PDCD10 programmed cell death 10 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PDCD10provided by HGNC
Official Full Name: programmed cell death 10provided by HGNC
Primary source: HGNC:HGNC:8761
See related: Ensembl:ENSG00000114209 MIM:609118; AllianceGenome:HGNC:8761
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: CCM3; TFAR15
Summary: This gene encodes an evolutionarily conserved protein associated with cell apoptosis. The protein interacts with the serine/threonine protein kinase MST4 to modulate the extracellular signal-regulated kinase (ERK) pathway. It also interacts with and is phosphoryated by serine/threonine kinase 25, and is thought to function in a signaling pathway essential for vascular developent. Mutations in this gene are one cause of cerebral cavernous malformations, which are vascular malformations that cause seizures and cerebral hemorrhages. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in colon (RPKM 13.1), lymph node (RPKM 11.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q26.1

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (167683298..167734892, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (170467195..170518819, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (167401086..167452680, complement)

Chromosome 3 - NC_000003.12 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?

Study on the role of CCM3 gene and lead exposure induced neurotoxicity through neurovascular units.
Title: Study on the role of CCM3 gene and lead exposure induced neurotoxicity through neurovascular units.
Programmed cell death 10 can be used as a potential biomarker for ankylosing spondylitis diagnosis and treatment.
Title: Programmed cell death 10 can be used as a potential biomarker for ankylosing spondylitis diagnosis and treatment.
Comprehensive CCM3 Mutational Analysis in Two Patients with Syndromic Cerebral Cavernous Malformation.
Title: Comprehensive CCM3 Mutational Analysis in Two Patients with Syndromic Cerebral Cavernous Malformation.
Knockdown of CCM3 promotes angiogenesis through activation and nuclear translocation of YAP/TAZ.
Title: Knockdown of CCM3 promotes angiogenesis through activation and nuclear translocation of YAP/TAZ.
PDCD10 promotes proliferation, migration, and invasion of osteosarcoma by inhibiting apoptosis and activating EMT pathway.
Title: PDCD10 promotes proliferation, migration, and invasion of osteosarcoma by inhibiting apoptosis and activating EMT pathway.
PDCD10 promotes the aggressive behaviors of pituitary adenomas by up-regulating CXCR2 and activating downstream AKT/ERK signaling.
Title: PDCD10 promotes the aggressive behaviors of pituitary adenomas by up-regulating CXCR2 and activating downstream AKT/ERK signaling.
Improving clinical interpretation of five KRIT1 and PDCD10 intronic variants.
Title: Improving clinical interpretation of five KRIT1 and PDCD10 intronic variants.
Programmed cell death 10 promotes metastasis and epithelial-mesenchymal transition of hepatocellular carcinoma via PP2Ac-mediated YAP activation.
Title: Programmed cell death 10 promotes metastasis and epithelial-mesenchymal transition of hepatocellular carcinoma via PP2Ac-mediated YAP activation.
CircSMARCA5 Facilitates the Progression of Prostate Cancer Through miR-432/PDCD10 Axis.
Title: CircSMARCA5 Facilitates the Progression of Prostate Cancer Through miR-432/PDCD10 Axis.
Programmed Cell Death 10 Mediated CXCL2-CXCR2 Signaling in Regulating Tumor-Associated Microglia/Macrophages Recruitment in Glioblastoma.
Title: Programmed Cell Death 10 Mediated CXCL2-CXCR2 Signaling in Regulating Tumor-Associated Microglia/Macrophages Recruitment in Glioblastoma.

Submit: New GeneRIF Correction See all GeneRIFs (80)

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
Cerebral cavernous malformation 3 MedGen: C1864040 OMIM: 603285 GeneReviews: Familial Cerebral Cavernous Malformation	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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:234579

