CDK5RAP3 CDK5 regulatory subunit associated protein 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CDK5RAP3provided by HGNC
Official Full Name: CDK5 regulatory subunit associated protein 3provided by HGNC
Primary source: HGNC:HGNC:18673
See related: Ensembl:ENSG00000108465 MIM:608202; AllianceGenome:HGNC:18673
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: C53; IC53; LZAP; HSF-27; MST016; PP1553; OK/SW-cl.114
Summary: This gene encodes a protein that has been reported to function in signaling pathways governing transcriptional regulation and cell cycle progression. It may play a role in tumorigenesis and metastasis. A pseudogene of this gene is located on the long arm of chromosome 20. Alternative splicing results in multiple transcript variants that encode different isoforms. [provided by RefSeq, May 2013]
Expression: Ubiquitous expression in spleen (RPKM 44.2), lymph node (RPKM 40.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q21.32

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (47967904..47981781)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (48829702..48843580)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (46047894..46059147)

Chromosome 17 - NC_000017.11 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?

CDK5RAP3 is a novel super-enhancer-driven gene activated by master TFs and regulates ER-Phagy in neuroblastoma.
Title: CDK5RAP3 is a novel super-enhancer-driven gene activated by master TFs and regulates ER-Phagy in neuroblastoma.
TSPAN6 reinforces the malignant progression of glioblastoma via interacting with CDK5RAP3 and regulating STAT3 signaling pathway.
Title: TSPAN6 reinforces the malignant progression of glioblastoma via interacting with CDK5RAP3 and regulating STAT3 signaling pathway.
CDK5RAP3 acts as a tumour suppressor in gastric cancer through the infiltration and polarization of tumour-associated macrophages.
Title: CDK5RAP3 acts as a tumour suppressor in gastric cancer through the infiltration and polarization of tumour-associated macrophages.
CDK5RAP3 acts as a putative tumor inhibitor in papillary thyroid carcinoma via modulation of Akt/GSK-3beta/Wnt/beta-catenin signaling.
Title: CDK5RAP3 acts as a putative tumor inhibitor in papillary thyroid carcinoma via modulation of Akt/GSK-3β/Wnt/β-catenin signaling.
CDK5RAP3 as tumour suppressor negatively regulates self-renewal and invasion and is regulated by ERK1/2 signalling in human gastric cancer.
Title: CDK5RAP3 as tumour suppressor negatively regulates self-renewal and invasion and is regulated by ERK1/2 signalling in human gastric cancer.
The current findings advance innovation in drug discovery and highlight C53 as a novel pGC-B activator with sustained in vivo activity and anti-fibrotic actions in vitro.
Title: C53: A novel particulate guanylyl cyclase B receptor activator that has sustained activity in vivo with anti-fibrotic actions in human cardiac and renal fibroblasts.
CDK5RAP3 is associated with autophagy and down-regulated in renal cancer.
Title: CDK5RAP3 Participates in Autophagy Regulation and Is Downregulated in Renal Cancer.
Study demonstrated that CDK5RAP3/C53 isoform d (IC53d) was upregulated in gastric cancer tissues and was associated with tumor Tstage. Furthermore, overexpression of IC53d promoted the proliferation, colony formation and G1/S phase transition of gastric cancer cells, leading to enhancement of tumorigenesis in vitro and in vivo.
Title: Overexpression of IC53d promotes the proliferation of gastric cancer cells by activating the AKT/GSK3β/cyclin D1 signaling pathway.
Our results demonstrated that CDK5RAP3 negatively regulates the Wnt/beta-catenin signaling pathway by repressing AKT phosphorylation, which leads to better survival of patients with gastric cancer.
Title: CDK5RAP3 suppresses Wnt/β-catenin signaling by inhibiting AKT phosphorylation in gastric cancer.
Prognostic analysis showed that the co-expression of CDK5RAP3 and DDRGK1 was an independent prognostic factor correlating with the overall survival of gastric cancer patients.
Title: Low expression of CDK5RAP3 and DDRGK1 indicates a poor prognosis in patients with gastric cancer.

Submit: New GeneRIF Correction See all GeneRIFs (27)

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

EBI GWAS Catalog

Description
Genome-wide association analysis of genetic generalized epilepsies implicates susceptibility loci at 1q43, 2p16.1, 2q22.3 and 17q21.32 EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D17S1721E (e-PCR)
- UniSTS:153954

WI-11758 (e-PCR)
- UniSTS:83325

RH65642 (e-PCR)
- UniSTS:57236

IB3577 (e-PCR)
- UniSTS:23450

G59781 (e-PCR)
- UniSTS:136934

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables MDM2/MDM4 family protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables NF-kappaB binding	IPI Inferred from Physical Interaction more info	PubMed
enables cyclin binding	IPI Inferred from Physical Interaction more info	PubMed
enables mitogen-activated protein kinase binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase binding	NAS Non-traceable Author Statement more info	PubMed
enables ubiquitin-like ligase-substrate adaptor activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin-like protein ligase binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in apoptotic nuclear changes	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in brain development	NAS Non-traceable Author Statement more info	PubMed
involved_in cell population proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in definitive erythrocyte differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in endoplasmic reticulum unfolded protein response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in liver development	ISS Inferred from Sequence or Structural Similarity more info
involved_in mitotic G2 DNA damage checkpoint signaling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitotic G2/M transition checkpoint	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of MAP kinase activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of NF-kappaB transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of protein catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of protein kinase activity by regulation of protein phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of protein phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of protein serine/threonine kinase activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein localization to nucleus	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of protein ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of reticulophagy	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of reticulophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of signal transduction by p53 class mediator	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
NOT involved_in positive regulation of ubiquitin-dependent protein catabolic process	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within protein ufmylation	IDA Inferred from Direct Assay more info	PubMed
involved_in protein ufmylation	IDA Inferred from Direct Assay more info	PubMed
involved_in protein ufmylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cyclin-dependent protein serine/threonine kinase activity	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of mitotic cell cycle	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of neuron differentiation	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of phosphatase activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in rescue of stalled ribosome	IDA Inferred from Direct Assay more info	PubMed
involved_in rescue of stalled ribosome	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to endoplasmic reticulum stress	ISS Inferred from Sequence or Structural Similarity more info
involved_in ribosome disassembly	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in centrosome	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
is_active_in endomembrane system	IBA Inferred from Biological aspect of Ancestor more info
is_active_in endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in membrane	HDA more info	PubMed
colocalizes_with microtubule	IDA Inferred from Direct Assay more info	PubMed
NOT located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: CDK5 regulatory subunit-associated protein 3

Names: CDK5 regulatory subunit associated protein IC53-2; LXXLL/leucine-zipper-containing ARF-binding protein; LXXLL/leucine-zipper-containing ARFbinding protein; ischemic heart CDK5 activator-binding protein C53

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_001278197.2 → NP_001265126.1 CDK5 regulatory subunit-associated protein 3 isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and has multiple coding region differences compared to variant 1. These differences cause translation initiation at an alternate AUG and result in an isoform (c) with a longer N-terminus, compared to isoform e.

Source sequence(s)

AA427702, AK300643, DA410409, DA410477

Consensus CDS

CCDS62232.1

UniProtKB/Swiss-Prot

Q96JB5

Related

ENSP00000438886.2, ENST00000536708.6

Conserved Domains (1) summary

pfam05600
Location:30 → 528

DUF773; Protein of unknown function (DUF773)
NM_001278198.2 → NP_001265127.1 CDK5 regulatory subunit-associated protein 3 isoform d

Status: REVIEWED

Description

Transcript Variant: This variant (5) includes an alternate penultimate exon, compared to variant 1, resulting in a novel 3' coding region and shorter 3' UTR. It encodes isoform d which has a distinct C-terminus, compared to isoform e.

Source sequence(s)

AA427702, AF217982, AK225274

UniProtKB/TrEMBL

J3QRM1

Related

ENST00000580287.5

Conserved Domains (1) summary

pfam05600
Location:1 → 287

DUF773; Protein of unknown function (DUF773)
NM_001278216.2 → NP_001265145.1 CDK5 regulatory subunit-associated protein 3 isoform e

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes isoform e.

Source sequence(s)

AA427702, AF217982

UniProtKB/TrEMBL

J3QRM1

Related

ENST00000584063.5

Conserved Domains (1) summary

pfam05600
Location:1 → 278

DUF773; Protein of unknown function (DUF773)
NM_001278217.2 → NP_001265146.1 CDK5 regulatory subunit-associated protein 3 isoform f

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and has multiple coding region differences compared to variant 1. These differences cause translation initiation at an alternate AUG and result in an isoform (f) with a longer N-terminus, compared to isoform e.

Source sequence(s)

AA427702, AF110322, AF217982

UniProtKB/Swiss-Prot

Q96JB5

Related

ENST00000585163.5

Conserved Domains (1) summary

pfam05600
Location:26 → 416

DUF773; Protein of unknown function (DUF773)
NM_176096.3 → NP_788276.1 CDK5 regulatory subunit-associated protein 3 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and has multiple coding region differences compared to variant 1. These differences cause translation initiation at an alternate AUG and result in an isoform (b) with a longer N-terminus, compared to isoform e.

Source sequence(s)

AA427702, AK023722

Consensus CDS

CCDS42356.1

UniProtKB/Swiss-Prot

B7Z6N4, D3DTU1, D3DTU2, F5H3I5, Q53FA2, Q96JB5, Q9H3F8, Q9H8G0, Q9HBR9

Related

ENSP00000344683.4, ENST00000338399.9

Conserved Domains (1) summary

pfam05600
Location:5 → 503

DUF773; Protein of unknown function (DUF773)

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_000017.11 Reference GRCh38.p14 Primary Assembly

Range

47967904..47981781

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011525297.1 → XP_011523599.1 CDK5 regulatory subunit-associated protein 3 isoform X1

UniProtKB/Swiss-Prot

Q96JB5

Conserved Domains (1) summary

pfam05600
Location:30 → 528

DUF773; Protein of unknown function (DUF773)
XM_017025166.3 → XP_016880655.1 CDK5 regulatory subunit-associated protein 3 isoform X2

Conserved Domains (1) summary

pfam05600
Location:1 → 410

DUF773; Protein of unknown function (DUF773)

Alternate T2T-CHM13v2.0

Genomic

NC_060941.1 Alternate T2T-CHM13v2.0

Range

48829702..48843580

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054317408.1 → XP_054173383.1 CDK5 regulatory subunit-associated protein 3 isoform X1
XM_054317409.1 → XP_054173384.1 CDK5 regulatory subunit-associated protein 3 isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_025197.2: Suppressed sequence

Description

NM_025197.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
NM_176095.1: Suppressed sequence

Description

NM_176095.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.