DPF1

Summary

DPF1 (double PHD fingers 1, HGNC:20225) is a protein-coding gene on chromosome 19q13.2, encoding Zinc finger protein neuro-d4 (Q92782). May have an important role in developing neurons by participating in regulation of cell survival, possibly as a neurospecific transcription factor.

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in nervous system development. Predicted to be located in chromatin and nucleoplasm. Predicted to be part of nBAF complex.

Source: NCBI Gene 8193 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 32 total
• MANE Select transcript: NM_001135155

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20225
Approved symbol	DPF1
Name	double PHD fingers 1
Location	19q13.2
Locus type	gene with protein product
Status	Approved
Aliases	neuro-d4, NEUD4, BAF45b, SMARCG1
Ensembl gene	ENSG00000011332
Ensembl biotype	protein_coding
OMIM	601670
Entrez	8193

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 19 protein_coding, 6 retained_intron, 1 nonsense_mediated_decay

ENST00000355526, ENST00000412732, ENST00000414789, ENST00000416611, ENST00000418517, ENST00000420980, ENST00000438060, ENST00000438365, ENST00000456296, ENST00000471976, ENST00000472656, ENST00000473716, ENST00000475938, ENST00000488378, ENST00000494031, ENST00000586624, ENST00000614244, ENST00000686058, ENST00000689228, ENST00000880212, ENST00000880213, ENST00000915610, ENST00000915611, ENST00000915612, ENST00000915613, ENST00000915614

RefSeq mRNA: 5 — MANE Select: NM_001135155 NM_001135155, NM_001135156, NM_001289978, NM_001363579, NM_004647

CCDS: CCDS33008, CCDS46064, CCDS46065, CCDS86760, CCDS92608

Canonical transcript exons

ENST00000355526 — 12 exons

Exon	Start	End
ENSE00001895106	38211006	38212133
ENSE00003467731	38216140	38216259
ENSE00003476168	38212280	38212361
ENSE00003487361	38218573	38218662
ENSE00003543432	38216353	38216403
ENSE00003568506	38222548	38222708
ENSE00003573917	38217798	38217876
ENSE00003580348	38213644	38213756
ENSE00003599334	38218931	38219058
ENSE00003665262	38222357	38222464
ENSE00003670055	38217460	38217591
ENSE00003921719	38224114	38224222

Expression profiles

Bgee: expression breadth ubiquitous, 184 present calls, max score 97.18.

FANTOM5 (CAGE): breadth broad, TPM avg 2.9853 / max 158.1234, expressed in 692 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
180745	2.3801	571
180746	0.2174	102
180744	0.2156	91
180743	0.1722	78

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	97.18	gold quality
right frontal lobe	UBERON:0002810	92.22	gold quality
prefrontal cortex	UBERON:0000451	91.86	gold quality
cingulate cortex	UBERON:0003027	90.73	gold quality
nucleus accumbens	UBERON:0001882	90.62	gold quality
anterior cingulate cortex	UBERON:0009835	90.57	gold quality
frontal cortex	UBERON:0001870	90.51	gold quality
neocortex	UBERON:0001950	90.31	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	89.56	gold quality
Brodmann (1909) area 9	UBERON:0013540	89.50	gold quality
cerebral cortex	UBERON:0000956	89.06	gold quality
ganglionic eminence	UBERON:0004023	88.98	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	88.64	gold quality
vena cava	UBERON:0004087	88.60	gold quality
telencephalon	UBERON:0001893	88.40	gold quality
Brodmann (1909) area 46	UBERON:0006483	88.28	gold quality
amygdala	UBERON:0001876	88.04	gold quality
lateral nuclear group of thalamus	UBERON:0002736	87.75	gold quality
superior frontal gyrus	UBERON:0002661	87.34	gold quality
temporal lobe	UBERON:0001871	86.84	gold quality
putamen	UBERON:0001874	86.75	gold quality
caudate nucleus	UBERON:0001873	86.66	gold quality
forebrain	UBERON:0001890	86.54	gold quality
Ammon’s horn	UBERON:0001954	86.43	gold quality
CA1 field of hippocampus	UBERON:0003881	86.42	silver quality
parietal lobe	UBERON:0001872	86.40	gold quality
subthalamic nucleus	UBERON:0001906	86.29	silver quality
ventral tegmental area	UBERON:0002691	86.28	silver quality
postcentral gyrus	UBERON:0002581	86.04	gold quality
body of tongue	UBERON:0011876	86.00	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.70

