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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:Q9NQY0AlphaFoldGenCCjaxSfariGnomADPubmed

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 (16 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.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous 0
missense 16 16
nonsense 0
start loss 0
frameshift 0
inframe indel 0
splice variant 1 1
non coding 0
Total 0 0 16 0 1

Variants in BIN3

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

Position Type Phenotype Significance ClinVar
8-22621430-C-T Inborn genetic diseases Uncertain significance (May 01, 2023)link
8-22621445-G-A Inborn genetic diseases Uncertain significance (Dec 05, 2022)link
8-22621487-G-A Inborn genetic diseases Uncertain significance (Mar 01, 2023)link
8-22621496-C-T Inborn genetic diseases Uncertain significance (Sep 14, 2022)link
8-22621498-G-T Inborn genetic diseases Uncertain significance (Jan 10, 2022)link
8-22621522-T-C Inborn genetic diseases Uncertain significance (May 31, 2023)link
8-22621555-G-A Inborn genetic diseases Uncertain significance (Sep 27, 2022)link
8-22623922-C-T Inborn genetic diseases Uncertain significance (Jan 03, 2022)link
8-22623956-C-A Inborn genetic diseases Uncertain significance (May 04, 2023)link
8-22623977-G-A Inborn genetic diseases Uncertain significance (Mar 16, 2022)link
8-22623979-G-A Inborn genetic diseases Uncertain significance (Sep 01, 2021)link
8-22623989-C-T Inborn genetic diseases Uncertain significance (Oct 03, 2022)link
8-22624250-G-A Inborn genetic diseases Uncertain significance (Feb 15, 2023)link
8-22624311-C-G Inborn genetic diseases Uncertain significance (Jun 10, 2022)link
8-22624319-C-T Inborn genetic diseases Uncertain significance (Nov 21, 2022)link
8-22624341-G-A Inborn genetic diseases Uncertain significance (Jun 18, 2021)link
8-22624356-T-G Inborn genetic diseases Uncertain significance (Jul 12, 2022)link
8-22630001-T-C Inborn genetic diseases Uncertain significance (Oct 04, 2022)link
8-22630437-G-A Benign (Dec 31, 2019)link
8-22630463-C-T Inborn genetic diseases Uncertain significance (Apr 19, 2023)link
8-22630467-C-G Inborn genetic diseases Uncertain significance (Mar 07, 2023)link
8-22630524-C-T Inborn genetic diseases Uncertain significance (Feb 10, 2022)link
8-22630531-G-A Inborn genetic diseases Uncertain significance (Feb 14, 2023)link
8-22630533-T-C Inborn genetic diseases Uncertain significance (Feb 07, 2023)link
8-22630555-T-A Inborn genetic diseases Uncertain significance (Aug 17, 2022)link

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