BANP

Summary

BANP (BTG3 associated nuclear protein, HGNC:13450) is a protein-coding gene on chromosome 16q24.2, encoding Protein BANP (Q8N9N5). Controls V(D)J recombination during T-cell development by repressing T-cell receptor (TCR) beta enhancer function. It is a common-essential gene (DepMap: required in 96.4% of cancer cell lines).

This gene encodes a protein that binds to matrix attachment regions. The protein forms a complex with p53 and negatively regulates p53 transcription, and functions as a tumor suppressor and cell cycle regulator. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 54971 — RefSeq curated summary.

At a glance

• GWAS associations: 12
• Clinical variants (ClinVar): 96 total — 3 pathogenic
• Cancer dependency (DepMap): dependent in 96.4% of screened cell lines (common-essential)
• MANE Select transcript: NM_001386991

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13450
Approved symbol	BANP
Name	BTG3 associated nuclear protein
Location	16q24.2
Locus type	gene with protein product
Status	Approved
Aliases	SMARBP1, SMAR1, FLJ20538, DKFZp761H172, FLJ10177, BEND1
Ensembl gene	ENSG00000172530
Ensembl biotype	protein_coding
OMIM	611564
Entrez	54971

Gene structure

Transcript identifiers

Ensembl transcripts: 96 — 83 protein_coding, 8 protein_coding_CDS_not_defined, 3 nonsense_mediated_decay, 2 retained_intron

ENST00000286122, ENST00000355022, ENST00000393207, ENST00000393208, ENST00000412691, ENST00000423252, ENST00000436274, ENST00000436970, ENST00000439677, ENST00000454563, ENST00000456902, ENST00000459966, ENST00000466197, ENST00000466847, ENST00000472964, ENST00000474563, ENST00000479780, ENST00000481948, ENST00000485772, ENST00000488074, ENST00000497491, ENST00000526460, ENST00000538234, ENST00000565242, ENST00000569400, ENST00000612301, ENST00000626016, ENST00000682872, ENST00000700483, ENST00000854712, ENST00000854713, ENST00000854714, ENST00000854715, ENST00000854716, ENST00000854717, ENST00000854718, ENST00000854719, ENST00000854720, ENST00000854721, ENST00000854722, ENST00000854723, ENST00000854724, ENST00000854725, ENST00000854726, ENST00000854727, ENST00000854728, ENST00000854729, ENST00000854730, ENST00000854731, ENST00000854732, ENST00000854733, ENST00000854734, ENST00000854735, ENST00000854736, ENST00000854737, ENST00000854738, ENST00000854739, ENST00000854740, ENST00000854741, ENST00000854742, ENST00000854743, ENST00000854744, ENST00000854745, ENST00000854746, ENST00000854747, ENST00000854748, ENST00000854749, ENST00000854750, ENST00000854751, ENST00000854752, ENST00000854753, ENST00000919339, ENST00000919340, ENST00000919341, ENST00000919342, ENST00000919343, ENST00000969707, ENST00000969708, ENST00000969709, ENST00000969710, ENST00000969711, ENST00000969712, ENST00000969713, ENST00000969714, ENST00000969715, ENST00000969716, ENST00000969717, ENST00000969718, ENST00000969719, ENST00000969720, ENST00000969721, ENST00000969722, ENST00000969723, ENST00000969724, ENST00000969725, ENST00000969726

RefSeq mRNA: 33 — MANE Select: NM_001386991 NM_001173539, NM_001173540, NM_001173541, NM_001173542, NM_001173543, NM_001384916, NM_001384918, NM_001384919, NM_001384920, NM_001384921, NM_001384922, NM_001384923, NM_001384925, NM_001384926, NM_001384927, NM_001384928, NM_001384929, NM_001384931, NM_001384935, NM_001384936, NM_001384937, NM_001384938, NM_001384939, NM_001384940, NM_001384941, NM_001384942, NM_001384943, NM_001384944, NM_001386991, NM_001386992, NM_001424170, NM_017869, NM_079837

CCDS: CCDS10966, CCDS42215, CCDS54052, CCDS54053, CCDS54054, CCDS54055, CCDS92203, CCDS92204

Canonical transcript exons

ENST00000682872 — 14 exons

Exon	Start	End
ENSE00001238421	88065267	88065332
ENSE00001238530	88006090	88006265
ENSE00002200065	87975048	87975185
ENSE00002213839	88035323	88035394
ENSE00002215853	88033109	88033245
ENSE00003485388	87981036	87981127
ENSE00003508142	88027483	88027650
ENSE00003510744	88018428	88018667
ENSE00003584876	87984060	87984259
ENSE00003611745	88072069	88072212
ENSE00003683876	88037973	88038011
ENSE00003922348	88076590	88077316
ENSE00003979934	87951434	87951515
ENSE00003979935	88004295	88004411

Expression profiles

Bgee: expression breadth ubiquitous, 277 present calls, max score 98.13.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.0024 / max 295.3971, expressed in 1812 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
155505	16.2994	1805
155506	2.6840	1030
155507	0.5200	272
155508	0.3382	151
155515	0.0659	29
155502	0.0656	19
155504	0.0172	8
155503	0.0120	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	98.13	gold quality
secondary oocyte	CL:0000655	97.56	gold quality
blood	UBERON:0000178	93.33	gold quality
pancreatic ductal cell	CL:0002079	93.25	silver quality
middle temporal gyrus	UBERON:0002771	92.84	gold quality
amniotic fluid	UBERON:0000173	91.79	gold quality
Brodmann (1909) area 23	UBERON:0013554	91.61	gold quality
tendon of biceps brachii	UBERON:0008188	91.49	gold quality
visceral pleura	UBERON:0002401	91.22	gold quality
epithelial cell of pancreas	CL:0000083	91.05	silver quality
tibia	UBERON:0000979	91.05	gold quality
cartilage tissue	UBERON:0002418	90.86	gold quality
thymus	UBERON:0002370	90.76	gold quality
esophagus squamous epithelium	UBERON:0006920	90.72	gold quality
periodontal ligament	UBERON:0008266	90.18	gold quality
renal medulla	UBERON:0000362	90.02	gold quality
bone marrow cell	CL:0002092	89.99	gold quality
squamous epithelium	UBERON:0006914	89.86	gold quality
parietal pleura	UBERON:0002400	89.77	gold quality
cervix squamous epithelium	UBERON:0006922	89.69	silver quality
pleura	UBERON:0000977	89.62	gold quality
choroid plexus epithelium	UBERON:0003911	89.27	gold quality
epithelium of esophagus	UBERON:0001976	89.20	gold quality
vena cava	UBERON:0004087	89.12	silver quality
renal glomerulus	UBERON:0000074	89.09	gold quality
placenta	UBERON:0001987	89.03	gold quality
granulocyte	CL:0000094	88.92	gold quality
gingival epithelium	UBERON:0001949	88.91	gold quality
pylorus	UBERON:0001166	88.79	gold quality
metanephric glomerulus	UBERON:0004736	88.77	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.92
E-MTAB-7303	no	200.05

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

Target	Regulation
STAT3

Upstream regulators (CollecTRI, top): CEBPB, NFKB, NFKBIA, TP53

miRNA regulators (miRDB)

25 targeting BANP, 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-548P	99.98	72.25	3784
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-320A-3P	99.77	69.73	2107
HSA-MIR-320B	99.77	69.73	2107
HSA-MIR-320C	99.77	69.73	2107
HSA-MIR-320D	99.77	69.73	2107
HSA-MIR-4429	99.77	69.62	2111
HSA-MIR-5700	99.64	69.88	2280
HSA-MIR-6757-3P	99.63	66.88	1089
HSA-MIR-425-5P	99.59	67.67	900
HSA-MIR-3120-3P	99.54	70.28	2669
HSA-MIR-5584-3P	99.23	68.79	1351
HSA-MIR-122B-3P	99.21	68.90	1333
HSA-MIR-21-3P	99.21	68.95	1312
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-922	99.02	67.23	1838
HSA-MIR-3619-5P	99.00	68.87	2308
HSA-MIR-4520-3P	98.75	66.55	963
HSA-MIR-6501-3P	98.71	67.45	1480
HSA-MIR-214-3P	98.71	68.12	2128
HSA-MIR-761	98.71	68.07	2051
HSA-MIR-5088-5P	97.97	64.28	487
HSA-MIR-3654	96.43	66.55	646

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 96.4% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 31)

