DPF2

Summary

DPF2 (double PHD fingers 2, HGNC:9964) is a protein-coding gene on chromosome 11q13.1, encoding Zinc finger protein ubi-d4 (Q92785). Plays an active role in transcriptional regulation by binding modified histones H3 and H4. It is a selective cancer dependency (DepMap: 34.1% of cell lines).

The protein encoded by this gene is a member of the d4 domain family, characterized by a zinc finger-like structural motif. This protein functions as a transcription factor which is necessary for the apoptotic response following deprivation of survival factors. It likely serves a regulatory role in rapid hematopoietic cell growth and turnover. This gene is considered a candidate gene for multiple endocrine neoplasia type I, an inherited cancer syndrome involving multiple parathyroid, enteropancreatic, and pituitary tumors.

Source: NCBI Gene 5977 — RefSeq curated summary.

At a glance

• Gene–disease (curated): Coffin-Siris syndrome (Definitive, ClinGen) — +1 more curated relationship
• GWAS associations: 3
• Clinical variants (ClinVar): 292 total — 7 pathogenic, 11 likely-pathogenic
• Regional missense constraint (gnomAD): 2 of 4 regions constrained (≈29% of expected missense variation)
• GTEx eGene: eQTL in 36 tissues, sQTL in 3 (q < 0.05)
• Phenotypes (HPO): 103
• Cancer dependency (DepMap): dependent in 34.1% of screened cell lines
• Constraint (gnomAD): pLI 1.00 (loss-of-function intolerant), LOEUF 0.29 (highly constrained)
• MANE Select transcript: NM_006268

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9964
Approved symbol	DPF2
Name	double PHD fingers 2
Location	11q13.1
Locus type	gene with protein product
Status	Approved
Aliases	ubi-d4, BAF45d, SMARCG2
Ensembl gene	ENSG00000133884
Ensembl biotype	protein_coding
OMIM	601671
Entrez	5977

Gene structure

Transcript identifiers

Ensembl transcripts: 33 — 15 protein_coding, 11 nonsense_mediated_decay, 6 retained_intron, 1 protein_coding_CDS_not_defined

MANE Select: ENST00000528416

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 6, TSL 3: 1, TSL 4: 1, TSL 5: 3

ENST00000528416, ENST00000252268, ENST00000415073, ENST00000444314, ENST00000524666, ENST00000530973, ENST00000530993, ENST00000531989, ENST00000532052, ENST00000532102, ENST00000532264, ENST00000532492, ENST00000703393, ENST00000703394, ENST00000703424, ENST00000703425, ENST00000703426, ENST00000703427, ENST00000938273, ENST00000979027, ENST00000979028, ENST00001049043, ENST00001049045, ENST00001084904, ENST00001084905, ENST00001084906, ENST00001084907, ENST00001084908, ENST00001084909, ENST00001084910, ENST00001115935, ENST00001117963, ENST00001142526

RefSeq mRNA: 2 — MANE Select: NM_006268 NM_001330308, NM_006268

CCDS: CCDS8100, CCDS81583

Canonical transcript exons

ENST00000528416 — 11 exons

Exon	Start	End
ENSE00003498334	65345666	65345803
ENSE00003502485	65340966	65341073
ENSE00003503966	65345930	65346058
ENSE00003526071	65340385	65340545
ENSE00003541428	65343745	65343837
ENSE00003653840	65341399	65341562
ENSE00003663834	65343991	65344069
ENSE00003988870	65346247	65346359
ENSE00003988872	65333852	65333918
ENSE00003988873	65348850	65348931
ENSE00003988876	65351683	65354262

Expression profiles

Bgee: expression breadth ubiquitous, 290 present calls, max score 98.69.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 38.1314 / max 234.2335, expressed in 1813 samples.

Highest expression (Bgee): oocyte, secondary oocyte, calcaneal tendon, ventricular zone, body of uterus.

Genetic regulation across tissues (GTEx eQTL / sQTL)

DPF2 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 36 tissues and its splicing (sQTL) in 3 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 39 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Testis	eqtl	1.6e-21	+0.25	11:65341762:A:C
Nerve Tibial	eqtl	6.2e-21	+0.26	11:65336906:T:A
Cells Cultured fibroblasts	eqtl	1.5e-18	+0.24	11:65341762:A:C
Skin Sun Exposed Lower leg	eqtl	7.8e-13	+0.23	11:65336906:T:A
Artery Tibial	eqtl	1.3e-10	+0.15	11:65336906:T:A
Esophagus Mucosa	eqtl	2.4e-09	+0.21	11:65336906:T:A
Pancreas	eqtl	2.7e-08	+0.26	11:65336906:T:A
Artery Aorta	eqtl	9.5e-08	+0.15	11:65336906:T:A
Adipose Visceral Omentum	eqtl	1.1e-07	+0.18	11:65336906:T:A
Adipose Subcutaneous	eqtl	3.2e-07	+0.16	11:65336906:T:A
Colon Transverse	eqtl	5.0e-07	+0.12	11:65336906:T:A
Thyroid	eqtl	1.4e-06	+0.15	11:65336906:T:A
Brain Nucleus accumbens basal ganglia	eqtl	3.0e-06	+0.28	11:65336906:T:A
Heart Left Ventricle	eqtl	3.1e-06	+0.18	11:65336906:T:A
Skin Not Sun Exposed Suprapubic	eqtl	4.0e-06	+0.16	11:65336906:T:A
Esophagus Muscularis	eqtl	4.5e-06	+0.11	11:65336906:T:A
Brain Amygdala	eqtl	5.9e-06	-0.41	11:65370683:G:C
Muscle Skeletal	eqtl	1.0e-05	+0.10	11:65336906:T:A
Brain Spinal cord cervical c-1	eqtl	1.5e-05	+0.26	11:65336906:T:A
Heart Atrial Appendage	eqtl	1.6e-05	+0.16	11:65336906:T:A

