BACH2

BTB domain and CNC homolog 2, the group of BTB domain containing|Basic leucine zipper proteins

Basic information

Region (hg38): 6:89926527-90296843

Links

ENSG00000112182 ∙ NCBI:60468 ∙ OMIM:605394 ∙ HGNC:14078 ∙ Uniprot:Q9BYV9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• immunodeficiency 60 (Limited), mode of inheritance: AD
• immunodeficiency 60 (Strong), mode of inheritance: AD
• immunodeficiency 60 (Moderate), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency 60 and autoimmunity	AD	Allergy/Immunology/Infectious	Individuals may manifest with findings such as inflammatory bowel disease and recurrent sinopulmonary infections and antiinfectious prophylaxis and early and aggressive treatment of infections may be beneficial	Allergy/Immunology/Infectious	28530713

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BACH2 gene.

• not provided (311 variants)
• Inborn genetic diseases (28 variants)
• Immunodeficiency 60 (12 variants)
• not specified (8 variants)
• BACH2-related condition (6 variants)
• Primary ciliary dyskinesia 3 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BACH2 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	109	13	123
missense			174	11	3	188
nonsense						0
start loss						0
frameshift			1			1
inframe indel			3			3
splice donor/acceptor (+/-2bp)						0
splice region			2	3		5
non coding				5	3	8
Total	0	0	179	125	19

Variants in BACH2

This is a list of pathogenic ClinVar variants found in the BACH2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-89932398-A-T		BACH2-related disorder	Benign (Feb 21, 2019)
6-89932401-C-T		BACH2-related disorder	Likely benign (Sep 18, 2019)
6-89932412-G-C			Uncertain significance (Feb 09, 2023)
6-89932414-A-G			Likely benign (Mar 15, 2022)
6-89932423-C-T			Likely benign (Mar 01, 2023)
6-89932429-C-T		not specified	Likely benign (Dec 18, 2023)
6-89932435-G-A			Likely benign (Jan 08, 2024)
6-89932453-A-T			Likely benign (Jan 11, 2022)
6-89932465-G-A			Likely benign (May 25, 2022)
6-89932476-C-G		not specified	Uncertain significance (Mar 23, 2022)
6-89932476-C-T			Likely benign (Jan 14, 2023)
6-89932477-G-A			Likely benign (Jan 25, 2024)
6-89932489-G-A			Likely benign (Jan 07, 2024)
6-89932506-G-A			Uncertain significance (Sep 23, 2021)
6-89932510-T-C			Likely benign (Oct 27, 2023)
6-89932516-C-G		Immunodeficiency 60	Likely benign (Dec 31, 2023)
6-89932518-C-G		Immunodeficiency 60	Uncertain significance (Feb 14, 2023)
6-89932523-A-G			Uncertain significance (Jan 10, 2024)
6-89932531-C-T			Likely benign (Sep 08, 2023)
6-89932532-G-A		not specified	Uncertain significance (Jan 03, 2024)
6-89932542-C-A			Uncertain significance (Jan 04, 2024)
6-89932548-G-C			Uncertain significance (Apr 06, 2023)
6-89932549-T-C			Likely benign (May 11, 2023)
6-89932568-T-G		not specified	Uncertain significance (Nov 17, 2023)
6-89932572-C-T		Immunodeficiency 60	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BACH2	protein_coding	protein_coding	ENST00000257749	4	370380

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00197	125739	0	4	125743	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.30	361	506	0.713	0.0000313	5523
Missense in Polyphen		83	165.59	0.50125		1858
Synonymous	0.00675	219	219	0.999	0.0000151	1673
Loss of Function	4.46	2	27.0	0.0740	0.00000133	343

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional regulator that acts as repressor or activator (By similarity). Binds to Maf recognition elements (MARE) (By similarity). Plays an important role in coordinating transcription activation and repression by MAFK (By similarity). Induces apoptosis in response to oxidative stress through repression of the antiapoptotic factor HMOX1 (PubMed:17018862). Positively regulates the nuclear import of actin (By similarity). {ECO:0000250|UniProtKB:P97303, ECO:0000269|PubMed:17018862}.

Recessive Scores

• pRec: 0.176

Intolerance Scores

• loftool: 0.0845
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.45

Haploinsufficiency Scores

• pHI: 0.966
• hipred: Y
• hipred_score: 0.749
• ghis: 0.493

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.761

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Bach2
• Phenotype: hematopoietic system phenotype; immune system phenotype; skeleton phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription, DNA-templated;import into nucleus
• Cellular component: nucleus;cytosol
• Molecular function: RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription factor activity