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 and regulation of DNA-templated transcription. Predicted to be located in chromatin and nucleoplasm. Predicted to be part of nBAF complex.

Source: NCBI Gene 8193 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 35 total
• GTEx eGene: eQTL in 11 tissues, sQTL in 15 (q < 0.05)
• Constraint (gnomAD): pLI 1.00 (loss-of-function intolerant), LOEUF 0.41 (moderately constrained)
• 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: 30 — 20 protein_coding, 6 retained_intron, 4 nonsense_mediated_decay

MANE Select: ENST00000355526

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 5, TSL 2: 6, TSL 3: 1, TSL 5: 5

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, ENST00001080873, ENST00001080874, ENST00001125133, ENST00001125134

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.

Highest expression (Bgee): cortical plate, frontal lobe, prefrontal cortex, cingulate cortex, nucleus accumbens.

Genetic regulation across tissues (GTEx eQTL / sQTL)

DPF1 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 11 tissues and its splicing (sQTL) in 15 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 26 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Brain Frontal Cortex BA9	sqtl	2.0e-23	+1.17	19:38218928:C:T
Brain Cortex	sqtl	3.7e-22	+1.08	19:38218928:C:T
Skin Sun Exposed Lower leg	eqtl	6.5e-16	+0.51	19:38200641:T:C
Brain Anterior cingulate cortex BA24	sqtl	9.6e-15	+1.03	19:38218928:C:T
Brain Nucleus accumbens basal ganglia	sqtl	7.6e-14	+0.89	19:38218928:C:T
Brain Caudate basal ganglia	sqtl	2.5e-12	+0.86	19:38218928:C:T
Skin Not Sun Exposed Suprapubic	eqtl	4.5e-12	+0.41	19:38143688:G:A
Brain Cerebellum	sqtl	1.4e-09	+0.83	19:38218928:C:T
Brain Hypothalamus	sqtl	2.7e-09	-0.79	19:38218928:C:T
Brain Cerebellar Hemisphere	sqtl	1.2e-08	-0.75	19:38218928:C:T
Testis	sqtl	8.5e-07	-0.57	19:38215288:T:C
Brain Putamen basal ganglia	sqtl	3.4e-06	-0.71	19:38218928:C:T
Brain Hippocampus	sqtl	1.9e-05	-0.77	19:38218928:C:T
Brain Amygdala	sqtl	2.2e-05	+0.92	19:38218928:C:T
Cells Cultured fibroblasts	sqtl	5.7e-04	+0.35	19:38218330:T:C
Esophagus Muscularis	eqtl	6.2e-04	-0.27	19:38247490:G:C
Brain Amygdala	eqtl	3.4e-03	-2.69	19:39102118:T:TCACACACA
Brain Substantia nigra	sqtl	5.0e-03	-0.73	19:38217758:A:C
Cells Cultured fibroblasts	eqtl	1.0e-02	+0.17	19:38877161:C:T
Esophagus Mucosa	eqtl	1.4e-02	-0.78	19:37394807:C:T

