BATF

Summary

BATF (basic leucine zipper ATF-like transcription factor, HGNC:958) is a protein-coding gene on chromosome 14q24.3, encoding Basic leucine zipper transcriptional factor ATF-like (Q16520). AP-1 family transcription factor that controls the differentiation of lineage-specific cells in the immune system: specifically mediates the differentiation of T-helper 17 cells (Th17), follicular T-helper cells (TfH), CD8(+) dendritic cells and class-switch recombination (CSR)….

The protein encoded by this gene is a nuclear basic leucine zipper protein that belongs to the AP-1/ATF superfamily of transcription factors. The leucine zipper of this protein mediates dimerization with members of the Jun family of proteins. This protein is thought to be a negative regulator of AP-1/ATF transcriptional events.

Source: NCBI Gene 10538 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 14 total — 1 pathogenic
• Transcription factor: yes — 17 downstream targets (CollecTRI)
• MANE Select transcript: NM_006399

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:958
Approved symbol	BATF
Name	basic leucine zipper ATF-like transcription factor
Location	14q24.3
Locus type	gene with protein product
Status	Approved
Aliases	B-ATF, SFA-2, BATF1
Ensembl gene	ENSG00000156127
Ensembl biotype	protein_coding
OMIM	612476
Entrez	10538

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000286639, ENST00000555504, ENST00000555795

RefSeq mRNA: 1 — MANE Select: NM_006399 NM_006399

CCDS: CCDS9843

Canonical transcript exons

ENST00000286639 — 3 exons

Exon	Start	End
ENSE00001024690	75546462	75546992
ENSE00001129828	75522469	75522745
ENSE00003600201	75525084	75525188

Expression profiles

Bgee: expression breadth ubiquitous, 181 present calls, max score 95.30.

FANTOM5 (CAGE): breadth broad, TPM avg 15.1964 / max 934.2669, expressed in 731 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
140681	9.7821	705
140682	4.6214	410
140683	0.6268	176
207301	0.1661	96

Top tissues by expression

272 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	95.30	gold quality
blood	UBERON:0000178	88.33	gold quality
leukocyte	CL:0000738	86.00	gold quality
monocyte	CL:0000576	85.51	gold quality
mononuclear cell	CL:0000842	85.48	gold quality
spleen	UBERON:0002106	85.47	gold quality
lymph node	UBERON:0000029	85.16	gold quality
vermiform appendix	UBERON:0001154	84.81	gold quality
palpebral conjunctiva	UBERON:0001812	84.29	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.11	gold quality
bone marrow	UBERON:0002371	82.05	gold quality
caecum	UBERON:0001153	80.67	gold quality
endometrium epithelium	UBERON:0004811	80.19	silver quality
olfactory segment of nasal mucosa	UBERON:0005386	79.94	gold quality
cartilage tissue	UBERON:0002418	79.93	silver quality
amniotic fluid	UBERON:0000173	79.35	gold quality
trabecular bone tissue	UBERON:0002483	78.81	gold quality
urinary bladder	UBERON:0001255	78.52	gold quality
mucosa of urinary bladder	UBERON:0001259	78.20	silver quality
nasal cavity epithelium	UBERON:0005384	78.20	silver quality
gluteal muscle	UBERON:0002000	76.64	gold quality
nasal cavity mucosa	UBERON:0001826	76.63	gold quality
bone marrow cell	CL:0002092	76.18	gold quality
triceps brachii	UBERON:0001509	75.71	gold quality
gall bladder	UBERON:0002110	75.43	gold quality
upper lobe of left lung	UBERON:0008952	75.38	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	75.31	gold quality
periodontal ligament	UBERON:0008266	74.97	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	74.82	gold quality
small intestine Peyer’s patch	UBERON:0003454	74.71	gold quality

Single-cell (SCXA)

Detected in 17 experiment(s), a significant marker in 14.