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

68 targeting DPF1, 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-6127	100.00	66.76	2188
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-7845-5P	99.88	64.88	771
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-1321	99.84	65.30	1811
HSA-MIR-4739	99.84	65.25	1832
HSA-MIR-4756-5P	99.84	64.98	1809
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-374C-5P	99.80	72.06	2910
HSA-MIR-655-3P	99.80	72.19	2909
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-204-5P	99.79	71.62	2439
HSA-MIR-211-5P	99.79	71.65	2440
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-4755-5P	99.71	70.34	2716
HSA-MIR-5006-3P	99.71	70.26	2728
HSA-MIR-6883-5P	99.69	68.05	3785

Literature-anchored findings (GeneRIF, showing 1)

• BAF45b Is Required for Efficient Zika Virus Infection of HAP1 Cells. (PMID:34696437)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	dpf1	ENSDARG00000099927
mus_musculus	Dpf1	ENSMUSG00000030584
rattus_norvegicus	Dpf1	ENSRNOG00000020687
drosophila_melanogaster	tth	FBGN0030502
drosophila_melanogaster	d4	FBGN0033015
caenorhabditis_elegans		WBGENE00016200

Paralogs (9): RSF1 (ENSG00000048649), KAT6A (ENSG00000083168), KAT8 (ENSG00000103510), PHF10 (ENSG00000130024), DPF2 (ENSG00000133884), KAT7 (ENSG00000136504), KAT6B (ENSG00000156650), KAT5 (ENSG00000172977), DPF3 (ENSG00000205683)

Protein

Protein identifiers

Zinc finger protein neuro-d4 — Q92782 (reviewed: Q92782)

Alternative names: BRG1-associated factor 45B, D4, zinc and double PHD fingers family 1

All UniProt accessions (12): Q92782, A0A804CCM0, A0A804CYY4, A0A8I5KWI2, A0A8I5QL29, C8C3P2, C9IZH8, C9JGC1, E9PDV3, F8WEC4, J3KQY6, K7EJD5

UniProt curated annotations — full annotation on UniProt →

Function. May have an important role in developing neurons by participating in regulation of cell survival, possibly as a neurospecific transcription factor. Belongs to the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a postmitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to postmitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth.

Subunit / interactions. Component of neuron-specific chromatin remodeling complex (nBAF complex) composed of at least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, DPF1/BAF45B, DPF3/BAF45C, ACTL6B/BAF53B and actin.

Subcellular location. Cytoplasm. Nucleus.

Similarity. Belongs to the requiem/DPF family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q92782-2	2	yes
Q92782-1	1
Q92782-3	3

RefSeq proteins (5): NP_001128627, NP_001128628, NP_001276907, NP_001350508, NP_004638 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001965	Znf_PHD	Domain
IPR011011	Znf_FYVE_PHD	Homologous_superfamily
IPR013083	Znf_RING/FYVE/PHD	Homologous_superfamily
IPR013087	Znf_C2H2_type	Domain
IPR019787	Znf_PHD-finger	Domain
IPR025750	DPF1-3_N	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00628, PF14051

UniProt features (27 total): binding site 16, zinc finger region 3, cross-link 3, splice variant 3, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q92782-F1	67.41	0.29

Functional residue map

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

Ligand- & substrate-binding residues (16): 322; 325; 328; 331; 343; 346; 351; 354; 369; 372; 274; 277 …

Post-translational modifications (3): 106, 129, 133

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-9824585	Regulation of MITF-M-dependent genes involved in pigmentation
R-HSA-9845323	Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs)
R-HSA-9933937	Formation of the canonical BAF (cBAF) complex
R-HSA-9934037	Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF)