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

showing 100 of 274 tissues 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
type B pancreatic cell	CL:0000169	85.83	gold quality
brain	UBERON:0000955	85.77	gold quality
globus pallidus	UBERON:0001875	85.62	silver quality
medial globus pallidus	UBERON:0002477	85.57	silver quality
central nervous system	UBERON:0001017	85.42	gold quality
dorsal plus ventral thalamus	UBERON:0001897	85.40	silver quality
lateral globus pallidus	UBERON:0002476	85.18	silver quality
cerebellar vermis	UBERON:0004720	85.17	silver quality
entorhinal cortex	UBERON:0002728	84.99	gold quality
right hemisphere of cerebellum	UBERON:0014890	84.97	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.79	gold quality
substantia nigra pars compacta	UBERON:0001965	84.71	silver quality
substantia nigra pars reticulata	UBERON:0001966	84.52	silver quality
pericardium	UBERON:0002407	84.51	silver quality
occipital lobe	UBERON:0002021	84.50	gold quality
inferior vagus X ganglion	UBERON:0005363	84.49	silver quality
cerebellar hemisphere	UBERON:0002245	84.44	gold quality
olfactory bulb	UBERON:0002264	84.44	gold quality
cerebellar cortex	UBERON:0002129	84.32	gold quality
pylorus	UBERON:0001166	84.06	gold quality
primary visual cortex	UBERON:0002436	83.68	gold quality
superior vestibular nucleus	UBERON:0007227	83.56	silver quality
pons	UBERON:0000988	83.54	silver quality
cerebellum	UBERON:0002037	83.54	gold quality
pharyngeal mucosa	UBERON:0000355	83.49	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	83.30	gold quality
ventricular zone	UBERON:0003053	82.89	gold quality
saphenous vein	UBERON:0007318	82.89	silver quality
medulla oblongata	UBERON:0001896	82.88	silver quality
Brodmann (1909) area 10	UBERON:0013541	82.83	gold quality
orbitofrontal cortex	UBERON:0004167	82.69	gold quality
oocyte	CL:0000023	82.41	gold quality
endothelial cell	CL:0000115	82.41	silver quality
hypothalamus	UBERON:0001898	81.88	gold quality
nipple	UBERON:0002030	81.76	gold quality
male germ cell	CL:0000015	81.60	gold quality
biceps brachii	UBERON:0001507	81.57	gold quality
buccal mucosa cell	CL:0002336	81.17	gold quality
sperm	CL:0000019	81.16	gold quality
renal medulla	UBERON:0000362	81.01	gold quality
midbrain	UBERON:0001891	80.25	gold quality
Brodmann (1909) area 23	UBERON:0013554	79.80	silver quality
substantia nigra	UBERON:0002038	79.63	gold quality
synovial joint	UBERON:0002217	79.46	gold quality
cervix squamous epithelium	UBERON:0006922	79.12	gold quality
frontal pole	UBERON:0002795	79.06	silver quality
myocardium	UBERON:0002349	78.42	gold quality
embryo	UBERON:0000922	78.25	gold quality
middle temporal gyrus	UBERON:0002771	78.08	silver quality
triceps brachii	UBERON:0001509	77.98	gold quality
paraflocculus	UBERON:0005351	77.72	gold quality
gluteal muscle	UBERON:0002000	77.71	gold quality
trabecular bone tissue	UBERON:0002483	77.50	gold quality
middle frontal gyrus	UBERON:0002702	77.47	gold quality
tongue squamous epithelium	UBERON:0006919	77.23	gold quality
penis	UBERON:0000989	77.03	gold quality
secondary oocyte	CL:0000655	75.97	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	75.56	silver quality
squamous epithelium	UBERON:0006914	75.54	gold quality
urethra	UBERON:0000057	75.45	gold quality
mammalian vulva	UBERON:0000997	75.38	gold quality
mucosa of sigmoid colon	UBERON:0004993	75.23	gold quality
parotid gland	UBERON:0001831	75.10	gold quality
gingival epithelium	UBERON:0001949	74.93	gold quality
thymus	UBERON:0002370	74.80	gold quality
spinal cord	UBERON:0002240	74.73	gold quality
colonic mucosa	UBERON:0000317	74.50	silver quality
epithelial cell of pancreas	CL:0000083	74.36	gold quality
gingiva	UBERON:0001828	74.33	gold quality
jejunum	UBERON:0002115	74.32	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

