BNIP2

protein-coding

BCL2 interacting protein 2, the group of BCH domain containing |BCL2 family

Gene summary

This gene is a member of the BCL2/adenovirus E1B 19 kd-interacting protein (BNIP) family. It interacts with the E1B 19 kDa protein, which protects cells from virally-induced cell death. The encoded protein also interacts with E1B 19 kDa-like sequences of BCL2, another apoptotic protector. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

MANE transcript

NM_004330.4

Inheritance

—

ClinVar variants

U:47B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.5

Max pathogenic AF

—

Genomic locus

chr15:59,659,146-59,689,339

External References & Databases

Ensembl (ENSG00000140299)

Transcript & Mutation Effects

hg38 • Region Span ~30.2 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 BNIP2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 46

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004330.4. 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						0
missense			46 clinvar	1 clinvar		47
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	47	1	0	48

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 46 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004330.4	RefSeq	NP_004321.3	9	MANE Select
ENST00000607373.6	Ensembl	ENSP00000475320.1	9	MANE Select
NM_001320674.2	RefSeq	NP_001307603.2	10	Standard
NM_001320675.4	RefSeq	NP_001307604.2	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Developmental Biology
CDO in myogenesis
Myogenesis

Biological Process

polyphosphate catabolic process
apoptotic process
negative regulation of apoptotic process
positive regulation of GTPase activity
positive regulation of muscle cell differentiation

Molecular Function

exopolyphosphatase activity
GTPase activator activity
calcium ion binding
protein binding

Cellular Component

nuclear envelope
cytoplasm
cytosol
intracellular membrane-bounded organelle
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000267859
Coding exons: 10
Length: 30389
Individuals with no LoFs: 125572
Homozygous LoFs: 0
Heterozygous LoFs: 13
Defined: 125585
p: 0.0000518

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.248	233	223	1.05	0.0000108	2787
Missense (PolyPhen)		87	92.396	0.9416		1218
Synonymous	-2.44	112	83.6	1.34	0.00000418	826
Loss of Function	2.06	10	19.9	0.502	9.41e-7	264

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000054	0.000053	rare
South Asian	0.00020	0.00020	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Implicated in the suppression of cell death. Interacts with the BCL-2 and adenovirus E1B 19 kDa proteins.;

Recessive Scores

pRec: 0.125

Intolerance Scores

RVIS EVS: -0.34
RVIS percentile EVS: 30.56

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.726

Gene Damage Prediction

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