• Identification of a novel mouse MAR-binding protein, named SMAR1, which shares homology with SATB1 and Cux in the MAR-binding domain/Cut repeat and also with the tetramerization domain of a B cell-specific MAR-binding protein, Bright. (PMID:10950932)
• SMAR1 plays an important role in the regulation of T cell development as well as V(D)J recombination (PMID:15623522)
• SMAR1 regulates cyclin D1 by modification of chromatin through the SIN3/histone deacetylase 1 complex (PMID:16166625)
• SMAR1 plays a central role in coordinating p53 and TGFbeta pathways in human breast cancer. (PMID:17668048)
• tumor suppressor SMAR1 downregulates Cytokeratin 8 gene expression by modulating p53-mediated transactivation of this gene (PMID:18822384)
• tumor suppressor protein SMAR1 can modulate NF-kappaB transactivation and inhibit tumorigenesis by regulating NF-kappaB target genes (PMID:18981184)
• Results highlight the role of SMAR1 in masking the active phosphorylation site of p53, enabling the deacetylation of p53 by HDAC1-MDM2 complex, thereby regulating the p53 transcriptional response during stress rescue. (PMID:19303885)
• Human breast cancer tissue sections that showed reduced SMAR1 expression exhibited increased surface roughness. (PMID:19799771)
• On mild DNA damage, SMAR1 selectively represses BAX and PUMA through binding to the MAR independently of inducing p53 deacetylation through HDAC1. (PMID:20075864)
• A novel mechanism of regulation of oxidative stress by ATM through modulation of SMAR1-AKR1a4 complex, is proposed. (PMID:20097305)
• report Prostaglandin A2 (PGA2) induced binding of HSP70 to a novel site on phi1 SMAR1 5’ UTR which stabilizes the wild type transcript and leads to subsequent increase in SMAR1 protein levels. (PMID:20153327)
• multiple roles of nuclear matrix associated protein SMAR1 in regulating various cellular target genes involved in cell growth, apoptosis and tumorigenesis.(REVIEW) (PMID:20709157)
• Results indicate that SMAR1 is an important player in p300-p53 regulated DNA damage signalling pathway and can exert its effect on apoptosis in a transcription independent manner. (PMID:22074660)
• TCF-4, beta-catenin, and SMAR1 tether at the -143-nucleotide site on the HIV LTR to inhibit HIV promoter activity. (PMID:22674979)
• During hemin-induced erythroid differentiation, enhanced expression of SMAR1 negatively correlates with miR-320a expression. (PMID:23876508)
• indicate a crucial role for SMAR1 in restraining breast cancer cell migration and suggest the candidature of this scaffold matrix-associated region-binding protein as a tumor suppressor. (PMID:25086032)
• SMAR1 has a role in repressing c-Fos-mediated HPV18 E6 transcription through alteration of chromatin histone deacetylation (PMID:25157104)
• Data indicate the role of SMAR1 protein in NF-kappaappa B dependent transcriptional regulation of pro-angiogenic chemokine interleukin-8 (IL-8). (PMID:25239884)
• SMAR1-mediated regulation of repair and apoptosis via a complex crosstalk involving Ku70, HDAC6 and Bax. (PMID:25299772)
• results reveal the complex molecular mechanism underlying SMAR1-mediated signal-dependent and -independent regulation of alternative splicing via Sam68 deacetylation (PMID:26080397)
• Dysregulated circ-BANP appears to have an important role in colorectal cancer cells. (PMID:28103507)
• Cdc20 functions as an important negative regulator of SMAR1 in higher grades of cancer (PMID:28617439)
• our observations establish that increased expression of SMAR1 in cancers can positively regulate MHC I surface expression thereby leading to higher chances of tumor regression and elimination of cancer cells. (PMID:31422285)
• SMAR1 repression by pluripotency factors and consequent chemoresistance in breast cancer stem-like cells is reversed by aspirin. (PMID:33082288)
• BANP opens chromatin and activates CpG-island-regulated genes. (PMID:34234345)
• SMAR1 suppresses the cancer stem cell population via hTERT repression in colorectal cancer cells. (PMID:34551340)
• Structural insights into DNA recognition by the BEN domain of the transcription factor BANP. (PMID:37086783)
• Nuclear Matrix-associated Protein SMAR1 Attenuated Acute Graft-versus-host Disease by Targeting JAK-STAT Signaling in CD4 + T Cells. (PMID:37817309)
• BANP Participates in the Chronic Intermittent Hypoxia-Induced Senescence of Vascular Endothelial Cells by Promoting P53 Phosphorylation and Nuclear Retention. (PMID:38168028)
• ZNF471 Interacts with BANP to Reduce Tumour Malignancy by Inactivating PI3K/AKT/mTOR Signalling but is Frequently Silenced by Aberrant Promoter Methylation in Renal Cell Carcinoma. (PMID:38169650)
• Structural basis of DNA recognition by BEN domain proteins reveals a role for oligomerization in unmethylated DNA selection by BANP. (PMID:39225042)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	banp	ENSDARG00000017562
mus_musculus	Banp	ENSMUSG00000025316
rattus_norvegicus	Banp	ENSRNOG00000019140

Protein

Protein identifiers

Protein BANP — Q8N9N5 (reviewed: Q8N9N5)

Alternative names: BEN domain-containing protein 1, Btg3-associated nuclear protein, Scaffold/matrix-associated region-1-binding protein

All UniProt accessions (15): A0A0S2Z5C2, A0A0S2Z5G4, A0A0S2Z5M2, A0A804HKG3, B4DE54, C9J811, C9JF73, C9JGM9, C9JLS0, C9JLT2, C9JTM8, C9JYB6, Q8N9N5, E9PIP2, E9PJI6

UniProt curated annotations — full annotation on UniProt →

Function. Controls V(D)J recombination during T-cell development by repressing T-cell receptor (TCR) beta enhancer function. Binds to scaffold/matrix attachment region beta (S/MARbeta), an ATC-rich DNA sequence located upstream of the TCR beta enhancer. Represses cyclin D1 transcription by recruiting HDAC1 to its promoter, thereby diminishing H3K9ac, H3S10ph and H4K8ac levels. Promotes TP53 activation, which causes cell cycle arrest. Plays a role in the regulation of alternative splicing. Binds to CD44 pre-mRNA and negatively regulates the inclusion of CD44 proximal variable exons v2-v6 but has no effect on distal variable exons v7-v10.