FANTOM5 promoters

1 alternative TSS:

Promoter ID	TPM avg	Samples expressed
115068	38.1314	1813

Top tissues by expression

showing 100 of 300 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	98.69	gold quality
secondary oocyte	CL:0000655	98.40	gold quality
calcaneal tendon	UBERON:0003701	96.48	gold quality
ventricular zone	UBERON:0003053	95.64	gold quality
body of uterus	UBERON:0009853	95.12	gold quality
right ovary	UBERON:0002118	94.98	gold quality
lower esophagus muscularis layer	UBERON:0035833	94.88	gold quality
lower esophagus	UBERON:0013473	94.86	gold quality
left ovary	UBERON:0002119	94.78	gold quality
endometrium epithelium	UBERON:0004811	94.78	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	94.65	gold quality
ganglionic eminence	UBERON:0004023	94.48	gold quality
endocervix	UBERON:0000458	94.14	gold quality
muscle layer of sigmoid colon	UBERON:0035805	94.11	gold quality
left uterine tube	UBERON:0001303	93.94	gold quality
smooth muscle tissue	UBERON:0001135	93.90	gold quality
right uterine tube	UBERON:0001302	93.78	gold quality
popliteal artery	UBERON:0002250	93.78	gold quality
mucosa of stomach	UBERON:0001199	93.77	gold quality
tibial artery	UBERON:0007610	93.77	gold quality
granulocyte	CL:0000094	93.69	gold quality
apex of heart	UBERON:0002098	93.64	gold quality
right coronary artery	UBERON:0001625	93.60	gold quality
descending thoracic aorta	UBERON:0002345	93.53	gold quality
stromal cell of endometrium	CL:0002255	93.39	gold quality
aorta	UBERON:0000947	93.32	gold quality
Brodmann (1909) area 10	UBERON:0013541	93.18	gold quality
right testis	UBERON:0004534	93.12	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	93.11	gold quality
right hemisphere of cerebellum	UBERON:0014890	93.08	gold quality
left testis	UBERON:0004533	93.02	gold quality
cerebellar hemisphere	UBERON:0002245	92.99	gold quality
ovary	UBERON:0000992	92.95	gold quality
cerebellar cortex	UBERON:0002129	92.90	gold quality
ectocervix	UBERON:0012249	92.90	gold quality
right lobe of thyroid gland	UBERON:0001119	92.89	gold quality
blood	UBERON:0000178	92.87	gold quality
embryo	UBERON:0000922	92.84	gold quality
islet of Langerhans	UBERON:0000006	92.81	gold quality
thoracic aorta	UBERON:0001515	92.79	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	92.73	gold quality
ascending aorta	UBERON:0001496	92.69	gold quality
tibial nerve	UBERON:0001323	92.68	gold quality
spinal cord	UBERON:0002240	92.52	gold quality
esophagus	UBERON:0001043	92.51	gold quality
left coronary artery	UBERON:0001626	92.51	gold quality
paraflocculus	UBERON:0005351	92.42	gold quality
coronary artery	UBERON:0001621	92.37	gold quality
cerebellum	UBERON:0002037	92.31	gold quality
monocyte	CL:0000576	92.29	gold quality
lymph node	UBERON:0000029	92.16	gold quality
leukocyte	CL:0000738	92.15	gold quality
testis	UBERON:0000473	92.12	gold quality
left lobe of thyroid gland	UBERON:0001120	92.10	gold quality
adult organism	UBERON:0007023	92.10	gold quality
middle frontal gyrus	UBERON:0002702	92.05	gold quality
right atrium auricular region	UBERON:0006631	91.99	gold quality
myometrium	UBERON:0001296	91.96	gold quality
mononuclear cell	CL:0000842	91.93	gold quality
spleen	UBERON:0002106	91.88	gold quality
heart left ventricle	UBERON:0002084	91.86	gold quality
lower esophagus mucosa	UBERON:0035834	91.82	gold quality
cartilage tissue	UBERON:0002418	91.78	gold quality
small intestine Peyer’s patch	UBERON:0003454	91.75	gold quality
thyroid gland	UBERON:0002046	91.72	gold quality
cardiac ventricle	UBERON:0002082	91.72	gold quality
cardiac atrium	UBERON:0002081	91.63	gold quality
right adrenal gland	UBERON:0001233	91.61	gold quality
right adrenal gland cortex	UBERON:0035827	91.59	gold quality
minor salivary gland	UBERON:0001830	91.48	gold quality
gastrocnemius	UBERON:0001388	91.46	gold quality
body of stomach	UBERON:0001161	91.43	gold quality
muscle of leg	UBERON:0001383	91.43	gold quality
heart	UBERON:0000948	91.39	gold quality
nucleus accumbens	UBERON:0001882	91.36	gold quality
corpus callosum	UBERON:0002336	91.29	gold quality
thymus	UBERON:0002370	91.27	silver quality
saliva-secreting gland	UBERON:0001044	91.26	gold quality
fundus of stomach	UBERON:0001160	91.21	gold quality
gall bladder	UBERON:0002110	91.21	gold quality
sigmoid colon	UBERON:0001159	91.14	gold quality
stomach	UBERON:0000945	91.13	gold quality
putamen	UBERON:0001874	91.08	gold quality
left adrenal gland	UBERON:0001234	90.96	gold quality
amygdala	UBERON:0001876	90.96	gold quality
transverse colon	UBERON:0001157	90.93	gold quality
pancreas	UBERON:0001264	90.93	gold quality
adenohypophysis	UBERON:0002196	90.93	gold quality
caudate nucleus	UBERON:0001873	90.85	gold quality
body of pancreas	UBERON:0001150	90.83	gold quality
urinary bladder	UBERON:0001255	90.81	gold quality
colonic epithelium	UBERON:0000397	90.77	gold quality
parotid gland	UBERON:0001831	90.77	gold quality
small intestine	UBERON:0002108	90.77	gold quality
right frontal lobe	UBERON:0002810	90.77	gold quality
frontal pole	UBERON:0002795	90.76	silver quality
cauda epididymis	UBERON:0004360	90.75	gold quality
prostate gland	UBERON:0002367	90.68	gold quality
substantia nigra	UBERON:0002038	90.66	gold quality
left adrenal gland cortex	UBERON:0035825	90.63	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.76

