CLIP3 CAP-Gly domain containing linker protein 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CLIP3provided by HGNC
Official Full Name: CAP-Gly domain containing linker protein 3provided by HGNC
Primary source: HGNC:HGNC:24314
See related: Ensembl:ENSG00000105270 MIM:607382; AllianceGenome:HGNC:24314
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: RSNL1; CLIPR59; CLIPR-59
Summary: This gene encodes a member of the cytoplasmic linker protein 170 family. Members of this protein family contain a cytoskeleton-associated protein glycine-rich domain and mediate the interaction of microtubules with cellular organelles. The encoded protein plays a role in T cell apoptosis by facilitating the association of tubulin and the lipid raft ganglioside GD3. The encoded protein also functions as a scaffold protein mediating membrane localization of phosphorylated protein kinase B. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Dec 2010]
Expression: Biased expression in brain (RPKM 97.6), endometrium (RPKM 19.6) and 9 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19q13.12

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (36014660..36032873, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (38560459..38578672, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (36505562..36523775, complement)

Chromosome 19 - NC_000019.10 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?

Downregulated CLIP3 induces radioresistance by enhancing stemness and glycolytic flux in glioblastoma.
Title: Downregulated CLIP3 induces radioresistance by enhancing stemness and glycolytic flux in glioblastoma.
this study indicates that inhibition of miRNA-593-3p by insulin promotes glucose metabolism through the regulation of Slc38a1 and CLIP3 expression, and provides a new insight into the role and mechanism of insulin-induced glycolysis.
Title: MicroRNA-593-3p regulates insulin-promoted glucose consumption by targeting Slc38a1 and CLIP3.
CLIPR-59 interacts with Spy1 resulting in its decreased association with a de-ubiquitinating enzyme in glioblastoma cells.
Title: Spy1 induces de-ubiquitinating of RIP1 arrest and confers glioblastoma's resistance to tumor necrosis factor (TNF-α)-induced apoptosis through suppressing the association of CLIPR-59 and CYLD.
DHHC17 is a ClipR-59 palmitoyltransferase that modulates ClipR-59 plasma membrane binding.
Title: DHHC17 palmitoylates ClipR-59 and modulates ClipR-59 association with the plasma membrane.
CLIPR-59 modulates ubiquitination of RIP1, resulting in the formation of Complex-II and thus promoting Caspase-8 activation to induce apoptosis by TNF-alpha.
Title: CLIPR-59 regulates TNF-α-induced apoptosis by controlling ubiquitination of RIP1.
CLIPR-59 may act as a typical chaperone, allowing a prompt interaction between tubulin and the raft component GD3 during cell apoptosis triggered by CD95/Fas
Title: Role of GD3-CLIPR-59 association in lymphoblastoid T cell apoptosis triggered by CD95/Fas.
CLIPR-59 prevents microtubule-raft interactions
Title: CLIPR-59 is a lipid raft-associated protein containing a cytoskeleton-associated protein glycine-rich domain (CAP-Gly) that perturbs microtubule dynamics.
play an important role in membrane-microtubule interactions.
Title: CLIPR-59, a new trans-Golgi/TGN cytoplasmic linker protein belonging to the CLIP-170 family.

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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

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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Replication interactions

Interaction	Pubs
Knockdown of CAP-GLY domain containing linker protein 3 (CLIP3) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D19S673E (e-PCR)
- UniSTS:49203

CLIPR-59__4586 (e-PCR)
- UniSTS:471394

WI-15016 (e-PCR)
- UniSTS:59625

RH12731 (e-PCR)
- UniSTS:54265

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ganglioside binding	IDA Inferred from Direct Assay more info	PubMed
enables microtubule binding	IDA Inferred from Direct Assay more info	PubMed
enables microtubule binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables microtubule plus-end binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cytoplasmic microtubule organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in fat cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in membrane biogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of microtubule polymerization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in peptidyl-L-cysteine S-palmitoylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of D-glucose transmembrane transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein localization to plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of protein phosphorylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein transport along microtubule	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi stack	IEA Inferred from Electronic Annotation more info
is_active_in cell cortex	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	TAS Traceable Author Statement more info
located_in early endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane raft	IDA Inferred from Direct Assay more info	PubMed
is_active_in microtubule plus-end	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IMP Inferred from Mutant Phenotype more info	PubMed
located_in recycling endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in trans-Golgi network	ISS Inferred from Sequence or Structural Similarity more info
located_in trans-Golgi network membrane	IDA Inferred from Direct Assay more info	PubMed
located_in trans-Golgi network membrane	IMP Inferred from Mutant Phenotype more info	PubMed

General protein information

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Preferred Names: CAP-Gly domain-containing linker protein 3

Names: CLIP-170-related 59 kDa protein; cytoplasmic linker protein 170-related 59 kDa protein; restin-like 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.

mRNA and Protein(s)

NM_001199570.2 → NP_001186499.1 CAP-Gly domain-containing linker protein 3

See identical proteins and their annotated locations for NP_001186499.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.

Source sequence(s)

AK289509, AL117468

Consensus CDS

CCDS12486.1

UniProtKB/Swiss-Prot

A8K0E4, Q8WWL1, Q96C99, Q96DZ5, Q9UFT7

UniProtKB/TrEMBL

B4DGS7

Related

ENSP00000466832.1, ENST00000593074.5

Conserved Domains (3) summary

sd00045
Location:120 → 157

ANK; ANK repeat [structural motif]

pfam01302
Location:418 → 482

CAP_GLY; CAP-Gly domain

pfam12796
Location:122 → 228

Ank_2; Ankyrin repeats (3 copies)
NM_015526.3 → NP_056341.1 CAP-Gly domain-containing linker protein 3

See identical proteins and their annotated locations for NP_056341.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.

Source sequence(s)

AJ427922, AL117468

Consensus CDS

CCDS12486.1

UniProtKB/Swiss-Prot

A8K0E4, Q8WWL1, Q96C99, Q96DZ5, Q9UFT7

UniProtKB/TrEMBL

B4DGS7

Related

ENSP00000353732.3, ENST00000360535.9

Conserved Domains (3) summary

sd00045
Location:120 → 157

ANK; ANK repeat [structural motif]

pfam01302
Location:418 → 482

CAP_GLY; CAP-Gly domain

pfam12796
Location:122 → 228

Ank_2; Ankyrin repeats (3 copies)