Subunit / interactions. Part of a corepressor complex containing BANP, HDAC1, SIN3A, SIN3B, RBL1 and RBL2. Forms a trimeric complex in the nucleus consisting of BANP, HDAC6 and KHDRBS1/SAM68; HDAC6 keeps KHDRBS1 in a deacetylated state which inhibits the inclusion of CD44 alternate exons. The complex is disrupted by MAPK1/MAPK3-mediated phosphorylation of BANP which results in BANP export to the cytoplasm. This facilitates acetylation of KHDRBS1 and CD44 variant exon inclusion. Interacts with TP53. Interacts with CUX1/CDP. Interacts with HDAC1.

Subcellular location. Nucleus. Nucleus speckle. Cytoplasm.

Tissue specificity. Down-regulated in breast cancer cell lines.

Post-translational modifications. MAPK1/MAPK3-mediated phosphorylation at Thr-337 and Thr-352 results in export to the cytoplasm.

Similarity. Belongs to the BANP/SMAR1 family.

Isoforms (7)

UniProt ID	Names	Canonical?
Q8N9N5-1	1	yes
Q8N9N5-2	2
Q8N9N5-3	3
Q8N9N5-4	4
Q8N9N5-5	5
Q8N9N5-6	6
Q8N9N5-7	7

RefSeq proteins (33): NP_001167010, NP_001167011, NP_001167012, NP_001167013, NP_001167014, NP_001371845, NP_001371847, NP_001371848, NP_001371849, NP_001371850, NP_001371851, NP_001371852, NP_001371854, NP_001371855, NP_001371856, NP_001371857, NP_001371858, NP_001371860, NP_001371864, NP_001371865, NP_001371866, NP_001371867, NP_001371868, NP_001371869, NP_001371870, NP_001371871, NP_001371872, NP_001371873, NP_001373920, NP_001373921, NP_001411099, NP_060339, NP_524576 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR018379	BEN_domain	Domain
IPR042343	BANP	Family

Pfam: PF10523

UniProt features (37 total): splice variant 7, modified residue 6, helix 6, compositionally biased region 4, region of interest 4, strand 3, sequence conflict 2, chain 1, domain 1, cross-link 1, turn 1, coiled-coil region 1

Structure

Experimental structures (PDB)

4 structures.

PDB	Method	Resolution (Å)
7YUG	X-RAY DIFFRACTION	1.1
7YUK	X-RAY DIFFRACTION	2.11
8YZT	X-RAY DIFFRACTION	2.58
8HTX	X-RAY DIFFRACTION	2.8

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N9N5-F1	54.71	0.22

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 (7): 19, 90, 100, 275, 337, 352, 133

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

ID	Pathway
R-HSA-6804759	Regulation of TP53 Activity through Association with Co-factors
R-HSA-9766229	Degradation of CDH1
R-HSA-212436	Generic Transcription Pathway
R-HSA-3700989	Transcriptional Regulation by TP53
R-HSA-5633007	Regulation of TP53 Activity
R-HSA-73857	RNA Polymerase II Transcription
R-HSA-74160	Gene expression (Transcription)

MSigDB gene sets: 152 (showing top): WANG_CLIM2_TARGETS_UP, TGCGCANK_UNKNOWN, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_UP, REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS, NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON, BLALOCK_ALZHEIMERS_DISEASE_UP, WHN_B, CCCNNGGGAR_OLF1_01, GOCC_NUCLEAR_SPECK, GOCC_NUCLEAR_BODY, GOCC_RIBONUCLEOPROTEIN_GRANULE, ZHENG_BOUND_BY_FOXP3, CAGCTTT_MIR320, AP2_Q6, REACTOME_CELL_JUNCTION_ORGANIZATION

GO Biological Process (2): chromatin organization (GO:0006325), positive regulation of DNA-templated transcription (GO:0045893)

GO Molecular Function (4): DNA binding (GO:0003677), RNA binding (GO:0003723), identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (5): nucleoplasm (GO:0005654), cytoplasm (GO:0005737), nuclear body (GO:0016604), nuclear speck (GO:0016607), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-6 pathways:

