BIN3

bridging integrator 3, the group of N-BAR domain containing

Basic information

Region (hg38): 8:22620418-22669148

Links

ENSG00000147439 ∙ NCBI:55909 ∙ OMIM:606396 ∙ HGNC:1054 ∙ Uniprot:Q9NQY0 ∙ 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 BIN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BIN3 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			27			27
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	27	0	0

Variants in BIN3

This is a list of pathogenic ClinVar variants found in the BIN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-22621430-C-T		not specified	Uncertain significance (May 01, 2023)
8-22621445-G-A		not specified	Uncertain significance (Dec 05, 2022)
8-22621472-C-T		not specified	Uncertain significance (May 28, 2024)
8-22621480-C-T		not specified	Uncertain significance (Apr 26, 2024)
8-22621487-G-A		not specified	Uncertain significance (Mar 01, 2023)
8-22621496-C-T		not specified	Uncertain significance (Sep 14, 2022)
8-22621498-G-T		not specified	Uncertain significance (Jan 10, 2022)
8-22621522-T-C		not specified	Uncertain significance (May 31, 2023)
8-22621555-G-A		not specified	Uncertain significance (Sep 27, 2022)
8-22623922-C-T		not specified	Uncertain significance (Jan 23, 2024)
8-22623943-G-A		not specified	Uncertain significance (Jan 31, 2024)
8-22623956-C-A		not specified	Uncertain significance (May 04, 2023)
8-22623977-G-A		not specified	Uncertain significance (Apr 09, 2024)
8-22623979-G-A		not specified	Uncertain significance (Sep 01, 2021)
8-22623981-C-T		not specified	Uncertain significance (Oct 14, 2023)
8-22623989-C-T		not specified	Uncertain significance (Oct 03, 2022)
8-22624031-G-C		not specified	Uncertain significance (Jun 10, 2024)
8-22624250-G-A		not specified	Uncertain significance (Feb 15, 2023)
8-22624311-C-G		not specified	Uncertain significance (Jun 10, 2022)
8-22624319-C-T		not specified	Uncertain significance (Nov 21, 2022)
8-22624341-G-A		not specified	Uncertain significance (Jun 18, 2021)
8-22624356-T-G		not specified	Uncertain significance (Jul 12, 2022)
8-22629991-T-C		not specified	Uncertain significance (Jun 16, 2024)
8-22630001-T-C		not specified	Uncertain significance (Oct 04, 2022)
8-22630437-G-A			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BIN3	protein_coding	protein_coding	ENST00000276416	9	48731

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.82e-13	0.0161	124611	1	31	124643	0.000128

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.298	166	156	1.07	0.00000974	1665
Missense in Polyphen		37	34.407	1.0754		426
Synonymous	-2.78	90	62.1	1.45	0.00000403	448
Loss of Function	-0.313	18	16.6	1.08	8.84e-7	188

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000434	0.000433
Ashkenazi Jewish	0.00	0.00
East Asian	0.000113	0.000111
Finnish	0.0000467	0.0000464
European (Non-Finnish)	0.0000894	0.0000885
Middle Eastern	0.000113	0.000111
South Asian	0.000297	0.000261
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in cytokinesis and septation where it has a role in the localization of F-actin.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.553
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24.33

Haploinsufficiency Scores

• pHI: 0.647
• hipred: N
• hipred_score: 0.282
• ghis: 0.564

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.675

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bin3
• Phenotype: immune system phenotype; respiratory system phenotype; liver/biliary system phenotype; neoplasm; hematopoietic system phenotype; vision/eye phenotype

Gene ontology

• Biological process: division septum assembly;endocytosis;actin filament organization;protein localization;unidimensional cell growth;regulation of lamellipodium assembly;myoblast migration involved in skeletal muscle regeneration;skeletal muscle fiber development;actin cortical patch localization;cytoskeleton-dependent cytokinesis;plasma membrane tubulation
• Cellular component: cytoplasm;actin filament;actin cortical patch
• Molecular function: protein binding;cytoskeletal protein binding;cytoskeletal adaptor activity;lipid binding