BIN3
Basic information
Region (hg38): 8:22620418-22669148
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 27 | 27 | ||||
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 | 27 | 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) | ||
8-22621445-G-A | not specified | Uncertain significance (Dec 05, 2022) | ||
8-22621472-C-T | not specified | Uncertain significance (May 28, 2024) | ||
8-22621480-C-T | not specified | Uncertain significance (Apr 26, 2024) | ||
8-22621487-G-A | not specified | Uncertain significance (Mar 01, 2023) | ||
8-22621496-C-T | not specified | Uncertain significance (Sep 14, 2022) | ||
8-22621498-G-T | not specified | Uncertain significance (Jan 10, 2022) | ||
8-22621522-T-C | not specified | Uncertain significance (May 31, 2023) | ||
8-22621555-G-A | not specified | Uncertain significance (Sep 27, 2022) | ||
8-22623922-C-T | not specified | Uncertain significance (Jan 23, 2024) | ||
8-22623943-G-A | not specified | Uncertain significance (Jan 31, 2024) | ||
8-22623956-C-A | not specified | Uncertain significance (May 04, 2023) | ||
8-22623977-G-A | not specified | Uncertain significance (Apr 09, 2024) | ||
8-22623979-G-A | not specified | Uncertain significance (Sep 01, 2021) | ||
8-22623981-C-T | not specified | Uncertain significance (Oct 14, 2023) | ||
8-22623989-C-T | not specified | Uncertain significance (Oct 03, 2022) | ||
8-22624031-G-C | not specified | Uncertain significance (Jun 10, 2024) | ||
8-22624250-G-A | not specified | Uncertain significance (Feb 15, 2023) | ||
8-22624311-C-G | not specified | Uncertain significance (Jun 10, 2022) | ||
8-22624319-C-T | not specified | Uncertain significance (Nov 21, 2022) | ||
8-22624341-G-A | not specified | Uncertain significance (Jun 18, 2021) | ||
8-22624356-T-G | not specified | Uncertain significance (Jul 12, 2022) | ||
8-22629991-T-C | not specified | Uncertain significance (Jun 16, 2024) | ||
8-22630001-T-C | not specified | Uncertain significance (Oct 04, 2022) | ||
8-22630437-G-A | Benign (Dec 31, 2019) |
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