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 79 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Corpus callosum	tissue	59.8
Spinal cord	tissue	57.1
Medulla oblongata	tissue	54.6
Substantia nigra	tissue	53.2
Superior colliculi	tissue	49.9
Midbrain	tissue	49.4
Thalamus	tissue	49.3
Hypothalamus	tissue	48.4
Periaqueductal gray	tissue	47.5
Pons	tissue	47.3
Putamen	tissue	46.9
Ventral forebrain	tissue	45.5
Septum	tissue	45.3
Basal ganglia	tissue	42.5	not detected
Cerebellum	tissue	42.0	high
Hippocampal formation	tissue	40.9
Cerebral cortex	tissue	40.1	medium
Occipital cortex	tissue	40.1
Prefrontal cortex	tissue	39.9
Somatosensory cortex	tissue	39.1
Olfactory bulb	tissue	37.8
Motor cortex	tissue	36.3
Amygdala	tissue	35.9
Retrosplenial cortex	tissue	35.5
Temporal cortex	tissue	35.4
Entorhinal cortex	tissue	34.8
Insular cortex	tissue	34.8
Retrosplenial and cingulate cortex	tissue	33.8
Caudate putamen	tissue	33.4
Ovary	tissue	30.6	medium
Thymus	tissue	30.3
Frontal cortex	tissue	29.7
Tongue	tissue	26.0
Vagina	tissue	23.6	medium
Skeletal muscle	tissue	23.6	high
Heart muscle	tissue	23.5	high
Endometrium 1	tissue	23.2	low
Nucleus accumbens	tissue	22.9
Testis	tissue	21.9	high
Seminal vesicle	tissue	21.6	low
Fallopian tube	tissue	21.3	medium
Bone marrow	tissue	21.0	high
Locus coeruleus	tissue	20.9
Pituitary gland	tissue	20.3
Smooth muscle	tissue	20.0	medium
Cervix	tissue	18.4	high
Epididymis	tissue	18.1	medium
Tonsil	tissue	17.3	low
Parathyroid gland	tissue	16.6	medium
Spleen	tissue	16.6	medium
Prostate	tissue	16.4	low
Hippocampus	tissue	16.3	low
Retina	tissue	16.0
Postcentral gyrus	tissue	16.0
Salivary gland	tissue	15.9	low
Lymph node	tissue	15.8	low
Placenta	tissue	14.6	medium
Thyroid gland	tissue	14.2	high
Esophagus	tissue	13.9	medium
Urinary bladder	tissue	13.9	medium

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — White matter (59.8), Ventral spinal cord (57.1), Dorsal spinal cord (55.7), Dorsal hippocampus (40.9), Ventral hippocampus (39.2).

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F1

miRNA regulators (miRDB)

Targeting DPF2 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 80 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-22-3P	99.93	68.13	917
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-4697-3P	99.89	67.09	1123
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-4517	99.76	69.19	1867
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-5004-5P	99.68	66.63	1294
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-6715B-5P	99.64	69.63	1420
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-298	99.63	67.56	1916
HSA-MIR-3153	99.55	67.59	2337
HSA-MIR-4269	99.55	69.89	1373
HSA-MIR-3616-5P	99.55	67.02	989
HSA-MIR-573	99.55	67.44	955
HSA-MIR-4708-3P	99.51	67.99	870
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-4325	99.49	72.20	1342
HSA-MIR-4688	99.48	64.68	828
HSA-MIR-6743-5P	99.48	63.60	721
HSA-MIR-766-5P	99.47	67.91	2225
HSA-MIR-3915	99.45	68.49	1905
HSA-MIR-3612	99.45	66.02	1333

Functional genomics

gnomAD constraint: pLI 1, LOEUF 0.287, missense Z 3.36 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD)

ENST00000528416 splits into 4 regions with different missense tolerance; 2 are missense-constrained (≈29% of the expected missense variation). Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. gnomAD

Region (GRCh38)	Missense obs / exp	o/e	Constrained
11:65,333,887–65,344,050	228 / 275.3	0.83	no
11:65,344,051–65,345,699	2 / 23.6	0.08	yes (p 8.6e-06)
11:65,345,700–65,346,041	58 / 84.6	0.69	no
11:65,346,042–65,351,756	27 / 125.8	0.21	yes (p 1.2e-18)
DepMap (CRISPR cell-line fitness): dependent in 34.1% of screened cell lines.

Most-dependent cell lines (DepMap gene-effect, lower = stronger; ≤ −0.5 shown): BT-549 (-1.792), KMS-26 (-1.426), CCK-81 (-1.336), CAMA-1 (-1.303), OCI-LY-19 (-1.288), OVCAR-5 (-1.246), RERF-LC-Ad2 (-1.243), RT4 (-1.22), NCI-H211 (-1.22), RT-112 (-1.215), Du4475 (-1.187), OCI-AML3 (-1.167), NCI-H1693 (-1.162), NCI-H2126 (-1.149), Panc 03.27 (-1.124).

