BNIP2

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

Basic information

Region (hg38): 15:59659146-59689339

Links

ENSG00000140299 ∙ NCBI:663 ∙ OMIM:603292 ∙ HGNC:1083 ∙ Uniprot:Q12982 ∙ 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 BNIP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BNIP2 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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5	1		6
Total	0	0	20	2	0

Variants in BNIP2

This is a list of pathogenic ClinVar variants found in the BNIP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-59668926-T-C		not specified	Uncertain significance (Aug 02, 2021)
15-59668988-G-A		not specified	Uncertain significance (Dec 02, 2022)
15-59669279-A-G		not specified	Uncertain significance (Feb 22, 2023)
15-59669301-G-C		not specified	Uncertain significance (Jun 27, 2023)
15-59669357-C-T		not specified	Uncertain significance (Aug 01, 2022)
15-59671252-C-T		not specified	Uncertain significance (Jan 23, 2023)
15-59671261-T-C		not specified	Uncertain significance (Oct 07, 2024)
15-59672727-T-A		not specified	Uncertain significance (Jul 31, 2024)
15-59672733-T-A		not specified	Uncertain significance (Aug 13, 2021)
15-59677934-T-C		not specified	Uncertain significance (Nov 18, 2022)
15-59677943-A-G		not specified	Uncertain significance (Oct 27, 2022)
15-59677989-T-C		not specified	Uncertain significance (Aug 05, 2024)
15-59677991-C-A		not specified	Uncertain significance (Aug 04, 2024)
15-59677991-C-T		not specified	Uncertain significance (Jun 12, 2023)
15-59679684-G-C		not specified	Uncertain significance (Oct 13, 2023)
15-59679690-T-A		not specified	Uncertain significance (Apr 08, 2024)
15-59679696-G-A		not specified	Uncertain significance (Jul 27, 2024)
15-59679730-G-C		not specified	Uncertain significance (Dec 03, 2021)
15-59680251-C-G		not specified	Uncertain significance (Mar 20, 2024)
15-59680255-G-T		not specified	Uncertain significance (Oct 05, 2023)
15-59680265-T-C		not specified	Likely benign (Mar 02, 2023)
15-59680288-C-G		not specified	Uncertain significance (Dec 21, 2023)
15-59680291-T-C		not specified	Uncertain significance (Jul 25, 2023)
15-59682459-C-G		not specified	Uncertain significance (Sep 14, 2022)
15-59682484-C-T		not specified	Uncertain significance (Aug 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BNIP2	protein_coding	protein_coding	ENST00000267859	10	30389

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000646	0.978	125572	0	13	125585	0.0000518

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.248	233	223	1.05	0.0000108	2787
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000994	0.0000993
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000535	0.0000529
Middle Eastern	0.00	0.00
South Asian	0.000202	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Implicated in the suppression of cell death. Interacts with the BCL-2 and adenovirus E1B 19 kDa proteins.
• Pathway: Developmental Biology;CDO in myogenesis;Myogenesis (Consensus)

Recessive Scores

• pRec: 0.125

Intolerance Scores

• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.56

Haploinsufficiency Scores

• pHI: 0.596
• hipred: N
• hipred_score: 0.475
• ghis: 0.625

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.726

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bnip2
• Phenotype: hematopoietic system phenotype; limbs/digits/tail phenotype; skeleton phenotype; immune system phenotype

Gene ontology

• Biological process: polyphosphate catabolic process;apoptotic process;negative regulation of apoptotic process;positive regulation of GTPase activity;positive regulation of muscle cell differentiation
• Cellular component: nuclear envelope;cytoplasm;cytosol;intracellular membrane-bounded organelle;perinuclear region of cytoplasm
• Molecular function: exopolyphosphatase activity;GTPase activator activity;calcium ion binding;protein binding