HPA expression

RNA tissue specificity: Tissue enriched

57 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Olfactory bulb	tissue	60.8
Caudate putamen	tissue	54.3
Frontal cortex	tissue	53.3
Postcentral gyrus	tissue	42.1
Prefrontal cortex	tissue	40.9
Cerebral cortex	tissue	40.9	medium
Motor cortex	tissue	37.0
Temporal cortex	tissue	37.0
Insular cortex	tissue	33.9
Retrosplenial and cingulate cortex	tissue	33.4
Hippocampal formation	tissue	33.1
Entorhinal cortex	tissue	32.3
Hippocampus	tissue	30.4	medium
Retrosplenial cortex	tissue	30.4
Amygdala	tissue	29.4
Somatosensory cortex	tissue	29.4
Septum	tissue	29.0
Nucleus accumbens	tissue	28.5
Occipital cortex	tissue	26.5
Basal ganglia	tissue	26.0	medium
Ventral forebrain	tissue	26.0
Hypothalamus	tissue	16.4
Midbrain	tissue	13.8
Thalamus	tissue	13.7
Putamen	tissue	13.5
Locus coeruleus	tissue	13.0
Pons	tissue	12.3
Periaqueductal gray	tissue	11.5
Superior colliculi	tissue	10.8
Corpus callosum	tissue	9.1
Substantia nigra	tissue	8.3
Medulla oblongata	tissue	8.0
Cerebellum	tissue	7.8	medium
Spinal cord	tissue	6.5
Pituitary gland	tissue	2.3
Retina	tissue	2.3
Choroid plexus	tissue	1.5
Testis	tissue	0.8	medium
Adrenal gland	tissue	0.4	not detected
Appendix	tissue	0.4	not detected
Skin 1	tissue	0.2	not detected
Salivary gland	tissue	0.2	not detected
Smooth muscle	tissue	0.2	not detected
Thymus	tissue	0.2
Lymph node	tissue	0.1	not detected
Heart muscle	tissue	0.1	not detected
Ovary	tissue	0.1	not detected
Vagina	tissue	0.1	not detected
Adipose tissue	tissue	0.1	not detected
Skeletal muscle	tissue	0.1	not detected
Colon	tissue	0.1	not detected
Endometrium 1	tissue	0.1	not detected
Placenta	tissue	0.1	low
Spleen	tissue	0.1	not detected
Small intestine	tissue	0.1	not detected
Bone marrow	tissue	0.1	not detected
Tonsil	tissue	0.1	not detected

Brain sub-regions (HPA Brain Atlas): detected in 189; highest nTPM — Precentral gyrus (49.9), Posterior cingulate cortex (43.5), Hippocampus, CA3 (42.7), Anterior cingulate cortex, supragenual-dorsal (42.6), Inferior frontal gyrus, opercular (42.6).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting DPF1 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 68 miRNAs:

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

Functional genomics

gnomAD constraint: pLI 1, LOEUF 0.415, missense Z 2.65 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000355526 — one region, missense o/e 0.65.

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)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:1352748) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 3 distinct phenotype terms.

Mouse phenotype (MP)	Records
hyperactivity	1
increased lean body mass	1
decreased grip strength	1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Pan troglodytes	Q5XUN4	98.8%	Diamond
Canis lupus familiaris	Q38JA7	97.6%	Diamond
Sus scrofa	A1YVX4	95.2%	Diamond
Gallus gallus	P58268	93.3%	Diamond
Bos taurus	Q2T9V9	92.9%	Diamond
Xenopus laevis	Q9W636	89.9%	Diamond
Arabidopsis thaliana	Q710E8	87.9%	Diamond
Xenopus tropicalis	F6UA42	87.2%	Diamond
Macaca fascicularis	Q8WML3	83.4%	Diamond
Ricinus communis	B9RU15	69.6%	Diamond
Oryza sativa Japonica Group	Q5SMU7	64.0%	Diamond
Schizosaccharomyces pombe 972h-	Q9HDV4	55.6%	Diamond
Saccharomyces cerevisiae S288C	P47156	53.3%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
SNORD152	snoRNA	109623473
SIPA1L3	protein-coding	23094
PPP1R14A	protein-coding	94274
C19orf33	protein-coding	64073
YIF1B	protein-coding	90522
KCNK6	protein-coding	9424
WDR87	protein-coding	83889
SPINT2	protein-coding	10653

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	Zf-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

Predicted structure (AlphaFold)

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

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): cytosol; nucleoplasm; mitochondria

Antibody reliability (HPA): IH enhanced · IF approved

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)

Position	Role
322	Zn(2+)
325	Zn(2+)
328	Zn(2+)
331	Zn(2+)
343	Zn(2+)
346	Zn(2+)
351	Zn(2+)
354	Zn(2+)
369	Zn(2+)
372	Zn(2+)
274	Zn(2+)
277	Zn(2+)
293	Zn(2+)
296	Zn(2+)
301	Zn(2+)
304	Zn(2+)