Literature-anchored findings (GeneRIF, showing 11)

• REQ functions as an efficient adaptor protein between the SWI/SNF complex and RelB/p52 and plays important roles in noncanonical NF-kappaB transcriptional activation and its associated oncogenic activity. (PMID:20460684)
• found that targeting Requiem and Alg-2 did not result in extended culture viability, but resulted in an increase in maximum viable cell numbers and cumulative IVCD under fed-batch conditions (PMID:20571937)
• crystal structure of the C2H2-type zinc finger domain of human DPF2 with a canonical C2H2 fold, which contains two beta strands and one alpha helix, was reported. (PMID:21888896)
• DPF2 decreases monomeric and mono-ubiquitinated OCT4, assembles poly-ubiquitin chains on OCT4 mainly through Ub-K48 linkage (PMID:26417682)
• the role of SMARCA4 and the two SWI/SNF subunits SMARCD2/BAF60B and DPF2/BAF45D in leukaemia, was investigated. (PMID:26571505)
• The demonstrate that the histone acetylation-binding double PHD finger (DPF) domains of human MOZ (also known as KAT6A) and DPF2 (also known as BAF45d) accommodate a wide range of histone lysine acylation with the strongest preference for propionylation (Kcr). (PMID:27775714)
• Upon influenza virus infection, DPF2 dysregulated IFN-beta induction and expression of cytokines/chemokines and antiviral proteins. This study provides evidence that influenza virus utilizes DPF2 to escape host innate immunity. (PMID:28404846)
• Authors show that DPF2 interacts with the acetylated tails of both histones 3 and 4 via bipartite binding pockets on the DPF2 surface. Blocking these interactions through targeted mutagenesis of DPF2 abolishes its recruitment to target chromatin regions as well as its ability to prevent myeloid differentiation in vivo. (PMID:28533407)
• de novo variants in DPF2 cause Coffin-Siris syndrome and propose a dominant-negative mechanism of pathogenicity. (PMID:29429572)
• BAF45D knockdown decreases cell viability, inhibits colony formation, induces cell apoptosis and S-phase arrest in human pancreatic cancer cells. (PMID:32024442)
• DPF2-related Coffin-Siris syndrome type 7 in two generations. (PMID:38697389)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	dpf2	ENSDARG00000012219
danio_rerio	dpf2l	ENSDARG00000037291
mus_musculus	Dpf2	ENSMUSG00000024826
rattus_norvegicus	Dpf2	ENSRNOG00000020892
drosophila_melanogaster	tth	FBGN0030502
drosophila_melanogaster	d4	FBGN0033015
caenorhabditis_elegans		WBGENE00016200

Paralogs (9): DPF1 (ENSG00000011332), RSF1 (ENSG00000048649), KAT6A (ENSG00000083168), KAT8 (ENSG00000103510), PHF10 (ENSG00000130024), KAT7 (ENSG00000136504), KAT6B (ENSG00000156650), KAT5 (ENSG00000172977), DPF3 (ENSG00000205683)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:109529) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 10 distinct phenotype terms.

Mouse phenotype (MP)	Records
abnormal heart morphology	1
abnormal craniofacial morphology	1
abnormal embryo size	1
edema	1
abnormal seminal vesicle morphology	1
abnormal limb morphology	1
abnormal tail morphology	1
abnormal kidney morphology	1
pallor	1
preweaning lethality, complete penetrance	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
Saccharomyces cerevisiae S288C	P32432	66.7%	Diamond
Schizosaccharomyces pombe 972h-	Q9HDV4	55.6%	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
POLA2	protein-coding	23649
TIGD3	protein-coding	220359
SLC25A45	protein-coding	283130
NEAT1	ncRNA	283131
MIR612	ncRNA	693197
FRMD8	protein-coding	83786
CDC42EP2	protein-coding	10435

Protein

Protein identifiers

Zinc finger protein ubi-d4 — Q92785 (reviewed: Q92785)

Alternative names: Apoptosis response zinc finger protein, BRG1-associated factor 45D, D4, zinc and double PHD fingers family 2, Protein requiem

All UniProt accessions (10): A0A994J3H5, A0A994J3P2, A0A994J414, A0A994J426, A0A994J6A8, A0A994J6N1, E9PN04, H0YEI1, J3KMZ8, Q92785

UniProt curated annotations — full annotation on UniProt →

Function. Plays an active role in transcriptional regulation by binding modified histones H3 and H4. Is a negative regulator of myeloid differentiation of hematopoietic progenitor cells. Might also have a role in the development and maturation of lymphoid cells. Involved in the regulation of non-canonical NF-kappa-B pathway.

Subunit / interactions. Interacts with the nucleosomes, in particular nucleosomes bearing histone H3 crotonylated at ‘Lys-14’ (H3K14cr) for which DPF2 has high affinity. Also interacts (via PHD-type zinc finger domains) with histone H3 butyrylated at ‘Lys-14’ (H3K14bu), histone H3 propionylated at ‘Lys-14’ (H3K14pr), and histone H3 acetylated at ‘Lys-14’ (H3K14ac). Interacts with histone H3 acetylated at ‘Lys-9’ (H3K9ac), histone H3 di-methylated at ‘Lys-9’ (H3K9me2), and histone H3 tri-methylated at ‘Lys-9’ (H3K9me3). Interacts with histone H4 acetylated at ‘Lys-12’ (H4K12ac). Interacts with histone H4 acetylated at ‘Lys-16’ (H4K16ac). Interacts with SWI/SNF complex components. Interacts with SMARCA2, SMARCA4, SMARCB1 and SMARCD1. Interacts with SMARCC1, SMARCC2 and ACTL6A. Interacts with RUNX1.

Subcellular location. Nucleus. Cytoplasm.

Tissue specificity. Ubiquitous.

