BATF2

basic leucine zipper ATF-like transcription factor 2, the group of Basic leucine zipper proteins

Basic information

Region (hg38): 11:64987945-64997018

Links

ENSG00000168062 ∙ NCBI:116071 ∙ OMIM:614983 ∙ HGNC:25163 ∙ Uniprot:Q8N1L9 ∙ 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 BATF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BATF2 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			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	27	0	0

Variants in BATF2

This is a list of pathogenic ClinVar variants found in the BATF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-64989160-G-A		not specified	Uncertain significance (Aug 14, 2024)
11-64989278-G-A		not specified	Uncertain significance (Nov 09, 2024)
11-64989295-C-T		not specified	Uncertain significance (Jan 15, 2025)
11-64989355-G-A		not specified	Uncertain significance (Feb 05, 2024)
11-64989385-G-C		not specified	Uncertain significance (Jul 13, 2022)
11-64989418-G-A		not specified	Uncertain significance (Sep 30, 2024)
11-64989421-G-T		not specified	Uncertain significance (Feb 12, 2024)
11-64989431-G-A		not specified	Uncertain significance (Oct 16, 2023)
11-64989452-C-G		not specified	Uncertain significance (Feb 27, 2024)
11-64989513-G-T		not specified	Uncertain significance (Apr 09, 2024)
11-64989527-G-A		not specified	Uncertain significance (Nov 24, 2024)
11-64989530-G-C		not specified	Uncertain significance (Mar 07, 2025)
11-64989536-G-A		not specified	Uncertain significance (Mar 07, 2024)
11-64989541-G-A		not specified	Uncertain significance (May 17, 2023)
11-64989550-G-A		not specified	Uncertain significance (Apr 28, 2022)
11-64989560-G-T		not specified	Uncertain significance (Aug 01, 2024)
11-64989577-G-A		not specified	Uncertain significance (Sep 14, 2022)
11-64989611-G-A		not specified	Uncertain significance (Jan 31, 2022)
11-64989695-C-T		not specified	Uncertain significance (Dec 07, 2024)
11-64989709-C-T		not specified	Uncertain significance (Mar 06, 2025)
11-64989731-G-A		not specified	Uncertain significance (Mar 24, 2023)
11-64989790-T-A		not specified	Uncertain significance (Aug 08, 2022)
11-64989803-A-G		not specified	Uncertain significance (Apr 29, 2024)
11-64994468-T-C		not specified	Uncertain significance (Nov 09, 2024)
11-64994491-C-T		not specified	Uncertain significance (Dec 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BATF2	protein_coding	protein_coding	ENST00000301887	3	9103

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.585	0.377	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.373	139	152	0.915	0.00000859	1720
Missense in Polyphen		20	30.736	0.65071		402
Synonymous	0.177	69	70.9	0.973	0.00000409	617
Loss of Function	1.53	0	2.73	0.00	1.16e-7	32

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: AP-1 family transcription factor that controls the differentiation of lineage-specific cells in the immune system. Following infection, participates in the differentiation of CD8(+) thymic conventional dendritic cells in the immune system. Acts via the formation of a heterodimer with JUN family proteins that recognizes and binds DNA sequence 5'-TGA[CG]TCA-3' and regulates expression of target genes (By similarity). Selectively suppresses CYR61/CCN1 transcription and hence blocks the downstream cell proliferation signals produced by CYR61 and inhibits CYR61-induced anchorage-independent growth and invasion in several cancer types, such as breast cancer, malignant glioma and metastatic melanoma. Possibly acts by interfering with AP-1 binding to CYR61 promoter. {ECO:0000250, ECO:0000269|PubMed:20531301}.

Recessive Scores

• pRec: 0.0761

Intolerance Scores

• loftool: 0.520
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.76

Haploinsufficiency Scores

• pHI: 0.0766
• hipred: N
• hipred_score: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.451

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Batf2
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;defense response to protozoan;myeloid dendritic cell differentiation
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding