BNIPL

BCL2 interacting protein like, the group of BCH domain containing

Basic information

Region (hg38): 1:151036321-151047720

Links

ENSG00000163141 ∙ NCBI:149428 ∙ OMIM:611275 ∙ HGNC:16976 ∙ Uniprot:Q7Z465 ∙ 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 BNIPL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BNIPL 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			21	2		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	0

Variants in BNIPL

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

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

Position	Type	Phenotype	Significance	ClinVar
1-151037610-A-G		not specified	Uncertain significance (Jun 16, 2023)
1-151037617-G-A		not specified	Uncertain significance (May 24, 2024)
1-151037622-T-G		not specified	Uncertain significance (Dec 10, 2024)
1-151038834-C-T		not specified	Uncertain significance (Jan 02, 2024)
1-151038843-C-T		not specified	Uncertain significance (Dec 24, 2024)
1-151038844-G-A		not specified	Uncertain significance (Nov 23, 2022)
1-151038870-C-T		not specified	Uncertain significance (Mar 20, 2023)
1-151038924-G-A		not specified	Likely benign (May 25, 2022)
1-151038954-C-A		not specified	Uncertain significance (Aug 21, 2023)
1-151038961-T-C		not specified	Uncertain significance (Jan 09, 2025)
1-151038961-T-G		not specified	Uncertain significance (Jan 21, 2025)
1-151038988-C-T		not specified	Uncertain significance (Feb 08, 2025)
1-151042967-C-G		not specified	Uncertain significance (Dec 17, 2024)
1-151043013-G-A		not specified	Likely benign (Jun 05, 2023)
1-151043046-G-A		not specified	Uncertain significance (Jun 06, 2022)
1-151043048-C-T		not specified	Uncertain significance (Feb 23, 2023)
1-151043051-C-T		not specified	Uncertain significance (Nov 03, 2022)
1-151043061-T-A		not specified	Uncertain significance (Sep 10, 2024)
1-151043067-G-A		not specified	Uncertain significance (Feb 13, 2024)
1-151043079-G-A		not specified	Uncertain significance (Oct 12, 2024)
1-151043087-C-T		not specified	Uncertain significance (Oct 04, 2022)
1-151043347-G-A		not specified	Uncertain significance (Jan 31, 2025)
1-151043596-G-T		not specified	Uncertain significance (Jan 09, 2025)
1-151043711-C-T		not specified	Uncertain significance (Aug 12, 2024)
1-151043726-C-T		not specified	Uncertain significance (Jan 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BNIPL	protein_coding	protein_coding	ENST00000368931	10	11031

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.03e-10	0.292	125572	0	175	125747	0.000696

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.919	169	206	0.820	0.0000117	2270
Missense in Polyphen		60	69.994	0.85722		835
Synonymous	0.677	66	73.4	0.899	0.00000353	739
Loss of Function	0.844	17	21.2	0.802	0.00000125	223

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00414	0.00399
Ashkenazi Jewish	0.00	0.00
East Asian	0.000599	0.000598
Finnish	0.00158	0.00157
European (Non-Finnish)	0.000286	0.000281
Middle Eastern	0.000599	0.000598
South Asian	0.0000980	0.0000980
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a bridge molecule between BCL2 and ARHGAP1/CDC42 in promoting cell death. {ECO:0000269|PubMed:12901880}.

Recessive Scores

• pRec: 0.0903

Intolerance Scores

• loftool: 0.985
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.88

Haploinsufficiency Scores

• pHI: 0.126
• hipred: N
• hipred_score: 0.437
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.572

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bnipl

Gene ontology

• Biological process: polyphosphate catabolic process;apoptotic process;negative regulation of cell population proliferation;regulation of growth rate
• Cellular component: nucleus;cytoplasm;cytosol
• Molecular function: exopolyphosphatase activity;protein binding;identical protein binding