BATF3

basic leucine zipper ATF-like transcription factor 3, the group of Basic leucine zipper proteins

Basic information

Region (hg38): 1:212686416-212699840

Links

ENSG00000123685

∙ NCBI:55509 ∙ OMIM:612470 ∙ HGNC:28915 ∙ Uniprot:Q9NR55 ∙ 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 BATF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BATF3 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			3 clinvar	1 clinvar		4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	1	0

Variants in BATF3

This is a list of pathogenic ClinVar variants found in the BATF3 region.

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

Position	Phenotype	Significance	ClinVar
1-212686819-T-C	not specified	Uncertain significance (Jun 24, 2022)	2366212
1-212686949-T-C	not specified	Likely benign (Sep 27, 2022)	2313966
1-212686960-T-C	not specified	Uncertain significance (Dec 15, 2023)	3133018
1-212699713-G-A	not specified	Uncertain significance (Apr 07, 2023)	2534888

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BATF3	protein_coding	protein_coding	ENST00000243440	3	13568

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0317	0.827	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	41	64.3	0.638	0.00000379	810
Missense in Polyphen		18	33.556	0.53641		369
Synonymous	0.489	24	27.2	0.881	0.00000163	250
Loss of Function	1.15	3	6.06	0.495	4.30e-7	68

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)	0.0000441	0.0000439
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 CD8(+) thymic conventional dendritic cells in the immune system. Required for development of CD8-alpha(+) classical dendritic cells (cDCs) and related CD103(+) dendritic cells that cross-present antigens to CD8 T-cells and produce interleukin-12 (IL12) in response to pathogens (By similarity). 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. {ECO:0000250, ECO:0000269|PubMed:10878360, ECO:0000269|PubMed:12087103, ECO:0000269|PubMed:15467742}.;
Pathway: Preimplantation Embryo;Development of pulmonary dendritic cells and macrophage subsets;Calcineurin-regulated NFAT-dependent transcription in lymphocytes;Calcium signaling in the CD4+ TCR pathway (Consensus)

Recessive Scores

pRec: 0.106

Intolerance Scores

loftool: 0.326
rvis_EVS: 0.08
rvis_percentile_EVS: 59.43

Haploinsufficiency Scores

pHI: 0.383
hipred: Y
hipred_score: 0.537
ghis: 0.592

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.363

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Batf3
Phenotype: immune system phenotype; hematopoietic system phenotype; cellular phenotype;

Gene ontology

Biological process: negative regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;response to virus;myeloid dendritic cell differentiation;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;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;transcription corepressor activity;protein binding