BCL2A1

BCL2 related protein A1, the group of Minor histocompatibility antigens|BCL2 family

Basic information

Region (hg38): 15:79960891-79971196

Previous symbols: [ "HBPA1" ]

Links

ENSG00000140379 ∙ NCBI:597 ∙ OMIM:601056 ∙ HGNC:991 ∙ Uniprot:Q16548 ∙ 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 BCL2A1 gene.

• Inborn genetic diseases (8 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCL2A1 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	8	0	1

Variants in BCL2A1

This is a list of pathogenic ClinVar variants found in the BCL2A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-79961086-A-G		not specified	Uncertain significance (Jul 15, 2021)
15-79961182-A-C			Benign (Dec 31, 2019)
15-79970765-A-C		not specified	Uncertain significance (Jun 06, 2023)
15-79970791-G-A		not specified	Uncertain significance (Jul 20, 2021)
15-79970792-G-A		not specified	Uncertain significance (Jun 12, 2023)
15-79970825-G-C		not specified	Uncertain significance (Aug 10, 2021)
15-79970906-T-C		not specified	Uncertain significance (Jun 23, 2023)
15-79970989-A-G		not specified	Uncertain significance (Jun 01, 2023)
15-79971021-C-T			Benign (Jun 21, 2018)
15-79971022-G-A		not specified	Uncertain significance (Oct 17, 2023)
15-79971050-G-T		not specified	Uncertain significance (May 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCL2A1	protein_coding	protein_coding	ENST00000267953	2	10558

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.208	0.755	125697	0	8	125705	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.13	62	92.6	0.670	0.00000470	1145
Missense in Polyphen		17	30.101	0.56476		383
Synonymous	-0.681	42	36.8	1.14	0.00000219	331
Loss of Function	1.73	2	6.92	0.289	3.95e-7	75

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000124	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Retards apoptosis induced by IL-3 deprivation. May function in the response of hemopoietic cells to external signals and in maintaining endothelial survival during infection (By similarity). Can inhibit apoptosis induced by serum starvation in the mammary epithelial cell line HC11 (By similarity). {ECO:0000250, ECO:0000250|UniProtKB:Q07440}.
• Pathway: Acute myeloid leukemia - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Apoptosis - Homo sapiens (human);NF-kappa B signaling pathway - Homo sapiens (human);Apoptosis Modulation and Signaling;Photodynamic therapy-induced HIF-1 survival signaling;Photodynamic therapy-induced NF-kB survival signaling;Regulation of Apoptosis by Parathyroid Hormone-related Protein;BCR signaling pathway;Direct p53 effectors (Consensus)

Recessive Scores

• pRec: 0.338

Intolerance Scores

• loftool: 0.461
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.01

Haploinsufficiency Scores

• pHI: 0.174
• hipred: N
• hipred_score: 0.418

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.809

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bcl2a1d

Gene ontology

• Biological process: aging;intrinsic apoptotic signaling pathway in response to DNA damage;cerebral cortex development;negative regulation of apoptotic process;extrinsic apoptotic signaling pathway in absence of ligand;negative regulation of intrinsic apoptotic signaling pathway
• Cellular component: mitochondrial outer membrane
• Molecular function: protein binding;protein homodimerization activity;protein heterodimerization activity;BH domain binding