BNIP1

BCL2 interacting protein 1, the group of BCL2 homology region 3 (BH3) only|SNAREs

Basic information

Region (hg38): 5:173144442-173164387

Links

ENSG00000113734 ∙ NCBI:662 ∙ OMIM:603291 ∙ HGNC:1082 ∙ Uniprot:Q12981 ∙ 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 BNIP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BNIP1 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			15
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	15	0	0

Variants in BNIP1

This is a list of pathogenic ClinVar variants found in the BNIP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-173144562-A-G		not specified	Uncertain significance (Dec 30, 2023)
5-173144586-A-C		not specified	Uncertain significance (May 27, 2022)
5-173144609-G-A		not specified	Uncertain significance (Oct 28, 2023)
5-173144632-A-T		Spondyloepiphyseal dysplasia congenita	Uncertain significance (Feb 23, 2021)
5-173146945-G-A		not specified	Uncertain significance (Jan 26, 2022)
5-173146954-T-C		not specified	Uncertain significance (Jun 16, 2024)
5-173151572-C-T		not specified	Uncertain significance (Nov 30, 2021)
5-173151653-C-A		not specified	Uncertain significance (Jun 18, 2021)
5-173154332-A-C		not specified	Uncertain significance (Jun 22, 2024)
5-173154400-A-C		not specified	Uncertain significance (Jun 09, 2022)
5-173158745-A-C		not specified	Uncertain significance (Dec 09, 2023)
5-173159968-G-A		not specified	Uncertain significance (Jun 22, 2021)
5-173160019-T-C		not specified	Uncertain significance (Nov 09, 2022)
5-173163779-G-T		not specified	Uncertain significance (Nov 29, 2021)
5-173163793-G-A		not specified	Uncertain significance (Oct 27, 2022)
5-173163796-C-T		not specified	Uncertain significance (Jan 30, 2024)
5-173163797-G-A		not specified	Uncertain significance (Apr 24, 2024)
5-173163821-G-A		not specified	Uncertain significance (Oct 18, 2021)
5-173163850-T-C		not specified	Uncertain significance (Dec 06, 2022)
5-173163902-G-A		not specified	Uncertain significance (May 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BNIP1	protein_coding	protein_coding	ENST00000231668	7	19946

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.68e-7	0.551	125600	0	147	125747	0.000585

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.467	130	146	0.891	0.00000768	1773
Missense in Polyphen		47	47.295	0.99377		561
Synonymous	-1.95	74	55.5	1.33	0.00000290	517
Loss of Function	0.877	11	14.6	0.752	7.12e-7	168

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000351	0.000351
Ashkenazi Jewish	0.00407	0.00408
East Asian	0.000436	0.000435
Finnish	0.000294	0.000277
European (Non-Finnish)	0.000576	0.000571
Middle Eastern	0.000436	0.000435
South Asian	0.000258	0.000229
Other	0.00163	0.00163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: As part of a SNARE complex may be involved in endoplasmic reticulum membranes fusion and be required for the maintenance of endoplasmic reticulum organization (PubMed:15272311). Plays also a role in apoptosis (PubMed:7954800, PubMed:15272311, PubMed:23896122). It is for instance required for endoplasmic reticulum stress-induced apoptosis (PubMed:23896122). As a substrate of RNF185 interacting with SQSTM1, might also be involved in mitochondrial autophagy (Probable). {ECO:0000269|PubMed:15272311, ECO:0000269|PubMed:23896122, ECO:0000269|PubMed:7954800, ECO:0000305|PubMed:21931693}.
• Pathway: SNARE interactions in vesicular transport - Homo sapiens (human);Vesicle-mediated transport;Membrane Trafficking;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• loftool: 0.874
• rvis_EVS: -0.12
• rvis_percentile_EVS: 45.13

Haploinsufficiency Scores

• pHI: 0.263
• hipred: N
• hipred_score: 0.422
• ghis: 0.611

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bnip1

Gene ontology

• Biological process: retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;apoptotic process;endoplasmic reticulum organization;endoplasmic reticulum membrane fusion;negative regulation of apoptotic process;execution phase of apoptosis
• Cellular component: nuclear envelope;cytoplasm;endoplasmic reticulum;endoplasmic reticulum membrane;integral component of endoplasmic reticulum membrane;SNARE complex;mitochondrial membrane;intracellular membrane-bounded organelle
• Molecular function: SNAP receptor activity;protein binding