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GeneBe

BIN3

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

Basic information

Region (hg38): 8:22620417-22669148

Links

ENSG00000147439NCBI:55909OMIM:606396HGNC:1054Uniprot:Q9NQY0AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BIN3 gene.

  • Inborn genetic diseases (25 variants)
  • not provided (1 variants)

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
25
clinvar
25
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 25 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)2514125
8-22621445-G-A not specified Uncertain significance (Dec 05, 2022)2391814
8-22621487-G-A not specified Uncertain significance (Mar 01, 2023)2462179
8-22621496-C-T not specified Uncertain significance (Sep 14, 2022)2356604
8-22621498-G-T not specified Uncertain significance (Jan 10, 2022)2271759
8-22621522-T-C not specified Uncertain significance (May 31, 2023)2519034
8-22621555-G-A not specified Uncertain significance (Sep 27, 2022)2313967
8-22623922-C-T not specified Uncertain significance (Jan 23, 2024)2393258
8-22623943-G-A not specified Uncertain significance (Jan 31, 2024)3134010
8-22623956-C-A not specified Uncertain significance (May 04, 2023)2561198
8-22623977-G-A not specified Uncertain significance (Mar 16, 2022)2352745
8-22623979-G-A not specified Uncertain significance (Sep 01, 2021)2248353
8-22623981-C-T not specified Uncertain significance (Oct 14, 2023)3134008
8-22623989-C-T not specified Uncertain significance (Oct 03, 2022)2315915
8-22624250-G-A not specified Uncertain significance (Feb 15, 2023)2459230
8-22624311-C-G not specified Uncertain significance (Jun 10, 2022)2359369
8-22624319-C-T not specified Uncertain significance (Nov 21, 2022)2411165
8-22624341-G-A not specified Uncertain significance (Jun 18, 2021)2215220
8-22624356-T-G not specified Uncertain significance (Jul 12, 2022)2392415
8-22630001-T-C not specified Uncertain significance (Oct 04, 2022)2316139
8-22630437-G-A Benign (Dec 31, 2019)776292
8-22630463-C-T not specified Uncertain significance (Apr 19, 2023)2516100
8-22630467-C-G not specified Uncertain significance (Mar 07, 2023)2459412
8-22630524-C-T not specified Uncertain significance (Feb 10, 2022)2400190
8-22630531-G-A not specified Uncertain significance (Feb 14, 2023)2483339

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
BIN3protein_codingprotein_codingENST00000276416 948731
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
5.82e-130.01611246111311246430.000128
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.2981661561.070.000009741665
Missense in Polyphen3734.4071.0754426
Synonymous-2.789062.11.450.00000403448
Loss of Function-0.3131816.61.088.84e-7188

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004340.000433
Ashkenazi Jewish0.000.00
East Asian0.0001130.000111
Finnish0.00004670.0000464
European (Non-Finnish)0.00008940.0000885
Middle Eastern0.0001130.000111
South Asian0.0002970.000261
Other0.0001660.000165

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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