Experiment	Marker?	Max mean expression
E-CURD-95	yes	1281.02
E-MTAB-8142	yes	1177.22
E-MTAB-8410	yes	981.71
E-MTAB-6653	yes	932.12
E-HCAD-15	yes	912.91
E-GEOD-139324	yes	879.18
E-CURD-46	yes	628.71
E-HCAD-8	yes	67.89
E-CURD-88	yes	36.62
E-CURD-120	yes	36.18
E-CURD-122	yes	36.05
E-ANND-3	yes	19.06
E-HCAD-1	yes	18.71
E-GEOD-130148	yes	7.16
E-CURD-97	no	1553.92

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

17 targets.

Target	Regulation
CCR9
CD2	Unknown
CD8A
IGBP1
IL10	Activation
IL17A	Activation
IL21	Activation
IL23A	Activation
IL4	Activation
IRF4	Activation
MAF	Activation
RARA
SIRT1
SLC11A1
SNCA
STAT3	Unknown
TBXT

JASPAR motifs

Motif	Name	Family
MA0462.1	BATF::JUN	B-ATF-related factors::Jun-related
MA0462.2	BATF::JUN	B-ATF-related factors::Jun-related
MA0462.3	BATF::JUN	B-ATF-related factors::Jun-related
MA1634.1	BATF	B-ATF-related factors
MA1634.2	BATF	B-ATF-related factors

JASPAR matrix evidence (PMIDs): PMID:22992523, PMID:29588546

Upstream regulators (CollecTRI, top): STAT3, STAT6

miRNA regulators (miRDB)

8 targeting BATF, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-6889-3P	98.84	67.35	1198
HSA-MIR-3194-3P	98.83	66.22	1167
HSA-MIR-6529-3P	98.68	66.76	1020
HSA-MIR-4749-3P	96.40	66.24	798
HSA-MIR-4734	88.28	63.44	87
HSA-MIR-4707-3P	86.55	62.02	99

Literature-anchored findings (GeneRIF, showing 24)