Category	Pathways
Regulation of TP53 Activity	1
Regulation of CDH1 Function	1
RNA Polymerase II Transcription	1
Generic Transcription Pathway	1
Transcriptional Regulation by TP53	1
Gene expression (Transcription)	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nucleic acid binding	2
cellular anatomical structure	2
cellular component organization	1
DNA-templated transcription	1
regulation of DNA-templated transcription	1
positive regulation of RNA biosynthetic process	1
protein binding	1
binding	1
nuclear lumen	1
intracellular anatomical structure	1
nucleoplasm	1
intracellular membraneless organelle	1
nuclear ribonucleoprotein granule	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

866 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BANP	HDAC1	Q13547	922
BANP	SETMAR	Q53H47	896
BANP	PRPF19	Q9UMS4	810
BANP	CUX1	P39880	741
BANP	CTNNB1	P35222	737
BANP	MDM2	Q00987	635
BANP	ZNF469	Q96JG9	571
BANP	BEND2	Q8NDZ0	570
BANP	TP53	P04637	550
BANP	SIN3A	Q96ST3	515
BANP	BEND5	Q7L4P6	483
BANP	FNDC3B	Q53EP0	483
BANP	TCF25	Q9BQ70	455
BANP	CCND1	P24385	454
BANP	LARP1	Q6PKG0	452

IntAct

313 interactions, top by confidence:

A	B	Type	Score
FHL2	BANP	psi-mi:“MI:0915”(physical association)	0.740
BANP	FHL2	psi-mi:“MI:0915”(physical association)	0.740
BANP	TNXB	psi-mi:“MI:0915”(physical association)	0.670
BANP	SP2	psi-mi:“MI:0915”(physical association)	0.670
BANP	TROAP	psi-mi:“MI:0915”(physical association)	0.670
BANP	NEDD9	psi-mi:“MI:0915”(physical association)	0.670
TRAF2	BANP	psi-mi:“MI:0915”(physical association)	0.670
CAMK2D	BANP	psi-mi:“MI:0915”(physical association)	0.670
BANP	C1orf94	psi-mi:“MI:0915”(physical association)	0.670
L3MBTL3	BANP	psi-mi:“MI:0915”(physical association)	0.670
PHF21A	BANP	psi-mi:“MI:0915”(physical association)	0.670
BANP	LENG1	psi-mi:“MI:0915”(physical association)	0.670
TROAP	BANP	psi-mi:“MI:0915”(physical association)	0.670
BANP	TRAF2	psi-mi:“MI:0915”(physical association)	0.670
BANP	PHF21A	psi-mi:“MI:0915”(physical association)	0.670
LENG1	BANP	psi-mi:“MI:0915”(physical association)	0.670
BANP	CAMK2D	psi-mi:“MI:0915”(physical association)	0.670
C1orf94	BANP	psi-mi:“MI:0915”(physical association)	0.670
SP2	BANP	psi-mi:“MI:0915”(physical association)	0.670

BioGRID (383): TP53 (Affinity Capture-Western), PARP1 (Affinity Capture-Western), EP300 (Affinity Capture-Western), BANP (Two-hybrid), BANP (Two-hybrid), BANP (Two-hybrid), BANP (Two-hybrid), BANP (Two-hybrid), BANP (Two-hybrid), BANP (Two-hybrid), BANP (Two-hybrid), BANP (Two-hybrid), BANP (Two-hybrid), BANP (Two-hybrid), BANP (Two-hybrid)

ESM2 similar proteins: A2BID7, B1AWL2, B4F6U4, H2L008, O08785, O15164, O15516, P57071, P70121, Q08BR4, Q0P5J0, Q0VCJ6, Q2TAL8, Q3UA37, Q3UTQ7, Q502P7, Q56R14, Q58NQ5, Q5FWL0, Q5NBY9, Q5RAK8, Q5RAX9, Q5RGA4, Q5XJV7, Q62415, Q64127, Q6DJT9, Q6E2N3, Q6INA9, Q6YGZ4, Q7Z3K3, Q8BZH4, Q8K0L9, Q8N187, Q8N9N5, Q8QG78, Q8QGQ6, Q8R515, Q8VBU8, Q91YB0

Diamond homologs: Q0VCW3, Q502P7, Q5FWL0, Q6P4Y1, Q8N9N5, Q8VBU8

SIGNOR signaling

5 interactions.

