BANK1

B cell scaffold protein with ankyrin repeats 1, the group of Ankyrin repeat domain containing

Basic information

Region (hg38): 4:101411285-102074812

Links

ENSG00000153064 ∙ NCBI:55024 ∙ OMIM:610292 ∙ HGNC:18233 ∙ Uniprot:Q8NDB2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BANK1 gene.

• Inborn genetic diseases (31 variants)
• not provided (3 variants)
• Systemic lupus erythematosus (1 variants)

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		1
missense			30	1	1	32
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	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)
4-101829857-G-C		Systemic lupus erythematosus	Benign (Feb 01, 2024)
4-101829889-T-C		not specified	Uncertain significance (Mar 14, 2023)
4-101829918-C-T		not specified	Uncertain significance (Sep 22, 2022)
4-101829919-G-A		Variant of unknown significance	Uncertain significance (Sep 15, 2023)
4-101830009-G-C		not specified	Uncertain significance (Nov 07, 2022)
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)
4-101830203-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)
4-101862610-A-C		not specified	Uncertain significance (Dec 20, 2023)
4-101870602-A-C		not specified	Uncertain significance (Dec 05, 2022)
4-101870640-G-T		not specified	Uncertain significance (Mar 14, 2023)
4-101895341-A-G		not specified	Uncertain significance (Jan 04, 2024)
4-101895356-A-G		not specified	Uncertain significance (Nov 17, 2023)
4-101895357-T-C		not specified	Uncertain significance (Mar 12, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

• 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
• Molecular function: signaling receptor binding;protein tyrosine kinase binding