626, updated on 5-Mar-2024

    Summary

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    Official Symbol
    DYNC2LI1provided by HGNC
    Official Full Name
    dynein cytoplasmic 2 light intermediate chain 1provided by HGNC
    Primary source
    HGNC:HGNC:24595
    See related
    Ensembl:ENSG00000138036 MIM:617083; AllianceGenome:HGNC:24595
    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
    LIC3; D2LIC; CGI-60
    Summary
    This gene encodes a protein that is a component of the dynein-2 microtubule motor protein complex that plays a role in the retrograde transport of cargo in primary cilia via the intraflagellar transport system. This gene is ubiquitously expressed and its protein, which localizes to the axoneme and Golgi apparatus, interacts directly with the cytoplasmic dynein 2 heavy chain 1 protein to form part of the multi-protein dynein-2 complex. Mutations in this gene produce defects in the dynein-2 complex which result in several types of ciliopathy including short-rib thoracic dysplasia 15 with polydactyly (SRTD15). Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Feb 2017]
    Expression
    Ubiquitous expression in testis (RPKM 10.0), thyroid (RPKM 6.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    2p21
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (43774039..43828347)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (43779369..43833678)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (44001178..44055486)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene pleckstrin homology, MyTH4 and FERM domain containing H2 Neighboring gene zinc finger protein 106 homolog (mouse) pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr2:43942164-43942363 Neighboring gene MPRA-validated peak3684 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr2:43973372-43973613 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15680 Neighboring gene uncharacterized LOC105374571 Neighboring gene RN7SK pseudogene 66 Neighboring gene ATP binding cassette subfamily G member 5 Neighboring gene uncharacterized LOC102725159 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11428 Neighboring gene ATP binding cassette subfamily G member 8 Neighboring gene RNA, U6 small nuclear 1048, pseudogene Neighboring gene leucine rich pentatricopeptide repeat containing

    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. Combinations of deletion and missense variations of the dynein-2 DYNC2LI1 subunit found in skeletal ciliopathies cause ciliary defects. Qiu H, et al. Sci Rep, 2022 Jan 7. PMID 34997029, Free PMC Article
    2. Whole-exome sequencing identified two novel mutations of DYNC2LI1 in fetal skeletal ciliopathy. Zhang X, et al. Mol Genet Genomic Med, 2020 Dec. PMID 33030252, Free PMC Article
    3. Biallelic mutations in DYNC2LI1 are a rare cause of Ellis-van Creveld syndrome. Niceta M, et al. Clin Genet, 2018 Mar. PMID 28857138
    4. DYNC2LI1 mutations broaden the clinical spectrum of dynein-2 defects. Kessler K, et al. Sci Rep, 2015 Jul 1. PMID 26130459, Free PMC Article
    5. Mutations in DYNC2LI1 disrupt cilia function and cause short rib polydactyly syndrome. Taylor SP, et al. Nat Commun, 2015 Jun 16. PMID 26077881, Free PMC Article

    See all (33) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Combinations of deletion and missense variations of the dynein-2 DYNC2LI1 subunit found in skeletal ciliopathies cause ciliary defects.
      Title: Combinations of deletion and missense variations of the dynein-2 DYNC2LI1 subunit found in skeletal ciliopathies cause ciliary defects.
    2. Whole-exome sequencing identified two novel mutations of DYNC2LI1 in fetal skeletal ciliopathy.
      Title: Whole-exome sequencing identified two novel mutations of DYNC2LI1 in fetal skeletal ciliopathy.
    3. Our findings indicate that DYNC2LI1 mutations are associated with a wider clinical spectrum than previously appreciated, including EvC, with the severity of the phenotype likely depending on the extent of defective DYNC2LI1 function.
      Title: Biallelic mutations in DYNC2LI1 are a rare cause of Ellis-van Creveld syndrome.
    4. depletion of DYNC2LI1 induced altered cilia morphology with broadened ciliary tips and accumulation of intraflagellar transport complexes (IFT-B) complex proteins in accordance with retrograde IFT defects.
      Title: DYNC2LI1 mutations broaden the clinical spectrum of dynein-2 defects.
    5. DYNC2LI1 is essential for dynein-2 complex stability and that mutations in DYNC2LI1 result in variable length, including hyperelongated, cilia, Hedgehog pathway impairment and ciliary IFT accumulations, causing short rib polydactyly syndrome.
      Title: Mutations in DYNC2LI1 disrupt cilia function and cause short rib polydactyly syndrome.
    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 15 with polydactyly
    MedGen: C4310724 OMIM: 617088 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)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    capsid gag HIV-1 CA uncoating is delayed in the presence of ciliobrevin D, a specific inhibitor of dynein-mediated motor function, indicating that dynein is involved in CA uncoating in cells PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • DKFZp564A033