Disease relevance. Coffin-Siris syndrome 7 (CSS7) [MIM:618027] A form of Coffin-Siris syndrome, a congenital multiple malformation syndrome with broad phenotypic and genetic variability. Cardinal features are intellectual disability, coarse facial features, hypertrichosis, and hypoplastic or absent fifth digit nails or phalanges. Additional features include malformations of the cardiac, gastrointestinal, genitourinary, and/or central nervous systems. Sucking/feeding difficulties, poor growth, ophthalmologic abnormalities, hearing impairment, and spinal anomalies are common findings. Both autosomal dominant and autosomal recessive inheritance patterns have been reported. CSS7 inheritance is autosomal dominant. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the requiem/DPF family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q92785-1	1	yes
Q92785-2	2

RefSeq proteins (2): NP_001317237, NP_006259* (*=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 (61 total): turn 11, strand 8, modified residue 7, cross-link 7, helix 7, sequence variant 5, compositionally biased region 4, zinc finger region 3, mutagenesis site 3, region of interest 3, initiator methionine 1, chain 1, splice variant 1

Structure

Experimental structures (PDB)

9 structures by resolution:

PDB	Title	Method	Resolution (Å)
5VDC	Crystal structure of the human DPF2 tandem PHD finger domain	X-RAY DIFFRACTION	1.6
3IUF	Crystal structure of the C2H2-type zinc finger domain of human ubi-d4	X-RAY DIFFRACTION	1.8
5B79	Crystal structure of DPF2 double PHD finger	X-RAY DIFFRACTION	2.6
6LTH	Structure of human BAF Base module	ELECTRON MICROSCOPY	3
9RL4	Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6	ELECTRON MICROSCOPY	3.5
6LTJ	Structure of nucleosome-bound human BAF complex	ELECTRON MICROSCOPY	3.7
9RN2	Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2	ELECTRON MICROSCOPY	4.1
9RMC	Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 1	ELECTRON MICROSCOPY	4.2
9RN1	Structure of BAF-nucleosome complex with OCT4-SOX2 at SHL+6 in ADP-bound state, BAF47 …	ELECTRON MICROSCOPY	5.9

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q92785-F1	69.62	0.30

Human Protein Atlas

Protein class: Predicted intracellular proteins, Plasma proteins, Disease related genes, Human disease related genes, Congenital malformations, Other congenital malformations

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nucleoplasm; centrosome; cytosol; vesicles

Antibody reliability (HPA): IH approved · IF supported

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 (14)

Type	Positions
N-acetylalanine	2
Phosphoserine	142, 200, 244, 280
Phosphotyrosine	172
Phosphothreonine	176
Glycyl lysine isopeptide (lys-gly) (interchain with g-cter in sumo2)	10, 99, 107, 108, 178, 196, 281

Mutagenesis-validated functional residues (3)

Position	Phenotype
275	strongly decreased interaction with histones h3 and h4 and loss of function; when associated with a-300 and a-346.
300	strongly decreased interaction with histones h3 and h4 and loss of function; when associated with a-275 and a-346.
346	strongly decreased interaction with histones h3 and h4 and loss of function; when associated with a-275 and a-300.

Function

Pathways and Gene Ontology

Reactome pathways

2 curated (TAS) of 15; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

15 pathways:

ID	Pathway	Evidence
R-HSA-9933937	Formation of the canonical BAF (cBAF) complex	curated
R-HSA-9933946	Formation of the embryonic stem cell BAF (esBAF) 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: 437 (showing top): GOBP_REGULATION_OF_DOUBLE_STRAND_BREAK_REPAIR, GOBP_CHROMOSOME_ORGANIZATION, GOBP_HEMATOPOIETIC_PROGENITOR_CELL_DIFFERENTIATION, LFA1_Q6, GOBP_CELL_CYCLE_PHASE_TRANSITION, chr11q13, CAGCTG_AP4_Q5, GOBP_REGULATION_OF_DNA_REPAIR, GOBP_NUCLEOTIDE_EXCISION_REPAIR, GCM_RING1, GOBP_NEGATIVE_REGULATION_OF_HEMATOPOIETIC_PROGENITOR_CELL_DIFFERENTIATION, GOBP_APOPTOTIC_SIGNALING_PATHWAY, GOBP_REGULATION_OF_CHROMOSOME_SEGREGATION, MORF_CCNI, GCM_DPF2

GO Biological Process (15): negative regulation of transcription by RNA polymerase II (GO:0000122), 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), regulation of mitotic metaphase/anaphase transition (GO:0030071), regulation of G0 to G1 transition (GO:0070316), apoptotic signaling pathway (GO:0097190), positive regulation of stem cell population maintenance (GO:1902459), negative regulation of myeloid progenitor cell differentiation (GO:1905454), 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), chromatin organization (GO:0006325)

GO Molecular Function (7): transcription coregulator activity (GO:0003712), transcription corepressor activity (GO:0003714), zinc ion binding (GO:0008270), histone H3K14ac reader activity (GO:0140015), histone H4K16ac reader activity (GO:0140046), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (5): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829), cytoplasm (GO:0005737)

Reactome top-level categories

10 top-level categories:

Category	Pathways
SWI/SNF chromatin remodelers	3
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

48 GO namespaces:

Category	Terms
cellular anatomical structure	4
transcription by RNA polymerase II	2
negative regulation of DNA-templated transcription	2
regulation of mitotic cell cycle phase transition	2
regulation of transcription by RNA polymerase II	1
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
programmed cell death	1
apoptotic signaling pathway	1
execution phase of apoptosis	1
metaphase/anaphase transition of mitotic cell cycle	1
regulation of metaphase/anaphase transition of cell cycle	1
regulation of cell cycle process	1
G0 to G1 transition	1
apoptotic process	1
signal transduction	1
stem cell population maintenance	1
positive regulation of developmental process	1
positive regulation of multicellular organismal process	1
regulation of stem cell population maintenance	1
myeloid progenitor cell differentiation	1
negative regulation of hematopoietic progenitor cell differentiation	1
regulation of myeloid progenitor cell differentiation	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
cellular component organization	1
transcription regulator activity	1
transcription coregulator activity	1
transition metal ion binding	1
histone H3 reader activity	1
histone H4 reader activity	1
binding	1
cation binding	1
chromosome	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cytoplasm	1
intracellular anatomical structure	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 7 of 27 annotations. The rest are phylogenetic / computational / electronic (IEA).

