BCL2L12

BCL2 like 12, the group of BCL2 family

Basic information

Region (hg38): 19:49665142-49673916

Links

ENSG00000126453 ∙ NCBI:83596 ∙ OMIM:610837 ∙ HGNC:13787 ∙ Uniprot:Q9HB09 ∙ 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 BCL2L12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCL2L12 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			7	1		8
Total	0	0	25	1	0

Variants in BCL2L12

This is a list of pathogenic ClinVar variants found in the BCL2L12 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-49665831-G-A		not specified	Uncertain significance (Aug 04, 2024)
19-49665836-G-T		not specified	Uncertain significance (Dec 10, 2024)
19-49665863-T-C		not specified	Uncertain significance (Dec 08, 2023)
19-49665875-C-T		Malignant melanoma of skin • Squamous cell carcinoma of the skin	Likely pathogenic (May 31, 2016)
19-49665918-C-T		not specified	Uncertain significance (Jul 27, 2022)
19-49665941-C-T		not specified	Uncertain significance (Aug 17, 2022)
19-49665948-C-T		not specified	Uncertain significance (Aug 23, 2021)
19-49665950-G-C		not specified	Likely benign (Jul 05, 2023)
19-49665953-T-A		not specified	Uncertain significance (Jun 18, 2021)
19-49665972-G-C		not specified	Uncertain significance (Dec 08, 2024)
19-49666041-G-C		not specified	Uncertain significance (Oct 25, 2022)
19-49666052-T-C		not specified	Uncertain significance (Jan 20, 2023)
19-49666774-G-A		not specified	Uncertain significance (Dec 06, 2024)
19-49666775-G-A		not specified	Uncertain significance (Nov 11, 2024)
19-49667024-C-T		not specified	Uncertain significance (Feb 28, 2024)
19-49667033-A-G		not specified	Uncertain significance (Jul 14, 2021)
19-49667063-G-C		not specified	Uncertain significance (Nov 14, 2023)
19-49667090-G-A		not specified	Uncertain significance (Dec 04, 2024)
19-49667113-C-T			Likely benign (Nov 01, 2024)
19-49667126-C-G		not specified	Uncertain significance (Apr 18, 2024)
19-49667147-A-G		not specified	Uncertain significance (Jan 10, 2022)
19-49668901-C-G		not specified	Uncertain significance (Mar 24, 2023)
19-49668926-C-T		not specified	Uncertain significance (Jul 26, 2022)
19-49669065-C-T		not specified	Uncertain significance (Dec 21, 2022)
19-49669066-G-A		not specified	Uncertain significance (Aug 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCL2L12	protein_coding	protein_coding	ENST00000246785	7	8351

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.83e-9	0.192	125588	0	159	125747	0.000632

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.139	196	202	0.973	0.0000122	2052
Missense in Polyphen		78	91.091	0.85628		911
Synonymous	-0.388	85	80.6	1.05	0.00000434	749
Loss of Function	0.435	14	15.9	0.882	9.14e-7	157

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00169	0.00169
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.000111	0.000109
Finnish	0.000370	0.000370
European (Non-Finnish)	0.000696	0.000695
Middle Eastern	0.000111	0.000109
South Asian	0.000266	0.000261
Other	0.000832	0.000815

dbNSFP

Source: dbNSFP

• Pathway: Regulation of Apoptosis by Parathyroid Hormone-related Protein (Consensus)

Recessive Scores

• pRec: 0.0973

Intolerance Scores

• loftool: 0.929
• rvis_EVS: 0.86
• rvis_percentile_EVS: 88.69

Haploinsufficiency Scores

• pHI: 0.310
• hipred: N
• hipred_score: 0.123
• ghis: 0.493

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.709

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bcl2l12

Gene ontology

• Biological process: apoptotic process;positive regulation of transcription by RNA polymerase II;negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator;inhibition of cysteine-type endopeptidase activity involved in apoptotic process;negative regulation of cellular senescence
• Cellular component: nucleus;membrane
• Molecular function: p53 binding