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

Summary

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

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_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.

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Phenotypes

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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)

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

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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

D8S2279 (e-PCR)
- UniSTS:473907

SHGC-8189 (e-PCR)
- UniSTS:70477

SHGC-67307 (e-PCR)
- UniSTS:89991

SHGC-36672 (e-PCR)
- UniSTS:65176

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

NG_053008.1 RefSeqGene

Range

5001..40972

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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)
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)
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)
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)
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

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

43774039..43828347

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

43779369..43833678

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GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

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.