MSigDB gene sets: 165 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_DN, GOBP_REGULATION_OF_DOUBLE_STRAND_BREAK_REPAIR, TGGTGCT_MIR29A_MIR29B_MIR29C, GOBP_CHROMOSOME_ORGANIZATION, PEREZ_TP63_TARGETS, AAGCCAT_MIR135A_MIR135B, GOBP_CELL_CYCLE_PHASE_TRANSITION, ROVERSI_GLIOMA_COPY_NUMBER_UP, RIZKI_TUMOR_INVASIVENESS_3D_DN, GGGTGGRR_PAX4_03, GGAMTNNNNNTCCY_UNKNOWN, GOBP_REGULATION_OF_DNA_REPAIR, GOBP_NUCLEOTIDE_EXCISION_REPAIR, GOBP_REGULATION_OF_CHROMOSOME_SEGREGATION, KOYAMA_SEMA3B_TARGETS_UP

GO Biological Process (10): chromatin remodeling (GO:0006338), regulation of transcription by RNA polymerase II (GO:0006357), apoptotic process (GO:0006915), nervous system development (GO:0007399), regulation of mitotic metaphase/anaphase transition (GO:0030071), positive regulation of cell differentiation (GO:0045597), regulation of G0 to G1 transition (GO:0070316), regulation of G1/S transition of mitotic cell cycle (GO:2000045), positive regulation of double-strand break repair (GO:2000781), regulation of nucleotide-excision repair (GO:2000819)

GO Molecular Function (4): zinc ion binding (GO:0008270), sequence-specific double-stranded DNA binding (GO:1990837), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (5): chromatin (GO:0000785), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), nBAF complex (GO:0071565), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
SWI/SNF chromatin remodelers	2
MITF-M-dependent gene expression	1
Regulation of endogenous retroelements	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
regulation of mitotic cell cycle phase transition	2
chromatin organization	1
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
programmed cell death	1
apoptotic signaling pathway	1
execution phase of apoptosis	1
system development	1
metaphase/anaphase transition of mitotic cell cycle	1
regulation of metaphase/anaphase transition of cell cycle	1
cell differentiation	1
regulation of cell differentiation	1
positive regulation of cellular process	1
positive regulation of developmental process	1
regulation of cell cycle process	1
G0 to G1 transition	1
G1/S transition of mitotic cell cycle	1
regulation of cell cycle G1/S phase transition	1
double-strand break repair	1
positive regulation of DNA repair	1
regulation of double-strand break repair	1
regulation of DNA repair	1
nucleotide-excision repair	1
transition metal ion binding	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
binding	1
cation binding	1
chromosome	1
nuclear lumen	1
intracellular anatomical structure	1
SWI/SNF superfamily-type complex	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

516 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DPF1	ACTL6B	O94805	999
DPF1	ARID1A	O14497	983
DPF1	DPF3	Q92784	982
DPF1	DPF2	Q92785	963
DPF1	ACTL6A	O96019	960
DPF1	ARID1B	Q8NFD5	948
DPF1	BANF1	O75531	888
DPF1	PHF10	Q8WUB8	868
DPF1	BRD9	Q9H8M2	865
DPF1	SS18L1	O75177	859
DPF1	SMARCC1	Q92922	813
DPF1	SMARCE1	Q969G3	812
DPF1	SMARCD3	Q6STE5	805
DPF1	BRD7	Q9NPI1	800
DPF1	SMARCC2	Q8TAQ2	797

IntAct

91 interactions, top by confidence:

A	B	Type	Score
SMARCB1	ARID1A	psi-mi:“MI:0914”(association)	0.860
SMARCE1	ARID1A	psi-mi:“MI:0914”(association)	0.840
SMARCD1	ARID1A	psi-mi:“MI:0914”(association)	0.790
SMARCC2	ARID1A	psi-mi:“MI:0914”(association)	0.790
SS18	ARID1A	psi-mi:“MI:0914”(association)	0.760
SMARCE1	SMARCA2	psi-mi:“MI:0914”(association)	0.730
BCL7C	ARID1A	psi-mi:“MI:0914”(association)	0.640
BCL7A	ARID1A	psi-mi:“MI:0914”(association)	0.640
DPF1	SMARCA2	psi-mi:“MI:0914”(association)	0.530
DPF1	ARID1A	psi-mi:“MI:0914”(association)	0.530
FOS	MYO1C	psi-mi:“MI:2364”(proximity)	0.480
SS18L2	ARID1A	psi-mi:“MI:0914”(association)	0.480
CDC37	DPF1	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (140): DPF1 (Affinity Capture-MS), DPF1 (Affinity Capture-MS), DPF1 (Affinity Capture-MS), DPF1 (Affinity Capture-MS), DPF1 (Affinity Capture-MS), DPF1 (Affinity Capture-MS), DPF1 (Affinity Capture-MS), DPF1 (Affinity Capture-MS), DPF1 (Affinity Capture-MS), DPF1 (Proximity Label-MS), DPF1 (Affinity Capture-MS), PHF1 (Two-hybrid), DPF1 (Two-hybrid), DPF1 (Affinity Capture-MS), DPF1 (Affinity Capture-MS)