7 experimentally-supported GO terms:

GO term	NS	Evidence
negative regulation of myeloid progenitor cell differentiation	BP	mutant phenotype
chromatin	CC	direct assay
cytosol	CC	direct assay
nucleoplasm	CC	direct assay
nucleus	CC	direct assay
histone H3K14ac reader activity	MF	direct assay
histone H4K16ac reader activity	MF	direct assay

Protein interactions and networks

STRING

showing 15 of 1,048 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DPF2	SMARCE1	Q969G3	745
DPF2	ARID2	Q68CP9	725
DPF2	SMARCC2	Q8TAQ2	714
DPF2	BRD9	Q9H8M2	698
DPF2	BRD7	Q9NPI1	697
DPF2	SMARCC1	Q92922	693
DPF2	ARID1A	O14497	692
DPF2	SMARCD1	Q96GM5	690
DPF2	ARID1B	Q8NFD5	689
DPF2	PBRM1	Q86U86	669
DPF2	SMARCB1	Q12824	667
DPF2	SMARCA4	P51532	663
DPF2	ACTL6A	O96019	659
DPF2	BANF1	O75531	651
DPF2	BICRA	Q9NZM4	621

IntAct

Human interaction partners of DPF2 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

18 partners by confidence:

Partner	Interaction type	MIscore	Records
ARID1A	association	0.730	4
LDOC1	physical association	0.720	6
SMARCA2	association	0.640	1
HSF2BP	physical association	0.560	6
GOLGA6L9	physical association	0.560	3
LNX1	physical association	0.560	3
MEOX2	physical association	0.560	3
PICK1	physical association	0.560	3
RINT1	physical association	0.560	3
RUBCN	physical association	0.560	3
TTC23L	physical association	0.560	3
TXNDC12	physical association	0.560	3
ZNF655	physical association	0.560	3
HMBOX1	association	0.350	1
NFKB1	association	0.350	1
FHL2	physical association	0.000	2
RELB	physical association	0.000	1
ZNF212	physical association	0.000	1

BioGRID (522 interactions; top human partners by supporting records): SMARCA4 (Affinity Capture-MS; 18 records), SMARCB1 (Affinity Capture-MS; 13 records), SMARCC1 (Affinity Capture-MS; 12 records), SMARCD1 (Affinity Capture-MS; 12 records), SMARCE1 (Affinity Capture-MS; 12 records), SMARCA2 (Affinity Capture-MS; 11 records), SMARCC2 (Affinity Capture-MS; 11 records), ARID1B (Affinity Capture-MS; 9 records), ACTL6A (Affinity Capture-MS; 8 records), ARID1A (Affinity Capture-MS; 8 records), SMARCD2 (Affinity Capture-MS; 8 records), BCL7C (Affinity Capture-MS; 7 records), SMARCD3 (Affinity Capture-MS; 5 records), SS18 (Affinity Capture-MS; 5 records), AR (Proximity Label-MS; 4 records)

SIGNOR signaling

6 signaling interactions:

A	Effect	B	Mechanism
DPF2	“up-regulates activity”	“SWI/SNF complex”	binding
DPF2	“up-regulates activity”	NfKb-p65/p50	binding
DPF2	“down-regulates activity”	RUNX1	binding
DPF2	down-regulates	Differentiation
DPF2	“down-regulates activity”	ESRRA	binding
DPF2	“form complex”	“Embryonic stem cell-specific SWI/SNF”	binding

Protein complexes (CORUM) (3)

Experimentally-characterized complexes this protein is a subunit of (★ = the complex contains a known drug target).

3 complexes by size:

Complex	Subunits	Members
★ LARC complex (LCR-associated remodeling complex)	19	SMARCC1, SMARCC2, SMARCD2, SMARCE1, ACTL6A, CHD4, MBD3, RBBP4, ACTB, MTA2, SMARCA4, HDAC1, HDAC2, HNRNPC, MBD2, ARID1A, DPF2, GATAD2B, SMARCB1
cBAF complex	14	ARID1A, ARID1B, BCL7A, BCL7C, SMARCA4, SMARCB1, SMARCC1, SMARCD2, ACTB, ACTL6A, DPF2, SMARCC2, SMARCD1, SMARCE1
cBAF complex	14	SMARCD1, SMARCD2, ACTB, ACTL6A, ARID1A, BCL7C, SMARCB1, SMARCE1, ARID1B, BCL7A, DPF2, SMARCA2, SMARCC1, SMARCC2

Disease & clinical

Genetic variants

Variant evidence for DPF2: 292 ClinVar records (18 pathogenic / likely pathogenic); 3 GWAS associations. Per-variant detail is on Sugi Variant.

ClinVar

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

Classification	Count (floor)
Pathogenic	7
Likely pathogenic	11
Uncertain significance	117
Likely benign	112
Benign	13

Top pathogenic / likely-pathogenic (15)

