BIN2
bridging integrator 2, the group of N-BAR domain containing
Basic information
Region (hg38): 12:51281037-51324668
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (10 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the BIN2 gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 8 | 2 | 10 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 2 | 0 |
Variants in BIN2
This is a list of pathogenic ClinVar variants found in the BIN2 region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-51281503-A-G | Inborn genetic diseases | Uncertain significance (Jun 06, 2023) | ||
| 12-51288155-C-T | Inborn genetic diseases | Uncertain significance (Nov 09, 2021) | ||
| 12-51291644-G-A | Inborn genetic diseases | Uncertain significance (Jun 03, 2022) | ||
| 12-51291862-C-T | Inborn genetic diseases | Likely benign (Jul 21, 2022) | ||
| 12-51291922-C-T | Inborn genetic diseases | Uncertain significance (Jun 23, 2023) | ||
| 12-51291931-C-T | Inborn genetic diseases | Uncertain significance (Nov 08, 2022) | ||
| 12-51291992-C-T | Inborn genetic diseases | Likely benign (Dec 17, 2021) | ||
| 12-51292001-A-T | Inborn genetic diseases | Uncertain significance (Jun 24, 2022) | ||
| 12-51292058-G-C | Inborn genetic diseases | Uncertain significance (Sep 12, 2023) | ||
| 12-51292205-G-T | Inborn genetic diseases | Uncertain significance (Mar 06, 2023) | ||
| 12-51292268-T-A | Inborn genetic diseases | Uncertain significance (Apr 13, 2022) | ||
| 12-51292268-T-C | Inborn genetic diseases | Uncertain significance (Jan 26, 2022) | ||
| 12-51292271-T-G | Inborn genetic diseases | Uncertain significance (Mar 24, 2023) | ||
| 12-51292279-G-A | Inborn genetic diseases | Uncertain significance (May 17, 2023) | ||
| 12-51295817-A-G | Inborn genetic diseases | Uncertain significance (May 24, 2023) | ||
| 12-51295827-T-A | Inborn genetic diseases | Uncertain significance (Nov 07, 2022) | ||
| 12-51302088-C-T | Inborn genetic diseases | Uncertain significance (Mar 06, 2023) | ||
| 12-51302725-G-C | Inborn genetic diseases | Uncertain significance (Aug 02, 2021) | ||
| 12-51302778-T-C | Inborn genetic diseases | Uncertain significance (Jun 22, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| BIN2 | protein_coding | protein_coding | ENST00000267012 | 13 | 43631 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 4.53e-11 | 0.793 | 125698 | 0 | 49 | 125747 | 0.000195 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.06 | 252 | 304 | 0.829 | 0.0000154 | 3687 |
| Missense in Polyphen | 45 | 66.051 | 0.68129 | 847 | ||
| Synonymous | -0.284 | 119 | 115 | 1.03 | 0.00000618 | 1100 |
| Loss of Function | 1.68 | 21 | 31.1 | 0.676 | 0.00000167 | 358 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000608 | 0.000608 |
| Ashkenazi Jewish | 0.000198 | 0.000198 |
| East Asian | 0.000490 | 0.000489 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000106 | 0.000105 |
| Middle Eastern | 0.000490 | 0.000489 |
| South Asian | 0.000328 | 0.000327 |
| Other | 0.000489 | 0.000489 |
dbNSFP
Source:
- Function
- FUNCTION: Promotes cell motility and migration, probably via its interaction with the cell membrane and with podosome proteins that mediate interaction with the cytoskeleton. Modulates membrane curvature and mediates membrane tubulation. Plays a role in podosome formation. Inhibits phagocytosis. {ECO:0000269|PubMed:23285027}.;
- Pathway
- TYROBP Causal Network;Neutrophil degranulation;endocytotic role of ndk phosphins and dynamin;Innate Immune System;Immune System
(Consensus)
Recessive Scores
- pRec
- 0.0610
Intolerance Scores
- loftool
- 0.747
- rvis_EVS
- 0.69
- rvis_percentile_EVS
- 85.18
Haploinsufficiency Scores
- pHI
- 0.0708
- hipred
- N
- hipred_score
- 0.233
- ghis
- 0.429
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.190
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Bin2
- Phenotype
Gene ontology
- Biological process
- phagocytosis, engulfment;neutrophil degranulation;cell chemotaxis;podosome assembly;plasma membrane tubulation
- Cellular component
- phagocytic cup;podosome;extracellular region;plasma membrane;cell cortex;cell junction;secretory granule lumen;cell projection;ficolin-1-rich granule lumen
- Molecular function
- protein binding;phospholipid binding