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables dynein heavy chain binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables dynein heavy chain binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in determination of left/right symmetry IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in intraciliary retrograde transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intraciliary transport involved in cilium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intraciliary transport involved in cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in apical part of cell ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in axoneme IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in axoneme ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in ciliary basal body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in ciliary basal body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    colocalizes_with ciliary basal body ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in ciliary tip TAS
    Traceable Author Statement
    more info
    		  
    located_in ciliary transition zone IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cilium TAS
    Traceable Author Statement
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of cytoplasmic dynein complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of cytoplasmic dynein complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of cytoplasmic dynein complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in microtubule IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in motile cilium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    cytoplasmic dynein 2 light intermediate chain 1

    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_053008.1 RefSeqGene

      Range
      5001..40972
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001193464.2 → NP_001180393.1  cytoplasmic dynein 2 light intermediate chain 1 isoform 4

      See identical proteins and their annotated locations for NP_001180393.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate in-frame splice site in the middle portion of the coding region, compared to variant 1. This results in a longer protein (isoform 4), compared to isoform 1.
      Source sequence(s)
      AK223432, BC006969
      Consensus CDS
      CCDS62903.1
      UniProtKB/TrEMBL
      H7BYC8
      Related
      ENSP00000474032.1, ENST00000605786.5
      Conserved Domains (1) summary
      pfam05783
      Location:2 → 269
      DLIC; Dynein light intermediate chain (DLIC)

    2. NM_001348912.2 → NP_001335841.1  cytoplasmic dynein 2 light intermediate chain 1 isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) has multiple differences at its 3' end, compared to variant 1. This results in a longer protein (isoform 5) with a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC011242, AC108476
      UniProtKB/TrEMBL
      H7BYC8
      Conserved Domains (1) summary
      pfam05783
      Location:2 → 268
      DLIC; Dynein light intermediate chain (DLIC)

    3. NM_001348913.2 → NP_001335842.1  cytoplasmic dynein 2 light intermediate chain 1 isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) uses an alternate in-frame splice site in the middle portion of the coding region and has multiple differences at its 3' end, compared to variant 1. This results in a longer protein (isoform 6) with a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC011242, AC108476
      UniProtKB/TrEMBL
      H7BYC8
      Conserved Domains (1) summary
      pfam05783
      Location:2 → 269
      DLIC; Dynein light intermediate chain (DLIC)

    4. NM_015522.4 → NP_056337.1  cytoplasmic dynein 2 light intermediate chain 1 isoform 2

      See identical proteins and their annotated locations for NP_056337.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (2) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AK223432, BC016324, CB528979
      Consensus CDS
      CCDS46270.1
      UniProtKB/Swiss-Prot
      Q8TCX1
      Related
      ENSP00000385738.3, ENST00000406852.7
      Conserved Domains (1) summary
      pfam05783
      Location:2 → 160
      DLIC; Dynein light intermediate chain (DLIC)

    5. NM_016008.4 → NP_057092.2  cytoplasmic dynein 2 light intermediate chain 1 isoform 1

      See identical proteins and their annotated locations for NP_057092.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform 1.
      Source sequence(s)
      AK223432, AY083346
      Consensus CDS
      CCDS1813.1
      UniProtKB/Swiss-Prot
      A8MVJ5, Q53F57, Q6PDB2, Q8IWA3, Q8TCX1, Q96B03, Q96J00, Q9Y370, Q9Y3S9
      UniProtKB/TrEMBL
      H7BYC8
      Related
      ENSP00000260605.8, ENST00000260605.12
      Conserved Domains (1) summary
      pfam05783
      Location:2 → 268
      DLIC; Dynein light intermediate chain (DLIC)

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      43774039..43828347
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      43779369..43833678
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001012665.1: Suppressed sequence

      Description
      NM_001012665.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TCX1.1 GenPept UniProtKB/Swiss-Prot:Q8TCX1

    Gene LinkOut

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

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