Showing the 15 best-reviewed of 18 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant ID	HGVS	Classification	Review	Submitters
985019	NM_006268.5(DPF2):c.904+1G>A	Pathogenic	criteria provided, multiple submitters, no conflicts	2
1200174	NM_006268.5(DPF2):c.1036G>A (p.Asp346Asn)	Likely pathogenic	criteria provided, multiple submitters, no conflicts	2
438643	NM_006268.5(DPF2):c.827G>T (p.Cys276Phe)	Pathogenic	criteria provided, single submitter	2
545685	NM_006268.5(DPF2):c.1037A>G (p.Asp346Gly)	Pathogenic	criteria provided, single submitter	2
1173064	NM_006268.5(DPF2):c.1066T>G (p.Cys356Gly)	Pathogenic	criteria provided, single submitter	1
4855788	NM_006268.5(DPF2):c.904+1G>T	Pathogenic	criteria provided, single submitter	1
986144	NM_006268.5(DPF2):c.1033T>G (p.Cys345Gly)	Likely pathogenic	criteria provided, single submitter	1
1198043	NM_006268.5(DPF2):c.964T>C (p.Trp322Arg)	Likely pathogenic	criteria provided, single submitter	1
1676450	NM_006268.5(DPF2):c.1099+2dup	Likely pathogenic	criteria provided, single submitter	1
1805984	NM_006268.5(DPF2):c.1067G>C (p.Cys356Ser)	Likely pathogenic	criteria provided, single submitter	1
2442163	NM_006268.5(DPF2):c.1094dup (p.Pro365_Glu366insTer)	Likely pathogenic	criteria provided, single submitter	1
3064790	NM_006268.5(DPF2):c.970T>G (p.Cys324Gly)	Likely pathogenic	criteria provided, single submitter	1
3376275	NM_006268.5(DPF2):c.899G>T (p.Arg300Leu)	Likely pathogenic	criteria provided, single submitter	1
3769178	NM_006268.5(DPF2):c.976G>A (p.Glu326Lys)	Likely pathogenic	criteria provided, single submitter	1
4850131	NM_006268.5(DPF2):c.706G>T (p.Glu236Ter)	Likely pathogenic	criteria provided, single submitter	1

Per-variant reference — Sugi Variant

Explore DPF2’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 37 predictions of 721):

Position(s)	Effect	Δscore	Sites
11:65340546–65340547	donor_loss	1.0000	5
11:65340963	acceptor_gain	1.0000
11:65340964–65340965	acceptor_loss	1.0000	3
11:65341074–65341075	donor_loss	1.0000	5
11:65343838–65343839	donor_loss	1.0000	5
11:65344070–65344071	donor_loss	1.0000	6
11:65344074	donor_loss	1.0000
11:65345661	acceptor_gain	1.0000
11:65345664–65345665	acceptor_loss	1.0000	5
11:65345804–65345805	donor_loss	1.0000	5

AlphaMissense

1,482 missense substitutions predicted likely pathogenic (of 2,563 scored), across 293 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
M313	9	0.985	0.999
M354	9	0.946	0.998
M57	9	0.927	0.996
H227	8	1.000	1.000
D339	8	1.000	1.000
F344	8	1.000	1.000
D349	8	1.000	1.000
H353	8	1.000	1.000
D43	8	0.999	1.000
D274	8	0.999	1.000
H303	8	0.999	1.000
D346	8	0.999	1.000
D347	8	0.999	1.000
F309	8	0.998	1.000
H232	8	0.997	0.999
F275	8	0.997	1.000
D297	8	0.997	0.999
N28	8	0.991	1.000
H230	8	0.984	1.000
S370	8	0.982	0.997

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

2 prognostic cancer types:

Cancer	Prognostic	p-value
Lung Adenocarcinoma (validation)	unfavorable	9.13e-07
Liver Hepatocellular Carcinoma (TCGA)	unfavorable	8.11e-05

Disease associations

OMIM: gene MIM:601671 | disease phenotypes: MIM:618027, MIM:135900, MIM:609943, MIM:614562

GenCC curated gene-disease

2 curated gene-disease records:

Disease	Classification	Inheritance	Records
Coffin-Siris syndrome 7	Strong	Autosomal dominant	5
Coffin-Siris syndrome	Supportive	Autosomal dominant

ClinGen Gene-Disease Validity

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

1 validity classifications:

Disease	Classification	Inheritance
Coffin-Siris syndrome	Definitive	AD

Genomics England panels (PanelApp)

Clinical diagnostic gene panels including this gene (7 panels, 6 green/diagnostic-grade). Confidence: green = diagnostic, amber = moderate.

7 panels:

Panel	Rating
DDG2P	green
Fetal anomalies	green
Hypotonic infant	green
Intellectual disability	green
Leukodystrophy, childhood onset	green
Paediatric disorders	green
Rare syndromic craniosynostosis or isolated multisuture synostosis	amber

Mondo (3): Coffin-Siris syndrome 7 (MONDO:0054831), Coffin-Siris syndrome 1 (MONDO:0007617), Coffin-Siris syndrome (MONDO:0015452)

Orphanet (1): Coffin-Siris syndrome (Orphanet:1465)

HPO phenotypes

showing 60 of 103 phenotypes (HPO-id order):

HPO	Term
HP:0000006	Autosomal dominant inheritance
HP:0000028	Cryptorchidism
HP:0000047	Hypospadias
HP:0000085	Horseshoe kidney
HP:0000119	Abnormality of the genitourinary system
HP:0000154	Wide mouth
HP:0000179	Thick lower lip vermilion
HP:0000219	Thin upper lip vermilion
HP:0000243	Trigonocephaly
HP:0000252	Microcephaly
HP:0000280	Coarse facial features
HP:0000286	Epicanthus
HP:0000289	Broad philtrum
HP:0000294	Low anterior hairline
HP:0000316	Hypertelorism
HP:0000322	Short philtrum
HP:0000358	Posteriorly rotated ears
HP:0000365	Hearing impairment
HP:0000369	Low-set ears
HP:0000400	Macrotia
HP:0000403	Recurrent otitis media
HP:0000444	Convex nasal ridge
HP:0000445	Wide nose
HP:0000455	Broad nasal tip
HP:0000463	Anteverted nares
HP:0000486	Strabismus
HP:0000494	Downslanted palpebral fissures
HP:0000505	Visual impairment
HP:0000508	Ptosis
HP:0000540	Hypermetropia
HP:0000545	Myopia
HP:0000574	Thick eyebrow
HP:0000684	Delayed eruption of teeth
HP:0000691	Microdontia
HP:0000708	Atypical behavior
HP:0000718	Aggressive behavior
HP:0000722	Compulsive behaviors
HP:0000729	Autistic behavior
HP:0000733	Motor stereotypy
HP:0000750	Delayed speech and language development
HP:0000752	Hyperactivity
HP:0000767	Pectus excavatum
HP:0000998	Hypertrichosis
HP:0001007	Hirsutism
HP:0001156	Brachydactyly
HP:0001195	Single umbilical artery
HP:0001249	Intellectual disability
HP:0001250	Seizure
HP:0001252	Hypotonia
HP:0001263	Global developmental delay
HP:0001270	Motor delay
HP:0001274	Agenesis of corpus callosum
HP:0001305	Dandy-Walker malformation
HP:0001344	Absent speech
HP:0001382	Joint hypermobility
HP:0001510	Growth delay
HP:0001511	Intrauterine growth retardation
HP:0001561	Polyhydramnios
HP:0001562	Oligohydramnios
HP:0001627	Abnormal heart morphology