SHGC-79363 (e-PCR)
- UniSTS:103261

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in Golgi reassembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in Golgi reassembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in angiogenesis	IEA Inferred from Electronic Annotation more info
involved_in cellular response to leukemia inhibitory factor	IEA Inferred from Electronic Annotation more info
involved_in endothelium development	NAS Non-traceable Author Statement more info	PubMed
involved_in establishment of Golgi localization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intrinsic apoptotic signaling pathway in response to hydrogen peroxide	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of apoptotic process	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cell migration involved in sprouting angiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of MAP kinase activity	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of Notch signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell migration	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell population proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of intracellular protein transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of peptidyl-serine phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein serine/threonine kinase activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of stress-activated MAPK cascade	IDA Inferred from Direct Assay more info	PubMed
involved_in protein stabilization	IMP Inferred from Mutant Phenotype more info	PubMed
NOT involved_in regulation of Rho protein signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of angiogenesis	NAS Non-traceable Author Statement more info	PubMed
NOT involved_in stress fiber assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in wound healing, spreading of cells	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of FAR/SIN/STRIPAK complex	IBA Inferred from Biological aspect of Ancestor more info
part_of FAR/SIN/STRIPAK complex	IDA Inferred from Direct Assay more info	PubMed
colocalizes_with Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi membrane	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: programmed cell death protein 10

Names: TF-1 cell apoptosis-related protein 15; apoptosis-related protein 15; cerebral cavernous malformations 3 protein

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_008158.1 RefSeqGene

Range

4972..56566

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_651

mRNA and Protein(s)

NM_007217.4 → NP_009148.2 programmed cell death protein 10

See identical proteins and their annotated locations for NP_009148.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2, and 3 encode the same isoform.

Source sequence(s)

AC079822

Consensus CDS

CCDS3202.1

UniProtKB/Swiss-Prot

A8K515, D3DNN5, O14811, Q9BUL8

UniProtKB/TrEMBL

C9J5C3

Related

ENSP00000376506.2, ENST00000392750.7

Conserved Domains (1) summary

pfam06840
Location:14 → 161

DUF1241; Protein of unknown function (DUF1241)
NM_145859.2 → NP_665858.1 programmed cell death protein 10

See identical proteins and their annotated locations for NP_665858.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same isoform.

Source sequence(s)

AC079822

Consensus CDS

CCDS3202.1

UniProtKB/Swiss-Prot

A8K515, D3DNN5, O14811, Q9BUL8

UniProtKB/TrEMBL

C9J5C3

Related

ENSP00000418317.2, ENST00000473645.6

Conserved Domains (1) summary

pfam06840
Location:14 → 161

DUF1241; Protein of unknown function (DUF1241)
NM_145860.2 → NP_665859.1 programmed cell death protein 10

See identical proteins and their annotated locations for NP_665859.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same isoform.

Source sequence(s)

AC079822

Consensus CDS

CCDS3202.1

UniProtKB/Swiss-Prot

A8K515, D3DNN5, O14811, Q9BUL8

UniProtKB/TrEMBL

C9J5C3

Related

ENSP00000420553.2, ENST00000497056.6

Conserved Domains (1) summary

pfam06840
Location:14 → 161

DUF1241; Protein of unknown function (DUF1241)

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_000003.12 Reference GRCh38.p14 Primary Assembly

Range

167683298..167734892 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005247086.6 → XP_005247143.1 programmed cell death protein 10 isoform X1

See identical proteins and their annotated locations for XP_005247143.1

UniProtKB/Swiss-Prot

A8K515, D3DNN5, O14811, Q9BUL8

UniProtKB/TrEMBL

C9J5C3

Related

ENSP00000417202.1, ENST00000470131.5

Conserved Domains (1) summary

pfam06840
Location:14 → 161

DUF1241; Protein of unknown function (DUF1241)
XM_011512368.4 → XP_011510670.1 programmed cell death protein 10 isoform X1

See identical proteins and their annotated locations for XP_011510670.1

UniProtKB/Swiss-Prot

A8K515, D3DNN5, O14811, Q9BUL8

UniProtKB/TrEMBL

C9J5C3

Conserved Domains (1) summary

pfam06840
Location:14 → 161

DUF1241; Protein of unknown function (DUF1241)
XM_005247087.6 → XP_005247144.1 programmed cell death protein 10 isoform X1

See identical proteins and their annotated locations for XP_005247144.1

UniProtKB/Swiss-Prot

A8K515, D3DNN5, O14811, Q9BUL8

UniProtKB/TrEMBL

C9J5C3

Conserved Domains (1) summary

pfam06840
Location:14 → 161

DUF1241; Protein of unknown function (DUF1241)
XM_011512369.4 → XP_011510671.1 programmed cell death protein 10 isoform X1

