BCL2L13

protein-coding

BCL2 like 13, the group of BCL2 family

Gene summary

This gene encodes a mitochondrially-localized protein with conserved B-cell lymphoma 2 homology motifs. Overexpression of the encoded protein results in apoptosis. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jul 2012]

MANE transcript

NM_015367.4

Inheritance

—

ClinVar variants

U:75B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.43

Max pathogenic AF

—

Genomic locus

chr22:17,628,855-17,730,855

External References & Databases

Ensembl (ENSG00000099968)

Transcript & Mutation Effects

hg38 • Region Span ~102.0 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BCL2L13 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 82

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015367.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			74 clinvar	8 clinvar	2 clinvar	84
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	75	8	2	85

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 91 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015367.4	RefSeq	NP_056182.2	6	MANE Select
ENST00000317582.10	Ensembl	ENSP00000318883.5	6	MANE Select
NM_001270726.1	RefSeq	NP_001257655.1	6	Standard
NM_001270727.1	RefSeq	NP_001257656.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Legionellosis - Homo sapiens (human)
Mitophagy - animal - Homo sapiens (human)
Regulation of Apoptosis by Parathyroid Hormone-related Protein

Biological Process

apoptotic process
activation of cysteine-type endopeptidase activity involved in apoptotic process

Molecular Function

protein binding
cysteine-type endopeptidase activator activity involved in apoptotic process

Cellular Component

nucleus
mitochondrion
integral component of membrane
mitochondrial membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000317582
Coding exons: 6
Length: 101768
Individuals with no LoFs: 125730
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 125746
p: 0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.301	244	258	0.947	0.0000136	3115
Missense (PolyPhen)		91	93.902	0.9691		1201
Synonymous	-1.02	122	108	1.13	0.00000653	1021
Loss of Function	2.15	7	16.4	0.427	7.92e-7	196

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.000092	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000054	0.000053	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May promote the activation of caspase-3 and apoptosis.;

Intolerance Scores

LoFtool: 0.644
RVIS EVS: 0.51
RVIS percentile EVS: 80.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.793

Gene Damage Prediction

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