• Overexpression of human BATF in transgenic mice disrupts the development of thymus-derived NKT cells (PMID:12594265)
• up-regulated dramatically within 24 h following the infection of established and primary human B cells with EBV by the action of EBNA2 and activated Notch protein (PMID:12719594)
• Phosphorylation of serine-43 converts BATF from a DNA binding into a non-DNA binding inhibitor of activator protein-1 activity. (PMID:12809553)
• PD-1 inhibits T cell function by upregulating BATF. (PMID:20890291)
• The activator protein 1 (AP1) family transcription factor BATF (B cell, activating transcription factor-like) was among the genes enriched in Th9 cells and was required for the expression of IL-9 and other Th9-associated genes. (PMID:24216482)
• increase expression in children with recurrent asthma (PMID:24290279)
• Increased expression of the Th17-IL-6R/pSTAT3/BATF/RorgammaT-axis in the tumoural region of adenocarcinoma as compared to squamous cell carcinoma of the lung (PMID:25491772)
• data strongly support a model in which EBNA3A is tethered to DNA through a BATF-containing protein complexes to enable continuous cell proliferation (PMID:25540416)
• BATF plays a key role in the differentiation of T helper cell subsets and Ig class-switching. Apart from that we suggest an important function in mast cell development and in murine models of allergic asthma, it was observed that mice deficient for Batf are protected from the disease. Hence, the previous findings on BATF make it an interesting target for the treatment of Th cell-derived-cytokine-driven diseases. (PMID:26970726)
• Retinoic acid signaling and BATF productions are activated in IgAN patients compared with controls. (PMID:27073891)
• BATF/JUN-B and BATF/C-JUN complexes play important roles in OA cartilage destruction through regulating anabolic and catabolic gene expression in chondrocytes. (PMID:27147707)
• Findings demonstrate that peripheral and intrahepatic BATF expressions are dramatically increased in chronic hepatitis B (CHB) patients, which might boost the differentiation of Th17 cells and the release of associated cytokine during chronic HBV infection. (PMID:29164410)
• BATF-dependent pathogenic GM-CSF+ effector T cells are critical promoters of intestinal inflammation in graft-versus-host disease (PMID:29376889)
• results reveal that JunB, c-Jun, and Bach2 cooperate with BATF to contribute to the specificity of BATF-dependent cytokine induction in Th subsets. (PMID:31451674)
• Prognostic Value of DNA Methylation-Driven Genes in Clear Cell Renal Cell Carcinoma: A Study Based on Methylation and Transcriptome Analyses. (PMID:32733620)
• Supervised machine learning algorithm identified KRT20, BATF and TP63 as biologically relevant biomarkers for bladder biopsy specimens from interstitial cystitis/bladder pain syndrome patients. (PMID:35102612)
• A systematic comparison of FOSL1, FOSL2 and BATF-mediated transcriptional regulation during early human Th17 differentiation. (PMID:35511484)
• BATF epigenetically and transcriptionally controls the activation program of regulatory T cells in human tumors. (PMID:36206353)
• Depletion of BATF in CAR-T cells enhances antitumor activity by inducing resistance against exhaustion and formation of central memory cells. (PMID:36240777)
• BATF reprograms the tumor immune status. (PMID:36640752)
• Relative Expression of BATF and CD112 in PBMC of Patients with Chronic Lymphocytic Leukemia. (PMID:37378949)
• Integrated BATF transcriptional network regulates suppressive intratumoral regulatory T cells. (PMID:37713508)
• BATF promotes extramedullary infiltration through TGF-beta1/Smad/MMPs axis in acute myeloid leukemia. (PMID:38477642)
• BATF is a major driver of NK cell epigenetic reprogramming and dysfunction in AML. (PMID:39259809)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	batf	ENSDARG00000011818
mus_musculus	Batf	ENSMUSG00000034266
rattus_norvegicus	Batf	ENSRNOG00000008588
drosophila_melanogaster	Atf3	FBGN0028550

Paralogs (8): FOSL2 (ENSG00000075426), BATF3 (ENSG00000123685), FOSB (ENSG00000125740), JDP2 (ENSG00000140044), ATF3 (ENSG00000162772), BATF2 (ENSG00000168062), FOS (ENSG00000170345), FOSL1 (ENSG00000175592)

Protein

Protein identifiers

Basic leucine zipper transcriptional factor ATF-like — Q16520 (reviewed: Q16520)

Alternative names: B-cell-activating transcription factor, SF-HT-activated gene 2 protein

All UniProt accessions (2): Q16520, G3V266

UniProt curated annotations — full annotation on UniProt →

Function. AP-1 family transcription factor that controls the differentiation of lineage-specific cells in the immune system: specifically mediates the differentiation of T-helper 17 cells (Th17), follicular T-helper cells (TfH), CD8(+) dendritic cells and class-switch recombination (CSR) in B-cells. Acts via the formation of a heterodimer with JUNB that recognizes and binds DNA sequence 5’-TGA[CG]TCA-3’. The BATF-JUNB heterodimer also forms a complex with IRF4 (or IRF8) in immune cells, leading to recognition of AICE sequence (5’-TGAnTCA/GAAA-3’), an immune-specific regulatory element, followed by cooperative binding of BATF and IRF4 (or IRF8) and activation of genes. Controls differentiation of T-helper cells producing interleukin-17 (Th17 cells) by binding to Th17-associated gene promoters: regulates expression of the transcription factor RORC itself and RORC target genes such as IL17 (IL17A or IL17B). Also involved in differentiation of follicular T-helper cells (TfH) by directing expression of BCL6 and MAF. In B-cells, involved in class-switch recombination (CSR) by controlling the expression of both AICDA and of germline transcripts of the intervening heavy-chain region and constant heavy-chain region (I(H)-C(H)). Following infection, can participate in CD8(+) dendritic cell differentiation via interaction with IRF4 and IRF8 to mediate cooperative gene activation. Regulates effector CD8(+) T-cell differentiation by regulating expression of SIRT1. Following DNA damage, part of a differentiation checkpoint that limits self-renewal of hematopoietic stem cells (HSCs): up-regulated by STAT3, leading to differentiation of HSCs, thereby restricting self-renewal of HSCs.

