BANK1
Basic information
Region (hg38): 4:101411286-102074812
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 BANK1 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 | 1 | |||||
missense | 50 | 52 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 51 | 2 | 1 |
Variants in BANK1
This is a list of pathogenic ClinVar variants found in the BANK1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
4-101790905-G-A | not specified | Uncertain significance (Aug 02, 2021) | ||
4-101790909-T-G | not specified | Uncertain significance (Mar 20, 2023) | ||
4-101790932-T-G | not specified | Uncertain significance (Feb 06, 2024) | ||
4-101790935-G-T | not specified | Uncertain significance (Oct 03, 2023) | ||
4-101790948-C-A | not specified | Uncertain significance (Jul 31, 2024) | ||
4-101829820-A-T | not specified | Uncertain significance (Apr 15, 2024) | ||
4-101829846-G-A | not specified | Uncertain significance (Jun 04, 2024) | ||
4-101829857-G-C | Systemic lupus erythematosus | Benign/Likely benign (Feb 01, 2024) | ||
4-101829889-T-C | not specified | Uncertain significance (Mar 14, 2023) | ||
4-101829918-C-T | not specified | Uncertain significance (Dec 10, 2024) | ||
4-101829919-G-A | Variant of unknown significance | Uncertain significance (Sep 15, 2023) | ||
4-101829964-C-T | not specified | Uncertain significance (May 23, 2024) | ||
4-101830009-G-C | not specified | Uncertain significance (Nov 07, 2022) | ||
4-101830023-A-G | not specified | Uncertain significance (Aug 04, 2024) | ||
4-101830062-A-C | not specified | Uncertain significance (Oct 12, 2021) | ||
4-101830146-A-G | not specified | Uncertain significance (Feb 05, 2024) | ||
4-101830146-A-T | not specified | Uncertain significance (Feb 23, 2023) | ||
4-101830192-G-A | not specified | Uncertain significance (Jun 16, 2022) | ||
4-101830194-A-G | not specified | Likely benign (Apr 17, 2024) | ||
4-101830203-A-G | not specified | Uncertain significance (Oct 25, 2023) | ||
4-101855067-A-G | not specified | Uncertain significance (Nov 07, 2022) | ||
4-101855070-G-T | not specified | Uncertain significance (Apr 19, 2023) | ||
4-101855085-C-T | not specified | Uncertain significance (Dec 05, 2022) | ||
4-101855099-A-G | not specified | Uncertain significance (Feb 23, 2023) | ||
4-101855125-T-C | not specified | Uncertain significance (Nov 22, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
BANK1 | protein_coding | protein_coding | ENST00000322953 | 16 | 663527 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
4.79e-12 | 0.985 | 125573 | 0 | 169 | 125742 | 0.000672 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.230 | 409 | 396 | 1.03 | 0.0000187 | 5200 |
Missense in Polyphen | 125 | 121.6 | 1.028 | 1615 | ||
Synonymous | -0.295 | 136 | 132 | 1.03 | 0.00000619 | 1392 |
Loss of Function | 2.45 | 25 | 42.1 | 0.593 | 0.00000231 | 535 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000677 | 0.000675 |
Ashkenazi Jewish | 0.00270 | 0.00258 |
East Asian | 0.000112 | 0.000109 |
Finnish | 0.0000466 | 0.0000462 |
European (Non-Finnish) | 0.000821 | 0.000809 |
Middle Eastern | 0.000112 | 0.000109 |
South Asian | 0.000840 | 0.000817 |
Other | 0.000833 | 0.000815 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in B-cell receptor (BCR)-induced Ca(2+) mobilization from intracellular stores. Promotes Lyn-mediated phosphorylation of IP3 receptors 1 and 2. {ECO:0000269|PubMed:11782428}.;
- Disease
- DISEASE: Systemic lupus erythematosus (SLE) [MIM:152700]: A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys and serosal membranes. It is of unknown etiology, but is thought to represent a failure of the regulatory mechanisms of the autoimmune system. The disease is marked by a wide range of system dysfunctions, an elevated erythrocyte sedimentation rate, and the formation of LE cells in the blood or bone marrow. {ECO:0000269|PubMed:18204447}. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry.;
- Pathway
- BCR
(Consensus)
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- loftool
- 0.998
- rvis_EVS
- 0.45
- rvis_percentile_EVS
- 78
Haploinsufficiency Scores
- pHI
- 0.123
- hipred
- N
- hipred_score
- 0.172
- ghis
- 0.459
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.816
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Bank1
- Phenotype
- immune system phenotype; hematopoietic system phenotype;
Gene ontology
- Biological process
- response to bacterium;B cell activation;positive regulation of MAPK cascade;negative regulation of translational initiation;positive regulation of peptidyl-tyrosine phosphorylation;negative regulation of B cell activation;negative regulation of protein kinase B signaling;negative regulation of interleukin-6 secretion
- Cellular component
- Molecular function
- signaling receptor binding;protein tyrosine kinase binding