See identical proteins and their annotated locations for XP_011510671.1

UniProtKB/Swiss-Prot

A8K515, D3DNN5, O14811, Q9BUL8

UniProtKB/TrEMBL

C9J5C3

Conserved Domains (1) summary

pfam06840
Location:14 → 161

DUF1241; Protein of unknown function (DUF1241)
XM_006713485.5 → XP_006713548.1 programmed cell death protein 10 isoform X1

See identical proteins and their annotated locations for XP_006713548.1

UniProtKB/Swiss-Prot

A8K515, D3DNN5, O14811, Q9BUL8

UniProtKB/TrEMBL

C9J5C3

Related

ENSP00000417118.2, ENST00000475915.6

Conserved Domains (1) summary

pfam06840
Location:14 → 161

DUF1241; Protein of unknown function (DUF1241)
XM_005247088.5 → XP_005247145.1 programmed cell death protein 10 isoform X1

See identical proteins and their annotated locations for XP_005247145.1

UniProtKB/Swiss-Prot

A8K515, D3DNN5, O14811, Q9BUL8

UniProtKB/TrEMBL

C9J5C3

Related

ENSP00000420021.1, ENST00000461494.5

Conserved Domains (1) summary

pfam06840
Location:14 → 161

DUF1241; Protein of unknown function (DUF1241)
XM_017005644.3 → XP_016861133.1 programmed cell death protein 10 isoform X1

UniProtKB/Swiss-Prot

A8K515, D3DNN5, O14811, Q9BUL8

UniProtKB/TrEMBL

C9J5C3

Conserved Domains (1) summary

pfam06840
Location:14 → 161

DUF1241; Protein of unknown function (DUF1241)
XM_047447375.1 → XP_047303331.1 programmed cell death protein 10 isoform X1

UniProtKB/Swiss-Prot

A8K515, D3DNN5, O14811, Q9BUL8

UniProtKB/TrEMBL

C9J5C3
XM_047447374.1 → XP_047303330.1 programmed cell death protein 10 isoform X1

UniProtKB/Swiss-Prot

A8K515, D3DNN5, O14811, Q9BUL8

UniProtKB/TrEMBL

C9J5C3

Alternate T2T-CHM13v2.0

Genomic

NC_060927.1 Alternate T2T-CHM13v2.0

Range

170467195..170518819 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054345101.1 → XP_054201076.1 programmed cell death protein 10 isoform X1

UniProtKB/Swiss-Prot

A8K515, D3DNN5, O14811, Q9BUL8

UniProtKB/TrEMBL

C9J5C3
XM_054345100.1 → XP_054201075.1 programmed cell death protein 10 isoform X1

UniProtKB/Swiss-Prot

A8K515, D3DNN5, O14811, Q9BUL8

UniProtKB/TrEMBL

C9J5C3
XM_054345098.1 → XP_054201073.1 programmed cell death protein 10 isoform X1

UniProtKB/Swiss-Prot

A8K515, D3DNN5, O14811, Q9BUL8

UniProtKB/TrEMBL

C9J5C3
XM_054345099.1 → XP_054201074.1 programmed cell death protein 10 isoform X1

UniProtKB/Swiss-Prot

A8K515, D3DNN5, O14811, Q9BUL8

UniProtKB/TrEMBL

C9J5C3
XM_054345094.1 → XP_054201069.1 programmed cell death protein 10 isoform X1

UniProtKB/Swiss-Prot

A8K515, D3DNN5, O14811, Q9BUL8

UniProtKB/TrEMBL

C9J5C3
XM_054345095.1 → XP_054201070.1 programmed cell death protein 10 isoform X1

UniProtKB/Swiss-Prot

A8K515, D3DNN5, O14811, Q9BUL8

UniProtKB/TrEMBL

C9J5C3
XM_054345093.1 → XP_054201068.1 programmed cell death protein 10 isoform X1

UniProtKB/Swiss-Prot

A8K515, D3DNN5, O14811, Q9BUL8

UniProtKB/TrEMBL

C9J5C3
XM_054345096.1 → XP_054201071.1 programmed cell death protein 10 isoform X1

UniProtKB/Swiss-Prot

A8K515, D3DNN5, O14811, Q9BUL8

UniProtKB/TrEMBL

C9J5C3
XM_054345097.1 → XP_054201072.1 programmed cell death protein 10 isoform X1

UniProtKB/Swiss-Prot

A8K515, D3DNN5, O14811, Q9BUL8

UniProtKB/TrEMBL

C9J5C3