BIN1
bridging integrator 1, the group of N-BAR domain containing
Basic information
Region (hg38): 2:127048027-127107288
Previous symbols: [ "AMPHL" ]
Links
Phenotypes
GenCC
Source:
- myopathy, centronuclear, 2 (Moderate), mode of inheritance: AR
- centronuclear myopathy (Definitive), mode of inheritance: Semidominant
- centronuclear myopathy (Definitive), mode of inheritance: AR
- centronuclear myopathy (Limited), mode of inheritance: AD
- myopathy, centronuclear, 2 (Strong), mode of inheritance: AR
- autosomal recessive centronuclear myopathy (Supportive), mode of inheritance: AR
- autosomal dominant centronuclear myopathy (Supportive), mode of inheritance: AD
- myopathy, centronuclear, 2 (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Myopathy, centronuclear, 2 | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Musculoskeletal | 17676042; 20142620; 22392505 |
ClinVar
This is a list of variants' phenotypes submitted to
- Myopathy,_centronuclear,_2 (641 variants)
- not_provided (119 variants)
- Inborn_genetic_diseases (58 variants)
- not_specified (34 variants)
- BIN1-related_disorder (12 variants)
- Autosomal_dominant_nonsyndromic_hearing_loss_22 (1 variants)
- See_cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the BIN1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000139343.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 8 | 146 | 154 | |||
| missense | 2 | 3 | 287 | 8 | 1 | 301 |
| nonsense | 1 | 1 | 5 | 7 | ||
| start loss | 0 | |||||
| frameshift | 1 | 7 | 8 | |||
| splice donor/acceptor (+/-2bp) | 6 | 8 | 14 | |||
| Total | 3 | 11 | 315 | 154 | 1 |
Highest pathogenic variant AF is 0.00001487599
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| BIN1 | protein_coding | protein_coding | ENST00000316724 | 19 | 59329 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 125733 | 0 | 15 | 125748 | 0.0000596 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.25 | 235 | 354 | 0.663 | 0.0000222 | 3856 |
| Missense in Polyphen | 70 | 123.62 | 0.56625 | 1425 | ||
| Synonymous | 0.260 | 157 | 161 | 0.974 | 0.0000122 | 1132 |
| Loss of Function | 4.46 | 7 | 35.8 | 0.196 | 0.00000171 | 394 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000178 | 0.000178 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000621 | 0.0000615 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000985 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in regulation of synaptic vesicle endocytosis. May act as a tumor suppressor and inhibits malignant cell transformation.;
- Disease
- DISEASE: Myopathy, centronuclear, 2 (CNM2) [MIM:255200]: A congenital muscle disorder characterized by progressive muscular weakness and wasting involving mainly limb girdle, trunk, and neck muscles. It may also affect distal muscles. Weakness may be present during childhood or adolescence or may not become evident until the third decade of life. Ptosis is a frequent clinical feature. The most prominent histopathologic features include high frequency of centrally located nuclei in muscle fibers not secondary to regeneration, radial arrangement of sarcoplasmic strands around the central nuclei, and predominance and hypotrophy of type 1 fibers. {ECO:0000269|PubMed:17676042}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Fc gamma R-mediated phagocytosis - Homo sapiens (human);Endocytosis - Homo sapiens (human);VEGFA-VEGFR2 Signaling Pathway;Vesicle-mediated transport;endocytotic role of ndk phosphins and dynamin;Membrane Trafficking;p73 transcription factor network;Clathrin-mediated endocytosis;Arf6 trafficking events
(Consensus)
Recessive Scores
- pRec
- 0.202
Intolerance Scores
- loftool
- 0.576
- rvis_EVS
- -0.75
- rvis_percentile_EVS
- 13.58
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.980
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Zebrafish Information Network
- Gene name
- bin1b
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- curved
Gene ontology
- Biological process
- endocytosis;nucleus organization;cytoskeleton organization;cell population proliferation;endosome to lysosome transport;viral process;regulation of endocytosis;positive regulation of actin filament polymerization;T-tubule organization;positive regulation of apoptotic process;regulation of neuron differentiation;positive regulation of astrocyte differentiation;nucleus localization;lipid tube assembly;membrane organization;regulation of cell cycle arrest;regulation of heart rate by cardiac conduction;negative regulation of potassium ion transmembrane transport;negative regulation of amyloid-beta formation;negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process;negative regulation of ventricular cardiac muscle cell action potential;negative regulation of calcium ion transmembrane transport via high voltage-gated calcium channel
- Cellular component
- nucleus;nuclear envelope;cytoplasm;cytosol;cytoskeleton;plasma membrane;synaptic vesicle;actin cytoskeleton;membrane;Z disc;T-tubule;axon;I band;node of Ranvier;axon initial segment;lipid tube
- Molecular function
- protease binding;protein binding;phospholipid binding;clathrin binding;identical protein binding;tau protein binding;actin filament binding;chaperone binding;RNA polymerase binding