BIN3
bridging integrator 3, the group of N-BAR domain containing
Basic information
Region (hg38): 8:22620417-22669148
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- 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) | ||
| 8-22621445-G-A | Inborn genetic diseases | Uncertain significance (Dec 05, 2022) | ||
| 8-22621487-G-A | Inborn genetic diseases | Uncertain significance (Mar 01, 2023) | ||
| 8-22621496-C-T | Inborn genetic diseases | Uncertain significance (Sep 14, 2022) | ||
| 8-22621498-G-T | Inborn genetic diseases | Uncertain significance (Jan 10, 2022) | ||
| 8-22621522-T-C | Inborn genetic diseases | Uncertain significance (May 31, 2023) | ||
| 8-22621555-G-A | Inborn genetic diseases | Uncertain significance (Sep 27, 2022) | ||
| 8-22623922-C-T | Inborn genetic diseases | Uncertain significance (Jan 03, 2022) | ||
| 8-22623956-C-A | Inborn genetic diseases | Uncertain significance (May 04, 2023) | ||
| 8-22623977-G-A | Inborn genetic diseases | Uncertain significance (Mar 16, 2022) | ||
| 8-22623979-G-A | Inborn genetic diseases | Uncertain significance (Sep 01, 2021) | ||
| 8-22623989-C-T | Inborn genetic diseases | Uncertain significance (Oct 03, 2022) | ||
| 8-22624250-G-A | Inborn genetic diseases | Uncertain significance (Feb 15, 2023) | ||
| 8-22624311-C-G | Inborn genetic diseases | Uncertain significance (Jun 10, 2022) | ||
| 8-22624319-C-T | Inborn genetic diseases | Uncertain significance (Nov 21, 2022) | ||
| 8-22624341-G-A | Inborn genetic diseases | Uncertain significance (Jun 18, 2021) | ||
| 8-22624356-T-G | Inborn genetic diseases | Uncertain significance (Jul 12, 2022) | ||
| 8-22630001-T-C | Inborn genetic diseases | Uncertain significance (Oct 04, 2022) | ||
| 8-22630437-G-A | Benign (Dec 31, 2019) | |||
| 8-22630463-C-T | Inborn genetic diseases | Uncertain significance (Apr 19, 2023) | ||
| 8-22630467-C-G | Inborn genetic diseases | Uncertain significance (Mar 07, 2023) | ||
| 8-22630524-C-T | Inborn genetic diseases | Uncertain significance (Feb 10, 2022) | ||
| 8-22630531-G-A | Inborn genetic diseases | Uncertain significance (Feb 14, 2023) | ||
| 8-22630533-T-C | Inborn genetic diseases | Uncertain significance (Feb 07, 2023) | ||
| 8-22630555-T-A | Inborn genetic diseases | Uncertain significance (Aug 17, 2022) |
GnomAD
Source:
| 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:
- 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