PDCD10
programmed cell death 10, the group of CCM adhesion complex|STRIPAK complex
Basic information
Region (hg38): 3:167683298-167734939
Previous symbols: [ "CCM3" ]
Links
Phenotypes
GenCC
Source:
- 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:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Cerebral cavernous malformations 3 | AD | Cardiovascular; Neurologic; Pharmacogenomic | Surveillance 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; Neurologic | 15543491; 16380626; 18060436; 19088123; 20301470; 21029238; 23485406; 23595507; 23663874 |
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 17 | 18 | ||||
| missense | 32 | 35 | ||||
| nonsense | 13 | 17 | ||||
| start loss | 1 | 1 | ||||
| frameshift | 29 | 36 | ||||
| splice donor/acceptor (+/-2bp) | 11 | 18 | ||||
| Total | 54 | 19 | 33 | 19 | 0 |
Highest pathogenic variant AF is 0.0000065765244
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PDCD10 | protein_coding | protein_coding | ENST00000392750 | 7 | 51642 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.962 | 0.0380 | 123959 | 0 | 1 | 123960 | 0.00000403 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.43 | 74 | 118 | 0.628 | 0.00000616 | 1426 |
| Missense in Polyphen | 11 | 27.185 | 0.40464 | 372 | ||
| Synonymous | 0.310 | 37 | 39.5 | 0.937 | 0.00000222 | 370 |
| Loss of Function | 3.30 | 1 | 14.6 | 0.0685 | 9.98e-7 | 146 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000291 | 0.0000291 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
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