PDCD2L

programmed cell death 2 like

Basic information

Region (hg38): 19:34404399-34426168

Links

ENSG00000126249 ∙ NCBI:84306 ∙ OMIM:615661 ∙ HGNC:28194 ∙ Uniprot:Q9BRP1 ∙ 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 PDCD2L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDCD2L 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 PDCD2L

This is a list of pathogenic ClinVar variants found in the PDCD2L region.

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

Position	Type	Phenotype	Significance	ClinVar
19-34404435-C-T		not specified	Uncertain significance (Feb 19, 2025)
19-34404440-G-T		not specified	Uncertain significance (Apr 08, 2022)
19-34404448-G-C		not specified	Uncertain significance (Jan 26, 2025)
19-34404450-C-T		not specified	Uncertain significance (Sep 04, 2024)
19-34404452-G-A		not specified	Uncertain significance (Feb 07, 2023)
19-34404461-G-A		not specified	Uncertain significance (Oct 04, 2024)
19-34404477-C-G		not specified	Uncertain significance (Dec 26, 2023)
19-34404484-C-A		not specified	Uncertain significance (Aug 26, 2024)
19-34404486-G-C		not specified	Uncertain significance (Dec 03, 2024)
19-34404504-G-T		not specified	Uncertain significance (Jun 05, 2024)
19-34404513-C-A		not specified	Uncertain significance (Sep 27, 2021)
19-34404652-G-T		not specified	Uncertain significance (Dec 02, 2022)
19-34404673-C-T		not specified	Uncertain significance (Sep 22, 2022)
19-34404692-G-C		not specified	Uncertain significance (Nov 11, 2024)
19-34404733-C-T		not specified	Uncertain significance (Mar 10, 2025)
19-34404734-C-T		not specified	Uncertain significance (Dec 17, 2024)
19-34404743-G-A		not specified	Uncertain significance (Nov 07, 2024)
19-34404746-C-T		not specified	Uncertain significance (Aug 08, 2022)
19-34404749-C-T		not specified	Uncertain significance (Apr 26, 2023)
19-34404769-G-T		not specified	Uncertain significance (Oct 12, 2021)
19-34404781-G-A		not specified	Uncertain significance (Apr 06, 2024)
19-34404785-G-T		not specified	Uncertain significance (Jan 10, 2023)
19-34409172-C-G		not specified	Uncertain significance (May 03, 2023)
19-34409296-T-A		not specified	Uncertain significance (Aug 12, 2022)
19-34409300-C-T		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDCD2L	protein_coding	protein_coding	ENST00000246535	7	21785

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.48e-7	0.760	125684	0	64	125748	0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.129	194	199	0.974	0.00000950	2337
Missense in Polyphen		48	58.909	0.81482		740
Synonymous	0.118	77	78.3	0.983	0.00000378	697
Loss of Function	1.28	12	17.8	0.674	8.47e-7	192

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000235	0.000235
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000110	0.000109
Finnish	0.000554	0.000554
European (Non-Finnish)	0.000293	0.000290
Middle Eastern	0.000110	0.000109
South Asian	0.000365	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Over-expression suppresses AP1, CREB, NFAT, and NF-kB transcriptional activation, and delays cell cycle progression at S phase. {ECO:0000269|PubMed:17393540}.

Recessive Scores

• pRec: 0.0955

Intolerance Scores

• loftool: 0.382
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.11

Haploinsufficiency Scores

• pHI: 0.465
• hipred: N
• hipred_score: 0.148
• ghis: 0.596

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.589

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdcd2l

Gene ontology

• Biological process: cell cycle
• Cellular component: cytoplasm;membrane