Subunit / interactions. Heterodimer; mainly heterodimerizes with JUNB. The BATF-JUNB heterodimer interacts with IRF4 and IRF8. Interacts (via bZIP domain) with IRF4 and IRF8; the interaction is direct. Also forms heterodimers with JUN and JUND. Also interacts with IFI35.

Subcellular location. Nucleus. Cytoplasm.

Tissue specificity. Expressed at highest levels in lung, and at lower levels in placenta, liver, kidney, spleen, and peripheral blood. Detected in SW480 colorectal cancer cell line and several hematopoietic tumor cell lines, including Raji Burkitt’s lymphoma. Strongly expressed in mature B- and T-lymphocytes. Also expressed in moderate levels in lymph node and appendix and at low levels in thymus and bone marrow.

Post-translational modifications. Phosphorylated on serine and threonine residues and at least one tyrosine residue. Phosphorylation at Ser-43 inhibit DNA binding activity and transforms it as a negative regulator of AP-1 mediated transcription. Phosphorylated.

Induction. Up-regulated by PDCD1 following infection by HIV-1 virus, leading to inhibit T-cell functions and exhaust T-cells. Up-regulated by Epstein-Barr virus (EBV) protein EBNA2 following infection by EBV.

Similarity. Belongs to the bZIP family.

RefSeq proteins (1): NP_006390* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000837	AP-1	Family
IPR004827	bZIP	Domain
IPR046347	bZIP_sf	Homologous_superfamily

Pfam: PF00170

UniProt features (8 total): region of interest 3, modified residue 2, chain 1, domain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q16520-F1	81.59	0.56

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 43, 48

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

ID	Pathway
R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling
R-HSA-9976102	Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells)
R-HSA-1280215	Cytokine Signaling in Immune system
R-HSA-168256	Immune System
R-HSA-449147	Signaling by Interleukins

MSigDB gene sets: 366 (showing top): GOBP_MYELOID_CELL_DIFFERENTIATION, GOBP_REGULATION_OF_CELL_ACTIVATION, GOBP_HEMATOPOIETIC_PROGENITOR_CELL_DIFFERENTIATION, GOBP_DENDRITIC_CELL_DIFFERENTIATION, GOBP_REGULATION_OF_ALPHA_BETA_T_CELL_ACTIVATION, LU_IL4_SIGNALING, REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM, GOBP_B_CELL_ACTIVATION, GOBP_T_CELL_ACTIVATION_INVOLVED_IN_IMMUNE_RESPONSE, GOBP_REGULATION_OF_ADAPTIVE_IMMUNE_RESPONSE, GOBP_ALPHA_BETA_T_CELL_DIFFERENTIATION, GOZGIT_ESR1_TARGETS_DN, GOBP_REGULATION_OF_T_HELPER_CELL_DIFFERENTIATION, GOBP_POSITIVE_REGULATION_OF_CYTOKINE_PRODUCTION, RACCACAR_AML_Q6

