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

Gene ID: 51626, updated on 14-Nov-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
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Genomic context

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See DYNC2LI1 in Genome Data Viewer
Location:
2p21
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (43774039..43828347)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (43779369..43833678)
RS_2024_09 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 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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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
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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 
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_2024_08

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

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