PDCD7

programmed cell death 7, the group of U11 small nuclear ribonucleoprotein|U11/U12 di-snRNP

Basic information

Region (hg38): 15:65117378-65133808

Links

ENSG00000090470 ∙ NCBI:10081 ∙ OMIM:608138 ∙ HGNC:8767 ∙ Uniprot:Q8N8D1 ∙ 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 PDCD7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDCD7 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						0
missense			33	1		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	1	0

Variants in PDCD7

This is a list of pathogenic ClinVar variants found in the PDCD7 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-65118734-C-G		not specified	Uncertain significance (Aug 23, 2021)
15-65118763-G-T		not specified	Uncertain significance (Feb 28, 2023)
15-65118767-G-A		not specified	Uncertain significance (May 07, 2024)
15-65118778-C-T		not specified	Uncertain significance (Aug 26, 2022)
15-65118799-T-C		not specified	Uncertain significance (Dec 21, 2022)
15-65119416-G-A		not specified	Uncertain significance (Jul 26, 2021)
15-65119462-A-C		not specified	Uncertain significance (May 24, 2023)
15-65119724-C-G		not specified	Uncertain significance (Jun 29, 2023)
15-65119903-C-T		not specified	Uncertain significance (Jun 11, 2021)
15-65129043-G-A		not specified	Uncertain significance (Sep 12, 2023)
15-65129109-T-A		not specified	Uncertain significance (May 23, 2023)
15-65132985-C-T		not specified	Uncertain significance (Oct 05, 2022)
15-65133031-C-T		not specified	Uncertain significance (Apr 20, 2023)
15-65133055-G-A		not specified	Uncertain significance (Jul 12, 2023)
15-65133060-C-G		not specified	Uncertain significance (May 18, 2023)
15-65133069-C-T		not specified	Uncertain significance (Jul 14, 2021)
15-65133090-T-C		not specified	Uncertain significance (Jun 02, 2023)
15-65133190-C-T		not specified	Uncertain significance (Feb 12, 2024)
15-65133243-C-T		not specified	Uncertain significance (Oct 22, 2021)
15-65133315-C-T		not specified	Uncertain significance (May 16, 2024)
15-65133382-C-A		not specified	Uncertain significance (Jul 25, 2023)
15-65133408-G-A		not specified	Uncertain significance (Jul 25, 2023)
15-65133424-G-A		not specified	Likely benign (Jun 23, 2023)
15-65133439-C-T		not specified	Uncertain significance (Mar 03, 2022)
15-65133453-G-T		not specified	Uncertain significance (Mar 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDCD7	protein_coding	protein_coding	ENST00000204549	5	16458

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000855	0.776	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.752	153	182	0.843	0.00000950	2997
Missense in Polyphen		52	68.094	0.76365		926
Synonymous	0.835	67	76.3	0.878	0.00000415	1078
Loss of Function	1.22	10	15.1	0.661	8.10e-7	200

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000361	0.000354
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000163	0.000163
South Asian	0.000233	0.000229
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes apoptosis when overexpressed. {ECO:0000250}.
• Pathway: Metabolism of RNA;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.106

Haploinsufficiency Scores

• pHI: 0.250
• hipred: Y
• hipred_score: 0.516
• ghis: 0.615

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.342

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pdcd7

Zebrafish Information Network

• Gene name: pdcd7
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: degenerate

Gene ontology

• Biological process: mRNA splicing, via spliceosome;apoptotic process;RNA splicing;response to glucocorticoid
• Cellular component: nucleoplasm;U12-type spliceosomal complex