BIN2

bridging integrator 2, the group of N-BAR domain containing

Basic information

Region (hg38): 12:51281037-51324668

Links

ENSG00000110934 ∙ NCBI:51411 ∙ OMIM:605936 ∙ HGNC:1053 ∙ Uniprot:Q9UBW5 ∙ 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 BIN2 gene.

• Inborn genetic diseases (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BIN2 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			17	2		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	2	0

Variants in BIN2

This is a list of pathogenic ClinVar variants found in the BIN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-51281503-A-G		Inborn genetic diseases	Uncertain significance (Jun 06, 2023)
12-51288155-C-T		Inborn genetic diseases	Uncertain significance (Nov 09, 2021)
12-51291644-G-A		Inborn genetic diseases	Uncertain significance (Jun 03, 2022)
12-51291862-C-T		Inborn genetic diseases	Likely benign (Jul 21, 2022)
12-51291922-C-T		Inborn genetic diseases	Uncertain significance (Jun 23, 2023)
12-51291931-C-T		Inborn genetic diseases	Uncertain significance (Nov 08, 2022)
12-51291992-C-T		Inborn genetic diseases	Likely benign (Dec 17, 2021)
12-51292001-A-T		Inborn genetic diseases	Uncertain significance (Jun 24, 2022)
12-51292058-G-C		Inborn genetic diseases	Uncertain significance (Sep 12, 2023)
12-51292205-G-T		Inborn genetic diseases	Uncertain significance (Mar 06, 2023)
12-51292268-T-A		Inborn genetic diseases	Uncertain significance (Apr 13, 2022)
12-51292268-T-C		Inborn genetic diseases	Uncertain significance (Jan 26, 2022)
12-51292271-T-G		Inborn genetic diseases	Uncertain significance (Mar 24, 2023)
12-51292279-G-A		Inborn genetic diseases	Uncertain significance (May 17, 2023)
12-51295817-A-G		Inborn genetic diseases	Uncertain significance (May 24, 2023)
12-51295827-T-A		Inborn genetic diseases	Uncertain significance (Nov 07, 2022)
12-51302088-C-T		Inborn genetic diseases	Uncertain significance (Mar 06, 2023)
12-51302725-G-C		Inborn genetic diseases	Uncertain significance (Aug 02, 2021)
12-51302778-T-C		Inborn genetic diseases	Uncertain significance (Jun 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BIN2	protein_coding	protein_coding	ENST00000267012	13	43631

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.53e-11	0.793	125698	0	49	125747	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	252	304	0.829	0.0000154	3687
Missense in Polyphen		45	66.051	0.68129		847
Synonymous	-0.284	119	115	1.03	0.00000618	1100
Loss of Function	1.68	21	31.1	0.676	0.00000167	358

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000608	0.000608
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000490	0.000489
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000490	0.000489
South Asian	0.000328	0.000327
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes cell motility and migration, probably via its interaction with the cell membrane and with podosome proteins that mediate interaction with the cytoskeleton. Modulates membrane curvature and mediates membrane tubulation. Plays a role in podosome formation. Inhibits phagocytosis. {ECO:0000269|PubMed:23285027}.
• Pathway: TYROBP Causal Network;Neutrophil degranulation;endocytotic role of ndk phosphins and dynamin;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.0610

Intolerance Scores

• loftool: 0.747
• rvis_EVS: 0.69
• rvis_percentile_EVS: 85.18

Haploinsufficiency Scores

• pHI: 0.0708
• hipred: N
• hipred_score: 0.233
• ghis: 0.429

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.190

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bin2

Gene ontology

• Biological process: phagocytosis, engulfment;neutrophil degranulation;cell chemotaxis;podosome assembly;plasma membrane tubulation
• Cellular component: phagocytic cup;podosome;extracellular region;plasma membrane;cell cortex;cell junction;secretory granule lumen;cell projection;ficolin-1-rich granule lumen
• Molecular function: protein binding;phospholipid binding