ESM2 similar proteins: A2WXR5, A2Y4R8, A7YY07, A9LMC0, B2KF05, B2RRD7, B8ADZ3, B8BJV8, G5E8P1, O81488, O95696, P55201, P56163, P58267, P58268, P58269, P58270, Q09477, Q0VDT2, Q12830, Q2R837, Q3U5C7, Q40359, Q567C6, Q5EA28, Q5U2Z0, Q5XEM9, Q60DW3, Q61103, Q6P1G2, Q6Z7F4, Q71QF9, Q7F2Z1, Q8BRB7, Q8NHM5, Q8S8M9, Q8UVR5, Q8WML3, Q92782, Q92784

Diamond homologs: A0A1W2PPD8, A1A5Q5, A1YVX4, A2A8L1, A2AUY4, A2BIL7, A6H619, A8DZJ1, A9LMC0, B2RXH2, B7ZS37, B9RU15, C0SUT9, D3ZD32, F4I240, F4I6G4, F4KIX0, O16102, O43918, O64752, O75164, O88379, O94953, O97159, P29375, P39956, P41228, P41229, P41230, P56163, P58268, P58269, P58270, Q03833, Q09477, Q10RP4, Q12873, Q14839, Q22516, Q23541

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 82 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
Formation of the canonical BAF (cBAF) complex	11	112.6×	2e-19
Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF)	12	88.4×	2e-19
Formation of the embryonic stem cell BAF (esBAF) complex	9	87.2×	1e-14
Formation of the non-canonical BAF (ncBAF) complex	8	86.7×	5e-13
Formation of the polybromo-BAF (pBAF) complex	8	81.9×	8e-13
Regulation of endogenous retroelements	11	65.4×	2e-16
Regulation of MITF-M-dependent genes involved in pigmentation	14	60.0×	1e-19
MITF-M-dependent gene expression	14	40.9×	1e-17

GO biological processes:

GO term	Partners	Fold	FDR
regulation of G0 to G1 transition	10	86.4×	1e-15
regulation of nucleotide-excision repair	10	77.2×	4e-15
regulation of mitotic metaphase/anaphase transition	10	63.5×	4e-14
nucleosome disassembly	6	61.7×	3e-08
positive regulation of T cell differentiation	9	52.5×	6e-12
neuron fate specification	5	45.0×	3e-06
positive regulation of double-strand break repair	10	44.1×	2e-12
positive regulation of myoblast differentiation	9	42.3×	4e-11

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	26
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1668 predictions. Top by Δscore:

Variant	Effect	Δscore
19:38213638:ACTC:A	donor_loss	1.0000
19:38213640:TCA:T	donor_loss	1.0000
19:38213641:CACGT:C	donor_loss	1.0000
19:38213642:A:AC	donor_gain	1.0000
19:38213642:A:AT	donor_loss	1.0000
19:38213642:ACGT:A	donor_gain	1.0000
19:38213643:C:CA	donor_gain	1.0000
19:38213643:CG:C	donor_gain	1.0000
19:38213643:CGT:C	donor_gain	1.0000
19:38213643:CGTC:C	donor_gain	1.0000
19:38213643:CGTCG:C	donor_gain	1.0000
19:38213757:C:CC	acceptor_gain	1.0000
19:38213765:C:CT	acceptor_gain	1.0000
19:38213765:C:T	acceptor_gain	1.0000
19:38213766:A:T	acceptor_gain	1.0000
19:38216138:ACC:A	donor_loss	1.0000
19:38216139:C:T	donor_loss	1.0000
19:38216255:CTTGG:C	acceptor_gain	1.0000
19:38216256:TTGG:T	acceptor_gain	1.0000
19:38216257:TGG:T	acceptor_gain	1.0000
19:38216258:GG:G	acceptor_gain	1.0000
19:38216260:C:CA	acceptor_loss	1.0000
19:38216260:C:CC	acceptor_gain	1.0000
19:38217454:GCTCA:G	donor_loss	1.0000
19:38217457:CACGT:C	donor_loss	1.0000
19:38217458:A:AC	donor_gain	1.0000
19:38217458:ACGT:A	donor_loss	1.0000
19:38217459:C:CA	donor_gain	1.0000
19:38217459:CG:C	donor_gain	1.0000
19:38217459:CGT:C	donor_gain	1.0000

