PDCD10

programmed cell death 10, the group of CCM adhesion complex|STRIPAK complex

Basic information

Region (hg38): 3:167683298-167734939

Previous symbols: [ "CCM3" ]

Links

ENSG00000114209NCBI:11235OMIM:609118HGNC:8761Uniprot:Q9BUL8AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • cerebral cavernous malformation 3 (Strong), mode of inheritance: AD
  • cerebral cavernous malformation 3 (Strong), mode of inheritance: AD
  • famililal cerebral cavernous malformations (Supportive), mode of inheritance: AD
  • cerebral cavernous malformation 3 (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Cerebral cavernous malformations 3ADCardiovascular; Neurologic; PharmacogenomicSurveillance measures (eg, spinal cord MRI, annual brain gradient echo or susceptibility-weighted imaging) has been advocated; Agents that increase risk of hemorrhage should be avoided (eg, aspirin, NSAIDs, heparin, warfarin)Cardiovascular; Neurologic15543491; 16380626; 18060436; 19088123; 20301470; 21029238; 23485406; 23595507; 23663874

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PDCD10 gene.

  • Cerebral_cavernous_malformation_3 (110 variants)
  • not_provided (43 variants)
  • Inborn_genetic_diseases (21 variants)
  • PDCD10-related_disorder (7 variants)
  • Cerebral_cavernous_malformation (4 variants)
  • not_specified (2 variants)
  • Hemiparesis (1 variants)
  • Cerebral_cavernous_malformation_1 (1 variants)
  • Hereditary_cavernous_hemangioma_of_brain (1 variants)
  • Cavernous_hemangioma (1 variants)
  • Seizure (1 variants)
  • Cerebral_arteriovenous_malformation (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDCD10 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000007217.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
17
clinvar
18
missense
1
clinvar
32
clinvar
2
clinvar
35
nonsense
13
clinvar
4
clinvar
17
start loss
1
1
frameshift
29
clinvar
7
clinvar
36
splice donor/acceptor (+/-2bp)
11
clinvar
7
clinvar
18
Total 54 19 33 19 0

Highest pathogenic variant AF is 0.0000065765244

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PDCD10protein_codingprotein_codingENST00000392750 751642
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9620.0380123959011239600.00000403
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.43741180.6280.000006161426
Missense in Polyphen1127.1850.40464372
Synonymous0.3103739.50.9370.00000222370
Loss of Function3.30114.60.06859.98e-7146

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002910.0000291
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Promotes cell proliferation. Modulates apoptotic pathways. Increases mitogen-activated protein kinase activity and STK26 activity (PubMed:27807006). Important for cell migration, and for normal structure and assembly of the Golgi complex (PubMed:27807006). Important for KDR/VEGFR2 signaling. Increases the stability of KDR/VEGFR2 and prevents its breakdown. Required for normal cardiovascular development. Required for normal angiogenesis, vasculogenesis and hematopoiesis during embryonic development (By similarity). {ECO:0000250|UniProtKB:Q8VE70, ECO:0000269|PubMed:15543491, ECO:0000269|PubMed:17360971, ECO:0000269|PubMed:20332113, ECO:0000269|PubMed:27807006}.;
Pathway
Validated targets of C-MYC transcriptional activation (Consensus)

Recessive Scores

pRec
0.124

Intolerance Scores

loftool
rvis_EVS
-0.03
rvis_percentile_EVS
51.04

Haploinsufficiency Scores

pHI
0.761
hipred
Y
hipred_score
0.768
ghis
0.679

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.942

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Pdcd10
Phenotype
vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); renal/urinary system phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; neoplasm; normal phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype;

Zebrafish Information Network

Gene name
pdcd10b
Affected structure
whole organism
Phenotype tag
abnormal
Phenotype quality
dead

Gene ontology

Biological process
angiogenesis;positive regulation of cell population proliferation;positive regulation of gene expression;negative regulation of gene expression;positive regulation of cell migration;positive regulation of stress-activated MAPK cascade;positive regulation of peptidyl-serine phosphorylation;regulation of Rho protein signal transduction;intrinsic apoptotic signaling pathway in response to hydrogen peroxide;response to hydrogen peroxide;negative regulation of apoptotic process;stress fiber assembly;positive regulation of MAP kinase activity;wound healing, spreading of cells;positive regulation of Notch signaling pathway;protein stabilization;establishment of Golgi localization;positive regulation of protein serine/threonine kinase activity;negative regulation of cell migration involved in sprouting angiogenesis;Golgi reassembly;positive regulation of intracellular protein transport;negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis;cellular response to leukemia inhibitory factor
Cellular component
Golgi membrane;cytoplasm;Golgi apparatus;cytosol;plasma membrane;extracellular exosome
Molecular function
protein binding;protein kinase binding;protein homodimerization activity;protein N-terminus binding