Post-translational modifications (3)

Type	Positions
Glycyl lysine isopeptide (lys-gly) (interchain with g-cter in sumo2)	106, 129, 133

Function

Pathways and Gene Ontology

Reactome pathways

1 curated (TAS) of 14; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

14 pathways:

ID	Pathway	Evidence
R-HSA-9933937	Formation of the canonical BAF (cBAF) complex	curated
R-HSA-9932444	ATP-dependent chromatin remodelers	—
R-HSA-4839726	Chromatin organization	—
R-HSA-1266738	Developmental Biology	—
R-HSA-212165	Epigenetic regulation of gene expression	—
R-HSA-9934037	Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF)	electronic
R-HSA-74160	Gene expression (Transcription)	—
R-HSA-9856651	MITF-M-dependent gene expression	—
R-HSA-9730414	MITF-M-regulated melanocyte development	—
R-HSA-9824585	Regulation of MITF-M-dependent genes involved in pigmentation	electronic
R-HSA-9842860	Regulation of endogenous retroelements	—
R-HSA-9845323	Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs)	electronic
R-HSA-9932451	SWI/SNF chromatin remodelers	—
R-HSA-9938024	Somatic hypermutation of immunoglobulin genes	electronic

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 (12): chromatin remodeling (GO:0006338), DNA-templated transcription (GO:0006351), regulation of DNA-templated transcription (GO:0006355), 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 (5): transcription coregulator activity (GO:0003712), 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

10 top-level categories:

Category	Pathways
SWI/SNF chromatin remodelers	2
MITF-M-dependent gene expression	1
Regulation of endogenous retroelements	1
Affinity selection of immunoglobulins	1
Gene expression (Transcription)	1
Developmental Biology	1
Epigenetic regulation of gene expression	1
MITF-M-regulated melanocyte development	1
Chromatin organization	1
ATP-dependent chromatin remodelers	1

GO top-level categories

41 GO namespaces:

Category	Terms
cellular anatomical structure	3
regulation of mitotic cell cycle phase transition	2
chromatin organization	1
gene expression	1
RNA biosynthetic process	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	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
animal gross anatomical part developmental process	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
transcription regulator activity	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

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 1 of 22 annotations. The rest are phylogenetic / computational / electronic (IEA).

1 experimentally-supported GO terms:

GO term	NS	Evidence
sequence-specific double-stranded DNA binding	MF	direct assay

Protein interactions and networks

STRING

showing 15 of 690 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DPF1	ACTL6B	O94805	942
DPF1	ACTL6A	O96019	918
DPF1	BANF1	O75531	890
DPF1	SMARCC1	Q92922	690
DPF1	BRD7	Q9NPI1	675
DPF1	SMARCC2	Q8TAQ2	665
DPF1	PBRM1	Q86U86	664
DPF1	BRD9	Q9H8M2	657
DPF1	ARID1A	O14497	645
DPF1	ARID2	Q68CP9	641
DPF1	SMARCD1	Q96GM5	637
DPF1	SS18L1	O75177	628
DPF1	DPF3	Q92784	627
DPF1	SMARCE1	Q969G3	619
DPF1	SMARCA4	P51532	598

IntAct

Human interaction partners of DPF1 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

7 partners by confidence:

Partner	Interaction type	MIscore	Records
ARID1A	association	0.530	1
SMARCA2	association	0.530	1
CDC37	physical association	0.400	1
PTGER4	physical association	0.370	1
NFKB1	association	0.350	1
DISC1	physical association	0.000	1
RPN1	physical association	0.000	1

BioGRID (140 interactions; top human partners by supporting records): SMARCA4 (Affinity Capture-MS; 6 records), SMARCE1 (Affinity Capture-MS; 6 records), SMARCA2 (Affinity Capture-MS; 4 records), SMARCB1 (Affinity Capture-MS; 4 records), SMARCD1 (Affinity Capture-MS; 4 records), SS18 (Affinity Capture-MS; 4 records), ARID1A (Affinity Capture-MS; 3 records), ARID1B (Affinity Capture-MS; 3 records), BCL7A (Affinity Capture-MS; 3 records), BCL7C (Affinity Capture-MS; 3 records), SMARCC1 (Affinity Capture-MS; 3 records), SMARCC2 (Affinity Capture-MS; 3 records), ACTL6A (Affinity Capture-MS; 2 records), AR (Proximity Label-MS; 2 records), ARID2 (Affinity Capture-MS; 2 records)

Disease & clinical

Genetic variants

Variant evidence for DPF1: 35 ClinVar records (0 pathogenic / likely pathogenic); 1 GWAS association.