GO Biological Process (17): positive regulation of cytokine production (GO:0001819), lymphoid progenitor cell differentiation (GO:0002320), regulation of transcription by RNA polymerase II (GO:0006357), DNA damage response (GO:0006974), DNA damage response, signal transduction by p53 class mediator (GO:0030330), defense response to protozoan (GO:0042832), myeloid dendritic cell differentiation (GO:0043011), T-helper 2 cell differentiation (GO:0045064), isotype switching (GO:0045190), hematopoietic stem cell differentiation (GO:0060218), T-helper 17 cell differentiation (GO:0072539), T-helper 17 cell lineage commitment (GO:0072540), integrated stress response signaling (GO:0140467), regulation of T-helper 17 cell differentiation (GO:2000319), regulation of DNA-templated transcription (GO:0006355), cell differentiation (GO:0030154), positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (8): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), DNA-binding transcription factor activity (GO:0003700), sequence-specific DNA binding (GO:0043565), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (5): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), RNA polymerase II transcription regulator complex (GO:0090575)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
Signaling by Interleukins	1
Differentiation of T cells	1
Immune System	1
Cytokine Signaling in Immune system	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA polymerase II transcription regulatory region sequence-specific DNA binding	3
cellular anatomical structure	3
hematopoietic progenitor cell differentiation	2
regulation of DNA-templated transcription	2
transcription by RNA polymerase II	2
cellular response to stress	2
alpha-beta T cell activation involved in immune response	2
T cell differentiation involved in immune response	2
T-helper cell differentiation	2
T-helper 17 cell differentiation	2
regulation of transcription by RNA polymerase II	2
cytokine production	1
regulation of cytokine production	1
positive regulation of gene expression	1
positive regulation of multicellular organismal process	1
signal transduction in response to DNA damage	1
signal transduction by p53 class mediator	1
response to protozoan	1
defense response to other organism	1
myeloid dendritic cell activation	1
myeloid leukocyte differentiation	1
dendritic cell differentiation	1
type 2 immune response	1
somatic recombination of immunoglobulin genes involved in immune response	1
B cell activation involved in immune response	1
stem cell differentiation	1
T-helper 17 type immune response	1
T-helper cell lineage commitment	1
intracellular signaling cassette	1
regulation of immune effector process	1
regulation of T-helper cell differentiation	1
regulation of T-helper 17 type immune response	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
cellular developmental process	1
positive regulation of DNA-templated transcription	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1

Protein interactions and networks

STRING

2256 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BATF	JUN	P05412	993
BATF	IRF4	Q15306	992
BATF	JUNB	P17275	924
BATF	JUND	P17535	887
BATF	FOS	P01100	865
BATF	RORC	P51449	815
BATF	PRDM1	O75626	790
BATF	MAF	O75444	781
BATF	PDCD1	Q15116	767
BATF	BACH2	Q9BYV9	761
BATF	BCL6	P41182	750
BATF	STAT3	P40763	747
BATF	JDP2	Q8WYK2	747
BATF	HSP90AA1	P07900	745
BATF	HSP90AB1	P08238	745

IntAct

142 interactions, top by confidence:

A	B	Type	Score
JUNB	BATF	psi-mi:“MI:0915”(physical association)	0.970
BATF	JUNB	psi-mi:“MI:0915”(physical association)	0.970
JUNB	BATF	psi-mi:“MI:0407”(direct interaction)	0.970
BATF	JUNB	psi-mi:“MI:0407”(direct interaction)	0.970
JUNB	BATF	psi-mi:“MI:2364”(proximity)	0.970

BioGRID (45): BATF (Two-hybrid), BATF (Two-hybrid), GOPC (Two-hybrid), BATF (Two-hybrid), BATF (Two-hybrid), JUNB (Two-hybrid), DDIT3 (Two-hybrid), BATF (FRET), JUNB (Affinity Capture-Luminescence), JUNB (FRET), BATF (Affinity Capture-Luminescence), JUNB (Two-hybrid), COX8A (Two-hybrid), BATF (Affinity Capture-Luminescence), IFI35 (Two-hybrid)

ESM2 similar proteins: A1L2X1, D4A7E1, E1BD44, F1QW76, F7EMX9, G5ECU7, G5EF76, O09015, O35284, O57598, O96642, P13096, P13097, P13098, P13903, P46505, P50539, P50540, P50541, P97831, P97876, Q00P32, Q01068, Q01069, Q01070, Q01071, Q04788, Q05195, Q07291, Q09771, Q09926, Q0VFI9, Q0VH34, Q10574, Q16520, Q18711, Q21361, Q23579, Q62282, Q8AW52