AlphaMissense

2721 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:38212111:A:C	C365W	1.000
19:38212112:C:A	C365F	1.000
19:38212112:C:G	C365S	1.000
19:38212112:C:T	C365Y	1.000
19:38212113:A:G	C365R	1.000
19:38212113:A:T	C365S	1.000
19:38212120:A:C	C362W	1.000
19:38212121:C:A	C362F	1.000
19:38212121:C:G	C362S	1.000
19:38212121:C:T	C362Y	1.000
19:38212122:A:G	C362R	1.000
19:38212122:A:T	C362S	1.000
19:38212126:C:A	W360C	1.000
19:38212126:C:G	W360C	1.000
19:38212127:C:G	W360S	1.000
19:38212128:A:G	W360R	1.000
19:38212128:A:T	W360R	1.000
19:38212309:A:G	L348P	1.000
19:38212311:G:C	C347W	1.000
19:38212312:C:A	C347F	1.000
19:38212312:C:G	C347S	1.000
19:38212312:C:T	C347Y	1.000
19:38212313:A:G	C347R	1.000
19:38212313:A:T	C347S	1.000
19:38212320:G:C	H344Q	1.000
19:38212320:G:T	H344Q	1.000
19:38212322:G:C	H344D	1.000
19:38212322:G:T	H344N	1.000
19:38212325:A:C	Y343D	1.000
19:38212327:C:T	G342D	1.000

dbSNP variants (sampled 300 via entrez): RS1000060673 (19:38223813 C>T), RS1000127529 (19:38228478 G>A), RS1000158500 (19:38210532 C>T), RS1000431775 (19:38223490 C>G), RS1000515808 (19:38221642 T>C), RS1000548654 (19:38221374 C>G,T), RS1000757724 (19:38211952 C>T), RS1001092837 (19:38212057 G>A), RS1001099715 (19:38227440 C>T), RS1001171174 (19:38210629 G>T), RS1001308525 (19:38210910 G>A), RS1001338673 (19:38222131 A>ATAAATAAATAAATAAC,ATAAATAAC), RS1001467839 (19:38225102 C>T), RS1001890022 (19:38216260 C>T), RS1001901654 (19:38219442 C>T)

Disease associations

OMIM: gene MIM:601670 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): breast ductal adenocarcinoma (MONDO:0005590)

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST002337_167	Amyotrophic lateral sclerosis (sporadic)	4.000000e-06

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D018270	Carcinoma, Ductal, Breast	C04.557.470.200.025.232.500; C04.557.470.615.132.500; C04.588.180.390; C17.800.090.500.390

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

Binding affinities (BindingDB)