A	Effect	B	Mechanism
BANP	“down-regulates activity”	KHDRBS1	binding
ERK1/2	“down-regulates activity”	BANP	phosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	0
Uncertain significance	71
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (3)

Variant ID	HGVS	Classification
1069841	NC_000016.9:g.(?87636753)(88505740_?)del	Pathogenic
2498685	GRCh37/hg19 16q24.1-24.2(chr16:86544176-88110267)x1	Pathogenic
4682889	GRCh37/hg19 16q24.1-24.2(chr16:85281141-88194304)x1	Pathogenic

SpliceAI

4621 predictions. Top by Δscore:

Variant	Effect	Δscore
16:87975044:GTA:G	acceptor_loss	1.0000
16:87975046:A:T	acceptor_loss	1.0000
16:87975047:G:GA	acceptor_loss	1.0000
16:87975047:GGT:G	acceptor_gain	1.0000
16:87975204:G:GG	donor_gain	1.0000
16:87981021:T:TA	acceptor_gain	1.0000
16:87981025:A:AG	acceptor_gain	1.0000
16:87981025:ACT:A	acceptor_gain	1.0000
16:87981026:C:G	acceptor_gain	1.0000
16:87981027:T:A	acceptor_gain	1.0000
16:87981031:TTCA:T	acceptor_loss	1.0000
16:87981032:TCAG:T	acceptor_loss	1.0000
16:87981033:CAG:C	acceptor_loss	1.0000
16:87981034:A:AG	acceptor_gain	1.0000
16:87981034:AGTT:A	acceptor_gain	1.0000
16:87981035:G:GG	acceptor_gain	1.0000
16:87981035:GT:G	acceptor_gain	1.0000
16:87981035:GTT:G	acceptor_gain	1.0000
16:87981035:GTTG:G	acceptor_gain	1.0000
16:87981035:GTTGT:G	acceptor_gain	1.0000
16:87981126:AGG:A	donor_loss	1.0000
16:87981129:T:G	donor_loss	1.0000
16:87984058:A:AC	acceptor_loss	1.0000
16:87984058:A:AG	acceptor_gain	1.0000
16:87984059:G:GG	acceptor_gain	1.0000
16:87984059:GT:G	acceptor_gain	1.0000
16:87984059:GTC:G	acceptor_gain	1.0000
16:87984059:GTCA:G	acceptor_gain	1.0000
16:87984059:GTCAT:G	acceptor_gain	1.0000
16:88004294:GCGTC:G	acceptor_gain	1.0000

AlphaMissense

3494 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:88006248:T:A	I205N	1.000
16:88006248:T:C	I205T	1.000
16:88006248:T:G	I205S	1.000
16:88006258:C:A	N208K	1.000
16:88006258:C:G	N208K	1.000
16:88018442:G:C	G216R	1.000
16:88018443:G:A	G216D	1.000
16:88018443:G:T	G216V	1.000
16:88018448:T:A	W218R	1.000
16:88018448:T:C	W218R	1.000
16:88018450:G:C	W218C	1.000
16:88018450:G:T	W218C	1.000
16:88018452:T:A	L219Q	1.000
16:88018452:T:C	L219P	1.000
16:88018454:G:C	G220R	1.000
16:88018454:G:T	G220C	1.000
16:88018455:G:A	G220D	1.000
16:88018455:G:T	G220V	1.000
16:88018484:C:A	R230S	1.000
16:88018484:C:G	R230G	1.000
16:88018529:T:C	C245R	1.000
16:88018541:G:A	E249K	1.000
16:88018542:A:T	E249V	1.000
16:88018544:A:G	K250E	1.000
16:88018550:G:C	A252P	1.000
16:88018551:C:A	A252E	1.000
16:88018554:T:A	L253H	1.000
16:88018554:T:C	L253P	1.000
16:88018560:T:C	L255P	1.000
16:88018560:T:G	L255R	1.000

dbSNP variants (sampled 300 via entrez): RS1000021724 (16:88051021 G>C), RS1000021849 (16:87955033 G>A,T), RS1000025888 (16:88026943 G>A), RS1000048018 (16:87958834 T>A,C), RS1000117934 (16:88067646 C>G,T), RS1000118257 (16:88074583 G>A,C), RS1000119136 (16:88034640 G>A), RS1000148810 (16:88024195 G>A), RS1000183915 (16:87986266 A>G), RS1000198383 (16:87975004 C>A,T), RS1000200386 (16:87991303 T>C,G), RS1000257696 (16:87959145 C>G,T), RS1000319115 (16:88052610 C>G,T), RS1000357750 (16:87967014 G>A), RS1000367930 (16:87974078 G>T)

Disease associations

OMIM: gene MIM:611564 | disease phenotypes: MIM:615751

GenCC curated gene-disease

Mondo (2): hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency (MONDO:0014332), ependymoma (MONDO:0016698)

Orphanet (2): Hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency (Orphanet:401948), Ependymoma (Orphanet:251636)

HPO phenotypes

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

GWAS associations

12 associations (top):