Diamond homologs: A1L2X1, D4A7E1, E1BD44, F1QW76, F7EMX9, O02761, O35284, O77628, O88479, O97930, P01100, P01101, P01102, P11939, P12841, P18847, P23050, P29176, P29596, P53450, Q16520, Q2KII1, Q56TN0, Q56TT7, Q60765, Q6DGM8, Q8HZP6, Q8N1L9, Q8WYK2, Q91496, Q9Z2Q8, B4PPK2, P79702, P97876, Q9D275, Q9NR55, A8MPH9, B3MTI9, B3P5D2, B4G652

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 37 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Response of EIF2AK1 (HRI) to heme deficiency	6	133.8×	6e-10
ATF4 activates genes in response to endoplasmic reticulum stress	5	63.7×	1e-06
Cellular response to starvation	5	25.9×	6e-05
Response of EIF2AK4 (GCN2) to amino acid deficiency	6	20.8×	2e-05
Signaling by Interleukins	5	10.0×	2e-03
Cellular responses to stress	8	9.2×	6e-05
Diseases of signal transduction by growth factor receptors and second messengers	5	8.9×	3e-03
Cellular responses to stimuli	8	7.9×	1e-04

GO biological processes:

GO term	Partners	Fold	FDR
integrated stress response signaling	10	195.1×	5e-19
response to endoplasmic reticulum stress	7	32.4×	2e-07
liver development	5	30.8×	5e-05
regulation of cell cycle	5	10.4×	3e-03
transcription by RNA polymerase II	5	9.8×	4e-03
positive regulation of gene expression	8	8.6×	2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

14 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	11
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
144734	GRCh38/hg38 14q24.1-31.1(chr14:69562099-81975384)x1	Pathogenic

SpliceAI

489 predictions. Top by Δscore:

Variant	Effect	Δscore
14:75525078:TCCCA:T	acceptor_loss	1.0000
14:75525079:CCCA:C	acceptor_loss	1.0000
14:75525080:CCAG:C	acceptor_loss	1.0000
14:75525081:CA:C	acceptor_loss	1.0000
14:75525082:A:AG	acceptor_gain	1.0000
14:75525082:A:C	acceptor_loss	1.0000
14:75525083:G:GG	acceptor_gain	1.0000
14:75525083:G:T	acceptor_loss	1.0000
14:75525184:ACCTG:A	donor_gain	1.0000
14:75525185:CCTG:C	donor_gain	1.0000
14:75525186:CTG:C	donor_gain	1.0000
14:75525187:TG:T	donor_gain	1.0000
14:75525188:GG:G	donor_gain	1.0000
14:75525188:GGTA:G	donor_loss	1.0000
14:75525189:G:GC	donor_loss	1.0000
14:75525189:G:GG	donor_gain	1.0000
14:75546459:CAG:C	acceptor_loss	1.0000
14:75546461:GGAGA:G	acceptor_gain	1.0000
14:75522744:AGGT:A	donor_loss	0.9900
14:75522745:GGT:G	donor_loss	0.9900
14:75522746:GTAGA:G	donor_loss	0.9900
14:75522747:T:A	donor_loss	0.9900
14:75525082:AG:A	acceptor_gain	0.9900
14:75525083:GG:G	acceptor_gain	0.9900
14:75525083:GGA:G	acceptor_gain	0.9900
14:75546458:ACAG:A	acceptor_gain	0.9900
14:75546459:CAGG:C	acceptor_gain	0.9900
14:75546460:A:AG	acceptor_gain	0.9900
14:75546460:AG:A	acceptor_gain	0.9900
14:75546460:AGGA:A	acceptor_gain	0.9900