144 measured of 144 human assays (226 total across all organisms); most potent 50 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value	Patent
6-(Dimethylamino)-N-((2-methylquinolin-8-yl)sulfonyl)-4-(trifluoromethyl)benzofuran-2-carboxamide	IC50	1.47 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 107	IC50	2.29 nM	US-12357603: Acyl sulfonamides for treating cancer
N-((5-(tert-butyl)-2-methoxyphenyl)sulfonyl)-6-(dimethylamino)benzofuran-2-carboxamide	IC50	2.63 nM	US-12357603: Acyl sulfonamides for treating cancer
N-[(5-(tert-butyl)-2-cyclobutoxyphenyl)sulfonyl]-6-(dimethylamino)benzofuran-2-carboxamide	IC50	2.67 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 227	IC50	4 nM	US-12357603: Acyl sulfonamides for treating cancer
N-((5-(tert-butyl)-2-(cyclopropylmethoxy)phenyl)sulfonyl)-6-(dimethylamino)benzofuran-2-carboxamide	IC50	4.36 nM	US-12357603: Acyl sulfonamides for treating cancer
6-(Dimethylamino)-N-(2-ethoxy-5-sec-butyl-phenyl)sulfonyl-benzofuran-2-carboxamide (rac)	IC50	4.4 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 108	IC50	4.6 nM	US-12357603: Acyl sulfonamides for treating cancer
6-(Dimethylamino)-N-((2-ethoxyphenyl)sulfonyl)-4-(trifluoromethyl)benzofuran-2-carboxamide	IC50	5.73 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 109	IC50	7.09 nM	US-12357603: Acyl sulfonamides for treating cancer
N-([1,1’-biphenyl]-2-ylsulfonyl)-6-(dimethylamino)-4-(trifluoromethyl)benzofuran-2-carboxamide	IC50	7.14 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 113	IC50	7.25 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 110	IC50	7.48 nM	US-12357603: Acyl sulfonamides for treating cancer
N-[2-(cyclopropylmethoxy)-5-isopropyl-phenyl]sulfonyl-6-(dimethylamino)benzofuran-2-carboxamide	IC50	7.91 nM	US-12357603: Acyl sulfonamides for treating cancer
N-((2-((2,2-difluorocyclopropyl)methoxy)-5-isopropylphenyl)sulfonyl)-6-(dimethylamino)benzofuran-2-carboxamide (rac)	IC50	8.47 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 111	IC50	8.93 nM	US-12357603: Acyl sulfonamides for treating cancer
N-[(2-(Benzyloxy)-5-(tert-butyl)phenyl)sulfonyl]-6-(dimethylamino)benzofuran-2-carboxamide	IC50	8.95 nM	US-12357603: Acyl sulfonamides for treating cancer
6-(Dimethylamino)-N-[5-isopropyl-2-(2,2,2-trifluoroethoxy)phenyl]sulfonyl-benzofuran-2-carboxamide	IC50	11 nM	US-12357603: Acyl sulfonamides for treating cancer
6-(Dimethylamino)-N-(2-ethoxy-5-phenoxy-phenyl)sulfonyl-benzofuran-2-carboxamide	IC50	11.8 nM	US-12357603: Acyl sulfonamides for treating cancer
N-[(5-(tert-butyl)-2-(2,2,2-trifluoroethoxy)phenyl)sulfonyl]-6-(dimethylamino)benzofuran-2-carboxamide	IC50	11.8 nM	US-12357603: Acyl sulfonamides for treating cancer
N-(2-Benzyloxy-5-isopropyl-phenyl)sulfonyl-6-(dimethylamino)benzofuran-2-carboxamide	IC50	12.8 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 129	IC50	13.5 nM	US-12357603: Acyl sulfonamides for treating cancer
N-((5-(tert-butyl)-2-isopropoxyphenyl)sulfonyl)-6-(dimethylamino)benzofuran-2-carboxamide	IC50	15.4 nM	US-12357603: Acyl sulfonamides for treating cancer
N-((2-Cyclobutoxy-5-isopropylphenyl)sulfonyl)-6-(dimethylamino)benzofuran-2-carboxamide	IC50	15.9 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 112	IC50	17.7 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 126	IC50	20.5 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 225	IC50	22.7 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 143	IC50	29.3 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 222	IC50	30.6 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 134	IC50	30.7 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 84	IC50	40.6 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 221	IC50	44.4 nM	US-12357603: Acyl sulfonamides for treating cancer
6-(Dimethylamino)-N-(phenylsulfonyl)-4-(trifluoromethyl)benzofuran-2-carboxamide	IC50	44.9 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 83	IC50	48.8 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 118	IC50	52.4 nM	US-12357603: Acyl sulfonamides for treating cancer
6-(Dimethylamino)-N-[2-ethoxy-5-(trifluoromethyl)phenyl]sulfonyl-benzofuran-2-carboxamide	IC50	54 nM	US-12357603: Acyl sulfonamides for treating cancer
N-(5-Aminoquinoline-8-sulfonyl)-6-(dimethylamino)-1-benzofuran-2-carboxamide	IC50	56.4 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 138	IC50	56.7 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 135	IC50	57.9 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 224	IC50	58.3 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 115	IC50	64.6 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 86	IC50	64.9 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 127	IC50	71.2 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 91	IC50	74.2 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 137	IC50	81.5 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 124	IC50	92.8 nM	US-12357603: Acyl sulfonamides for treating cancer
6-(Dimethylamino)-N-(2-ethoxy-4-fluoro-phenyl)sulfonyl-benzofuran-2-carboxamide	IC50	94.9 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 87	IC50	97.3 nM	US-12357603: Acyl sulfonamides for treating cancer
6-(Dimethylamino)-N-(2-ethoxy-5-fluoro-phenyl)sulfonyl-benzofuran-2-carboxamide	IC50	97.3 nM	US-12357603: Acyl sulfonamides for treating cancer
US12357603, Example 147	IC50	98.6 nM	US-12357603: Acyl sulfonamides for treating cancer