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	29
Likely benign	2
Benign	0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 34 predictions of 976):

Position(s)	Effect	Δscore	Sites
19:38213642	donor_loss	1.0000
19:38213765	acceptor_gain	1.0000
19:38216138–38216139	donor_loss	1.0000	5
19:38216260–38216261	acceptor_loss	1.0000	4
19:38217458–38217459	donor_loss	1.0000	4
19:38217877–38217878	acceptor_loss	1.0000	5
19:38218576	donor_gain	1.0000
19:38218663–38218664	acceptor_loss	1.0000	6
19:38218669–38218670	acceptor_gain	1.0000	2
19:38218929–38218930	donor_loss	1.0000	5

AlphaMissense

1,319 missense substitutions predicted likely pathogenic (of 2,721 scored), across 265 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
M294	9	0.989	0.999
M83	9	0.961	0.998
M345	9	0.889	0.995
D337	8	1.000	1.000
D340	8	1.000	1.000
D69	8	0.999	1.000
H284	8	0.999	1.000
D338	8	0.999	1.000
H344	8	0.999	1.000
D258	8	0.998	1.000
F290	8	0.998	1.000
F335	8	0.997	1.000
D278	8	0.996	0.999
F259	8	0.994	1.000
N54	8	0.990	1.000
F67	8	0.987	1.000
S361	8	0.987	0.998
N78	8	0.918	0.998
S359	8	0.873	0.983
H49	8	0.834	0.996

HPA cancer prognostics

RNA cancer specificity: Group enriched (Glioblastoma Multiforme, Testicular Germ Cell Tumor)

Disease associations

OMIM: gene MIM:601670 | disease phenotypes:

GWAS associations

1 associations:

Study	Trait	p-value
GCST002337_142	Amyotrophic lateral sclerosis (sporadic)	4e-6

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

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	increases expression, decreases expression, increases abundance	2
aristolochic acid I	increases expression	1
bisphenol A	affects cotreatment, decreases methylation	1
trichostatin A	affects expression	1
beta-lapachone	increases expression, decreases expression	1
manganese chloride	increases abundance, decreases expression	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	increases abundance, decreases expression	1
Ascorbic Acid	affects cotreatment, decreases expression	1
Calcitriol	decreases expression, affects cotreatment	1
Dexamethasone	decreases expression, affects cotreatment	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)

Via MONDO — disease-level, not drug-specific.

12 trials:

NCT	Phase	Status	Title
NCT03414970	Phase 3	ACTIVE_NOT_RECRUITING	Hypofractionated Radiation Therapy After Mastectomy in Preventing Recurrence in Patients With Stage IIa-IIIa Breast Cancer
NCT00461344	Phase 2	TERMINATED	Docetaxel + Doxorubicin as Neoadjuvant Chemotherapy in Patients With Breast Cancer
NCT07499999	Phase 2	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	Phase 1/2	SUSPENDED	High Intensity Focused Ultrasound Tumor Treatment for Pancreatic Cancer Pain
NCT02779855	Phase 1/2	COMPLETED	Talimogene Laherparepvec in Combination With Neoadjuvant Chemotherapy in Triple Negative Breast Cancer
NCT01753908	Early Phase 1	COMPLETED	Broccoli Sprout Extract in Treating Patients With Breast Cancer
NCT01796041	Early Phase 1	COMPLETED	Intraoperative Imaging of Breast Cancer With Indocyanine Green
NCT07628634	Early Phase 1	RECRUITING	Feasibility Study on the Effect of a Methionine-Reduced Diet on Serum Levels in Pts w/ Solid Tumors
NCT01208974	Not specified	COMPLETED	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