Study	Trait	p-value
GCST000775_5	Central corneal thickness	6.000000e-22
GCST001806_25	Corneal structure	2.000000e-49
GCST003856_2	Central corneal thickness	2.000000e-08
GCST005170_43	Intraocular pressure	4.000000e-12
GCST006628_30	Systolic blood pressure	1.000000e-10
GCST010241_354	Apolipoprotein A1 levels	3.000000e-11
GCST010242_27	HDL cholesterol levels	5.000000e-16
GCST010244_386	Triglyceride levels	1.000000e-10
GCST90002397_717	Mean spheric corpuscular volume	3.000000e-09
GCST90002400_189	Plateletcrit	9.000000e-10
GCST90002402_473	Platelet count	1.000000e-11
GCST90013442_26	Keratoconus	4.000000e-20

EFO canonical traits (10, from GWAS)

EFO ID	Trait name
EFO:0004731	eye measurement
EFO:0004345	corneal topography
EFO:0005213	central corneal thickness
EFO:0004695	intraocular pressure measurement
EFO:0006335	systolic blood pressure
EFO:0004614	apolipoprotein A 1 measurement
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004530	triglyceride measurement
EFO:0007985	platelet crit
EFO:0004309	platelet count

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D004806	Ependymoma	C04.557.465.625.600.380.290; C04.557.470.670.380.290; C04.557.580.625.600.380.290

