PDCD2

programmed cell death 2, the group of Zinc fingers MYND-type

Basic information

Region (hg38): 6:170575295-170584692

Links

ENSG00000071994 ∙ NCBI:5134 ∙ OMIM:600866 ∙ HGNC:8762 ∙ Uniprot:Q16342 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PDCD2 gene.

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	1
missense			29		1	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: gnomAD

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: dbNSFP

• 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