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, increases methylation	3
Valproic Acid	affects expression, decreases expression, increases methylation	3
sodium arsenite	decreases expression, increases abundance, increases expression	2
aristolochic acid I	increases expression	1
bisphenol A	affects cotreatment, decreases methylation	1
trichostatin A	affects expression	1
beta-lapachone	decreases expression, increases expression	1
manganese chloride	decreases expression, increases abundance	1
benzo(e)pyrene	affects methylation	1
beta-glycerophosphoric acid	affects cotreatment, decreases expression	1
CGP 52608	affects binding, increases reaction	1
abrine	increases expression	1
mono-isobutyl phthalate	decreases methylation, increases abundance	1
Temozolomide	decreases expression	1
Sunitinib	decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Arsenic	decreases expression, increases abundance	1
Ascorbic Acid	affects cotreatment, decreases expression	1
Calcitriol	decreases expression, affects cotreatment	1
Dexamethasone	affects cotreatment, decreases expression	1
Manganese	decreases expression, increases abundance	1
Methapyrilene	affects methylation	1
Oxygen	decreases expression	1
Phthalic Acids	decreases methylation, increases abundance	1
Plant Extracts	decreases expression	1
Smoke	decreases expression	1
Testosterone	affects cotreatment, decreases expression	1
Tunicamycin	decreases expression	1
Urethane	increases expression	1
Thapsigargin	decreases expression	1

Cellosaurus cell lines

5 cell lines: 3 embryonic stem cell, 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_A1A9	SEES3-1V human DPF1, clone1	Embryonic stem cell	Male
CVCL_A1B0	SEES3-1V human DPF1, clone2	Embryonic stem cell	Male
CVCL_A1B1	SEES3-1V human DPF1, clone3	Embryonic stem cell	Male
CVCL_SL09	HAP1 DPF1 (-) 1	Cancer cell line	Male
CVCL_SL10	HAP1 DPF1 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT03414970	PHASE3	ACTIVE_NOT_RECRUITING	Hypofractionated Radiation Therapy After Mastectomy in Preventing Recurrence in Patients With Stage IIa-IIIa Breast Cancer
NCT00461344	PHASE2	TERMINATED	Docetaxel + Doxorubicin as Neoadjuvant Chemotherapy in Patients With Breast Cancer
NCT07499999	PHASE2	NOT_YET_RECRUITING	Randomized Double-Blind Phase II Trial of Baby Exemestane Versus Baby Tamoxifen in Post-Menopausal Women at High Risk for Breast Cancer
NCT00637364	PHASE1/PHASE2	SUSPENDED	High Intensity Focused Ultrasound Tumor Treatment for Pancreatic Cancer Pain
NCT02779855	PHASE1/PHASE2	COMPLETED	Talimogene Laherparepvec in Combination With Neoadjuvant Chemotherapy in Triple Negative Breast Cancer
NCT01753908	EARLY_PHASE1	COMPLETED	Broccoli Sprout Extract in Treating Patients With Breast Cancer
NCT01796041	EARLY_PHASE1	COMPLETED	Intraoperative Imaging of Breast Cancer With Indocyanine Green
NCT01208974	Not specified	ACTIVE_NOT_RECRUITING	Nipple-Areola Complex (NAC) Irradiation After Nipple-Sparing Mastectomy and Reconstruction
NCT01875198	Not specified	TERMINATED	Oncologic Impact of Splenectomy-omitting Radical Pancreatectomy in Well-selected Left-sided Pancreatic Cancer
NCT03543397	Not specified	UNKNOWN	MRI in Ductal Carcinoma in Situ (DCIS)
NCT03834532	Not specified	COMPLETED	Living Well After Breast Surgery