PDCD2
Basic information
Region (hg38): 6:170575295-170584692
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDCD2 gene is commonly pathogenic or not.
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.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 1 | |||||
missense | 29 | 30 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 29 | 0 | 2 |
Variants in PDCD2
This is a list of pathogenic ClinVar variants found in the PDCD2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
6-170577563-G-A | not specified | Uncertain significance (Sep 14, 2022) | ||
6-170577593-A-C | not specified | Uncertain significance (Dec 02, 2022) | ||
6-170577605-T-C | not specified | Uncertain significance (Nov 11, 2024) | ||
6-170577629-T-C | not specified | Uncertain significance (Jan 09, 2024) | ||
6-170577635-C-T | not specified | Uncertain significance (Nov 19, 2022) | ||
6-170577714-T-A | not specified | Uncertain significance (Jul 25, 2023) | ||
6-170578925-C-T | not specified | Uncertain significance (Dec 20, 2021) | ||
6-170578945-G-A | not specified | Uncertain significance (Sep 27, 2022) | ||
6-170580003-T-C | not specified | Uncertain significance (May 06, 2022) | ||
6-170580024-T-C | not specified | Uncertain significance (Jan 29, 2025) | ||
6-170580036-T-C | not specified | Uncertain significance (Feb 05, 2024) | ||
6-170580060-G-A | not specified | Uncertain significance (Oct 06, 2024) | ||
6-170583134-A-G | not specified | Uncertain significance (Jun 07, 2024) | ||
6-170583147-G-A | not specified | Uncertain significance (Jan 04, 2024) | ||
6-170583153-G-A | not specified | Uncertain significance (Jun 16, 2023) | ||
6-170583154-G-T | not specified | Uncertain significance (Feb 26, 2025) | ||
6-170583573-T-C | not specified | Uncertain significance (Dec 15, 2023) | ||
6-170583576-G-C | not specified | Uncertain significance (Jan 23, 2025) | ||
6-170583603-G-C | not specified | Uncertain significance (Jan 03, 2024) | ||
6-170583624-C-T | not specified | Uncertain significance (Dec 15, 2023) | ||
6-170583719-G-C | not specified | Uncertain significance (Dec 11, 2023) | ||
6-170584320-G-A | not specified | Uncertain significance (Oct 27, 2022) | ||
6-170584362-C-T | not specified | Uncertain significance (Feb 08, 2025) | ||
6-170584366-C-T | Benign (Aug 02, 2017) | |||
6-170584376-G-C | Benign (Aug 02, 2017) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PDCD2 | protein_coding | protein_coding | ENST00000541970 | 6 | 9398 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
3.90e-7 | 0.370 | 125666 | 0 | 82 | 125748 | 0.000326 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.0515 | 149 | 151 | 0.988 | 0.00000654 | 2216 |
Missense in Polyphen | 47 | 45.453 | 1.034 | 714 | ||
Synonymous | -0.0367 | 55 | 54.7 | 1.01 | 0.00000250 | 642 |
Loss of Function | 0.573 | 11 | 13.3 | 0.830 | 5.60e-7 | 183 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00134 | 0.00134 |
Ashkenazi Jewish | 0.0000992 | 0.0000992 |
East Asian | 0.000163 | 0.000163 |
Finnish | 0.0000465 | 0.0000462 |
European (Non-Finnish) | 0.000380 | 0.000378 |
Middle Eastern | 0.000163 | 0.000163 |
South Asian | 0.0000653 | 0.0000653 |
Other | 0.000820 | 0.000815 |
dbNSFP
Source:
- Function
- FUNCTION: May be a DNA-binding protein with a regulatory function. May play an important role in cell death and/or in regulation of cell proliferation.;
- Pathway
- TNFalpha
(Consensus)
Recessive Scores
- pRec
- 0.189
Intolerance Scores
- loftool
- 0.336
- rvis_EVS
- 0.31
- rvis_percentile_EVS
- 72.23
Haploinsufficiency Scores
- pHI
- 0.253
- hipred
- N
- hipred_score
- 0.197
- ghis
- 0.526
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.747
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pdcd2
- Phenotype
- embryo phenotype; normal phenotype; 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); vision/eye phenotype; skeleton phenotype; growth/size/body region 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);
Zebrafish Information Network
- Gene name
- pdcd2
- Affected structure
- nucleate erythrocyte
- Phenotype tag
- abnormal
- Phenotype quality
- immature
Gene ontology
- Biological process
- apoptotic process;activation of cysteine-type endopeptidase activity involved in apoptotic process;positive regulation of apoptotic process;regulation of hematopoietic progenitor cell differentiation;positive regulation of hematopoietic stem cell proliferation
- Cellular component
- nucleus;cytoplasm;extracellular exosome
- Molecular function
- DNA binding;protein binding;enzyme binding;metal ion binding