AlphaMissense

824 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:75525119:G:C	R33S	1.000
14:75525119:G:T	R33S	1.000
14:75525126:A:G	N36D	1.000
14:75525128:T:A	N36K	1.000
14:75525128:T:G	N36K	1.000
14:75525129:C:A	R37S	1.000
14:75525130:G:C	R37P	1.000
14:75525135:G:C	A39P	1.000
14:75525136:C:A	A39D	1.000
14:75525139:C:A	A40D	1.000
14:75525150:C:G	R44G	1.000
14:75525171:G:C	A51P	1.000
14:75525181:T:C	L54P	1.000
14:75525183:C:G	H55D	1.000
14:75546475:T:C	L61P	1.000
14:75546496:T:C	L68P	1.000
14:75546517:T:C	L75P	1.000
14:75525116:G:C	R32S	0.999
14:75525116:G:T	R32S	0.999
14:75525127:A:C	N36T	0.999
14:75525127:A:G	N36S	0.999
14:75525127:A:T	N36I	0.999
14:75525129:C:G	R37G	0.999
14:75525129:C:T	R37C	0.999
14:75525138:G:A	A40T	0.999
14:75525138:G:C	A40P	0.999
14:75525139:C:T	A40V	0.999
14:75525142:A:C	Q41P	0.999
14:75525144:A:G	K42E	0.999
14:75525147:A:C	S43R	0.999

dbSNP variants (sampled 300 via entrez): RS1000042581 (14:75530461 G>C), RS1000241022 (14:75546499 G>A,C,T), RS1000318056 (14:75533402 A>T), RS1000454172 (14:75527464 G>T), RS1000520201 (14:75532459 T>G), RS1000532090 (14:75534902 T>A,C), RS1000554136 (14:75530819 T>A), RS1000583827 (14:75533892 C>T), RS1000691228 (14:75546751 T>TGTCC), RS1000694032 (14:75526145 C>T), RS1000749197 (14:75541205 A>G), RS1000757707 (14:75525507 A>C), RS1000786394 (14:75522443 A>G), RS1000838725 (14:75522218 G>A), RS1000852183 (14:75543304 T>C)

Disease associations

OMIM: gene MIM:612476 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST001198_5	Multiple sclerosis	2.000000e-08
GCST005038_87	Allergic disease (asthma, hay fever or eczema)	9.000000e-09
GCST005531_81	Multiple sclerosis	2.000000e-07
GCST009597_120	Multiple sclerosis	6.000000e-13
GCST009617_1	LDL cholesterol levels x thiazide or thiazide-like diuretics use interaction	1.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004611	low density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

32 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases methylation, increases expression	3
Nickel	increases expression	2
TL8-506	affects cotreatment, increases expression	1
octa-2,4,6-trienoic acid	increases expression	1
di-n-butylphosphoric acid	affects expression	1
cylindrospermopsin	increases expression	1
CGP 52608	affects binding, increases reaction	1
K 7174	decreases expression	1
abrine	increases expression	1
LG 100815	increases expression	1
gardiquimod	increases expression, decreases reaction	1
(+)-JQ1 compound	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Clodronic Acid	decreases expression	1
Ozone	increases expression	1
Selenium	increases expression	1
Silicon Dioxide	increases expression	1
Smoke	decreases expression, increases abundance	1
Tetrachlorodibenzodioxin	increases expression	1
Tobacco Smoke Pollution	affects expression	1
Tretinoin	increases expression	1
Urethane	decreases expression	1
Valproic Acid	decreases expression	1
Vincristine	increases expression	1
Vitamin E	increases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	increases expression	1
Antirheumatic Agents	decreases expression	1
Palmitic Acid	decreases expression	1
Okadaic Acid	increases expression	1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_A0G9	SEES3-1V human BATF, clone1	Embryonic stem cell	Male
CVCL_A0H0	SEES3-1V human BATF, clone2	Embryonic stem cell	Male
CVCL_A0H1	SEES3-1V human BATF, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.