BCL2L2

BCL2 like 2, the group of Protein phosphatase 1 regulatory subunits|BCL2 family

Basic information

Region (hg38): 14:23298789-23311751

Links

ENSG00000129473 ∙ NCBI:599 ∙ OMIM:601931 ∙ HGNC:995 ∙ Uniprot:Q92843 ∙ 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 BCL2L2 gene.

• Inborn genetic diseases (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCL2L2 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in BCL2L2

This is a list of pathogenic ClinVar variants found in the BCL2L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-23307940-G-A		not specified	Uncertain significance (Jun 16, 2023)
14-23308149-G-T		not specified	Uncertain significance (Aug 31, 2022)
14-23308829-C-T		not specified	Uncertain significance (Apr 18, 2023)
14-23308859-C-T		not specified	Uncertain significance (Jul 20, 2021)
14-23308865-G-A		not specified	Uncertain significance (Aug 02, 2021)
14-23308865-G-C		not specified	Uncertain significance (Mar 05, 2024)
14-23308939-G-A		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCL2L2	protein_coding	protein_coding	ENST00000250405	2	12970

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.469	0.509	123857	0	10	123867	0.0000404

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.05	75	105	0.712	0.00000671	1219
Missense in Polyphen		15	24.694	0.60744		306
Synonymous	-0.230	45	43.1	1.04	0.00000251	435
Loss of Function	1.83	1	5.74	0.174	2.47e-7	66

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000628	0.0000628
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000360	0.0000360
Middle Eastern	0.00	0.00
South Asian	0.000164	0.000164
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes cell survival. Blocks dexamethasone-induced apoptosis. Mediates survival of postmitotic Sertoli cells by suppressing death-promoting activity of BAX. {ECO:0000269|PubMed:8761287}.
• Pathway: MicroRNAs in cancer - Homo sapiens (human);Apoptosis Modulation and Signaling;Apoptosis;Photodynamic therapy-induced NF-kB survival signaling;Apoptotic Signaling Pathway;Regulation of Apoptosis by Parathyroid Hormone-related Protein;Direct p53 effectors (Consensus)

Recessive Scores

• pRec: 0.201

Intolerance Scores

• loftool: 0.388
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.4

Haploinsufficiency Scores

• pHI: 0.689
• hipred: Y
• hipred_score: 0.567
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.965

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bcl2l2
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype; growth/size/body region 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: spermatogenesis;intrinsic apoptotic signaling pathway in response to DNA damage;negative regulation of apoptotic process;Sertoli cell proliferation;extrinsic apoptotic signaling pathway in absence of ligand;negative regulation of intrinsic apoptotic signaling pathway
• Cellular component: mitochondrial outer membrane;cytosol;Bcl-2 family protein complex
• Molecular function: protein binding;identical protein binding;protein homodimerization activity;protein heterodimerization activity;BH domain binding;disordered domain specific binding