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
cobaltous chloride	increases expression	2
Benzo(a)pyrene	decreases expression, increases methylation	2
Valproic Acid	affects expression, decreases expression	2
aristolochic acid I	increases expression	1
GSK-J4	increases expression	1
selenomethylselenocysteine	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, increases methylation, decreases methylation	1
terbufos	increases methylation	1
beta-lapachone	decreases expression	1
beta-methylcholine	affects expression	1
abrine	increases expression	1
PCI 5002	increases expression, affects cotreatment	1
Sunitinib	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Vorinostat	decreases expression	1
Air Pollutants	affects expression, increases abundance	1
Arsenic	affects methylation	1
Diazinon	increases methylation	1
Doxorubicin	decreases expression	1
Fonofos	increases methylation	1
Hydrogen Peroxide	decreases expression	1
Lead	affects methylation	1
Ozone	affects expression, increases abundance	1
Parathion	increases methylation	1
Phenobarbital	affects expression	1
Phthalic Acids	decreases methylation	1
Silver	increases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	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_A0G0	SEES3-1V human BANP, clone1	Embryonic stem cell	Male
CVCL_A0G1	SEES3-1V human BANP, clone2	Embryonic stem cell	Male
CVCL_A0G2	SEES3-1V human BANP, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00517959	PHASE3	UNKNOWN	SCRT Versus Conventional RT in Children and Young Adults With Low Grade and Benign Brain Tumors
NCT01096368	PHASE3	COMPLETED	Maintenance Chemotherapy or Observation Following Induction Chemotherapy and Radiation Therapy in Treating Patients With Newly Diagnosed Ependymoma
NCT00003479	PHASE2	TERMINATED	Antineoplaston Therapy in Treating Patients With Ependymoma
NCT00520936	PHASE2	COMPLETED	A Study of Pemetrexed in Children With Recurrent Cancer
NCT00840047	PHASE2	ACTIVE_NOT_RECRUITING	Methionine PET/CT Studies In Patients With Cancer
NCT01088035	PHASE2	TERMINATED	Carboplatin as a Radiosensitizer in Treating Childhood Ependymoma
NCT01247922	PHASE2	TERMINATED	Single-agent Erlotinib in Patients Previously Treated With Oral Etoposide in Protocol OSI-774-205
NCT01288235	PHASE2	COMPLETED	Proton Radiotherapy for Pediatric Brain Tumors Requiring Partial Brain Irradiation
NCT01295944	PHASE2	COMPLETED	Carboplatin and Bevacizumab for Recurrent Ependymoma
NCT01356290	PHASE2	RECRUITING	Antiangiogenic Therapy for Children With Recurrent Medulloblastoma, Ependymoma, ATRT and Rare CNS Tumors
NCT01836549	PHASE2	TERMINATED	Imetelstat Sodium in Treating Younger Patients With Recurrent or Refractory Brain Tumors
NCT02125786	PHASE2	ACTIVE_NOT_RECRUITING	A Trial of Surgery and Fractionated Re-Irradiation for Recurrent Ependymoma
NCT02689336	PHASE2	WITHDRAWN	Erlotinib in Combination With Temozolomide in Treating Relapsed/Recurrent/Refractory Pediatric Solid Tumors
NCT03095248	PHASE2	TERMINATED	Trial of Selumetinib in Patients With Neurofibromatosis Type II Related Tumors
NCT03155620	PHASE2	ACTIVE_NOT_RECRUITING	Targeted Therapy Directed by Genetic Testing in Treating Pediatric Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphomas, or Histiocytic Disorders (The Pediatric MATCH Screening Trial)
NCT03173950	PHASE2	COMPLETED	Immune Checkpoint Inhibitor Nivolumab in People With Recurrent Select Rare CNS Cancers
NCT03194906	PHASE2	COMPLETED	Memantine for Prevention of Cognitive Late Effects in Pediatric Patients Receiving Cranial Radiation Therapy for Localized Brain Tumors
NCT03210714	PHASE2	ACTIVE_NOT_RECRUITING	Erdafitinib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With FGFR Mutations (A Pediatric MATCH Treatment Trial)
NCT03213652	PHASE2	ACTIVE_NOT_RECRUITING	Ensartinib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With ALK or ROS1 Genomic Alterations (A Pediatric MATCH Treatment Trial)
NCT03213665	PHASE2	COMPLETED	Tazemetostat in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With EZH2, SMARCB1, or SMARCA4 Gene Mutations (A Pediatric MATCH Treatment Trial)
NCT03213678	PHASE2	COMPLETED	Samotolisib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With TSC or PI3K/MTOR Mutations (A Pediatric MATCH Treatment Trial)
NCT03213704	PHASE2	ACTIVE_NOT_RECRUITING	Larotrectinib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With NTRK Fusions (A Pediatric MATCH Treatment Trial)
NCT03220035	PHASE2	COMPLETED	Vemurafenib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With BRAF V600 Mutations (A Pediatric MATCH Treatment Trial)
NCT03233204	PHASE2	COMPLETED	Olaparib in Treating Patients With Relapsed or Refractory Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With Defects in DNA Damage Repair Genes (A Pediatric MATCH Treatment Trial)
NCT03526250	PHASE2	COMPLETED	Palbociclib in Treating Patients With Relapsed or Refractory Rb Positive Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With Activating Alterations in Cell Cycle Genes (A Pediatric MATCH Treatment Trial)
NCT03698994	PHASE2	ACTIVE_NOT_RECRUITING	Ulixertinib in Treating Patients With Advanced Solid Tumors, Non-Hodgkin Lymphoma, or Histiocytic Disorders With MAPK Pathway Mutations (A Pediatric MATCH Treatment Trial)
NCT03727841	PHASE2	TERMINATED	Marizomib for Recurrent Low-Grade and Anaplastic Supratentorial, Infratentorial, and Spinal Cord Ependymoma
NCT04049669	PHASE2	ACTIVE_NOT_RECRUITING	Pediatric Trial of Indoximod With Chemotherapy and Radiation for Relapsed Brain Tumors or Newly Diagnosed DIPG
NCT04195555	PHASE2	ACTIVE_NOT_RECRUITING	Ivosidenib in Treating Patients With Advanced Solid Tumors, Lymphoma, or Histiocytic Disorders With IDH1 Mutations (A Pediatric MATCH Treatment Trial)
NCT04284774	PHASE2	ACTIVE_NOT_RECRUITING	Tipifarnib for the Treatment of Advanced Solid Tumors, Lymphoma, or Histiocytic Disorders With HRAS Gene Alterations, a Pediatric MATCH Treatment Trial
NCT04320888	PHASE2	ACTIVE_NOT_RECRUITING	Selpercatinib for the Treatment of Advanced Solid Tumors, Lymphomas, or Histiocytic Disorders With Activating RET Gene Alterations, a Pediatric MATCH Treatment Trial
NCT04374305	PHASE2	RECRUITING	Innovative Trial for Understanding the Impact of Targeted Therapies in NF2-Related Schwannomatosis (INTUITT-NF2)
NCT04743661	PHASE2	ACTIVE_NOT_RECRUITING	131I-Omburtamab, in Recurrent Medulloblastoma and Ependymoma
NCT06804655	PHASE2	NOT_YET_RECRUITING	Pharmacoscopy for Patients With Refractory Primary Brain Tumors
NCT07424092	PHASE2	RECRUITING	Intratumoral DNX-2401 for High Grade Pediatric Brain Tumors
NCT00634231	PHASE1	COMPLETED	A Phase I Study of AdV-tk + Prodrug Therapy in Combination With Radiation Therapy for Pediatric Brain Tumors
NCT00994071	PHASE1	COMPLETED	A Phase I Study of ABT-888, an Oral Inhibitor of Poly(ADP-ribose) Polymerase and Temozolomide in Children With Recurrent/Refractory CNS Tumors
NCT01171469	PHASE1	COMPLETED	Vaccination With Dendritic Cells Loaded With Brain Tumor Stem Cells for Progressive Malignant Brain Tumor
NCT01331135	PHASE1	COMPLETED	Aflac ST0901 CHOANOME - Sirolimus in Solid Tumors
NCT01498783	PHASE1	COMPLETED	Phase I Study of 5-Fluorouracil in Children and Young Adults With Recurrent Ependymoma