GWAS associations

3 associations:

Study	Trait	p-value
GCST90002397_139	Mean spheric corpuscular volume	8e-16
GCST002481_8	Acne (severe)	3e-11
GCST008972_219	Urate levels	2e-9

EFO canonical traits (from GWAS)

1 canonical traits:

EFO ID	Trait name
EFO:0004531	urate measurement

MeSH disease descriptors

1 disease descriptors:

Descriptor	Name	Tree numbers
C536436	Coffin-Siris syndrome *(supp.)*

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	decreases expression, affects cotreatment, increases abundance, increases expression	2
Valproic Acid	affects expression, decreases expression	2
aristolochic acid I	increases expression	1
FR900359	affects phosphorylation	1
TAK-243	decreases sumoylation	1
N-(1,3-dimethylbutyl)-N’-phenyl-p-phenylenediamine quinone	affects expression	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases expression, increases abundance	1
bisphenol A	increases expression	1
salinomycin	decreases expression	1
sodium arsenite	increases expression	1
cobaltous chloride	increases expression	1
coumarin	affects phosphorylation	1
methacrylaldehyde	affects cotreatment, increases expression, increases abundance	1
JP8 aviation fuel	decreases expression	1
ICG 001	increases expression	1
abrine	increases expression	1
Acetaminophen	increases expression	1
Acrolein	affects cotreatment, increases expression, increases abundance	1
Caffeine	decreases phosphorylation	1
Cocaine	increases expression	1
Ethyl Methanesulfonate	increases expression	1
Menthol	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Ozone	affects cotreatment, increases expression, increases abundance	1
Quercetin	decreases phosphorylation	1
Urethane	increases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	increases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B1C2	Abcam A-431 DPF2 KO	Cancer cell line	Female
CVCL_SL11	HAP1 DPF2 (-)	Cancer cell line	Male

Clinical trials (associated diseases)

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

showing 60 of 301 trials:

NCT	Phase	Status	Title
NCT00391261	Phase 4	COMPLETED	An Open-label Trial of Metformin for Weight Control of Pediatric Patients on Antipsychotic Medications.
NCT01028820	Phase 4	COMPLETED	FMRI Brain Activation of Aripiprazole Treatment in Autism Spectrum Disorders
NCT01333865	Phase 4	COMPLETED	A Study of Memantine Hydrochloride (Namenda®) for Cognitive and Behavioral Impairment in Adults With Autism Spectrum Disorders
NCT01337700	Phase 4	COMPLETED	Milnacipran in Autism and the Functional Locus Coeruleus and Noradrenergic Model of Autism
NCT01695200	Phase 4	COMPLETED	Omega-3 Fatty Acids in Autism Spectrum Disorders
NCT02096952	Phase 4	COMPLETED	Methylphenidate ER Liquid Formulation in Adults With ASD and ADHD
NCT02235467	Phase 4	COMPLETED	Multisite Study: Parental Training Using Video Modelling to Develop Social Skills in Children With Autism
NCT02940574	Phase 4	COMPLETED	Neural and Behavioral Effects of Oxytocin in Autism Spectrum Disorders
NCT03333629	Phase 4	COMPLETED	Promoting Positive Outcomes for Individuals With ASD: Linking Early Detection, Treatment, and Long-term Outcomes
NCT03337646	Phase 4	COMPLETED	Evaluation of the Effect and Safety of Lisdexamfetamine in Children Aged 6-12 With ADHD and Autism
NCT03538431	Phase 4	COMPLETED	Improving Driving in Young People With Autism Spectrum Disorders
NCT03757585	Phase 4	COMPLETED	Natural Treatments for the Management of Emotional Dysregulation in Youth With Non-verbal Learning Disability (NVLD) and/or Autism Spectrum Disorders (ASD)
NCT04903353	Phase 4	COMPLETED	Pragmatic Trial Comparing Weight Gain in Children With Autism Taking Risperidone Versus Aripiprazole
NCT05063656	Phase 4	COMPLETED	Biomarker-Driven Pharmacological Treatment of Adolescents With Autism Spectrum Disorder With Gabapentin
NCT05146245	Phase 4	UNKNOWN	Safety and Pharmacokinetics of Antipsychotics in Children 2: Studying TDM in an RCT
NCT05916339	Phase 4	RECRUITING	AWARE: Management of ADHD in Autism Spectrum Disorder
NCT05954052	Phase 4	TERMINATED	A Study of Glutathione in Children With Autism Spectrum Disorder
NCT06853665	Phase 4	RECRUITING	The TEAM Study - Treatment Efficacy for Autism/Attention Using Mixed Amphetamine
NCT07054697	Phase 4	COMPLETED	Pilot-RCT With Individualized Homeopathic Treatment in the Children With Autism Spectrum Disorder
NCT07161804	Phase 4	COMPLETED	Pilot RCT Using Homeopathic Medicines in ASD
NCT07439042	Phase 4	RECRUITING	Buspirone for Anxiety in Autistic Youth
NCT07770152	Phase 4	NOT_YET_RECRUITING	Semaglutide in Youth With Autism Spectrum Disorder
NCT01302964	Phase 3	COMPLETED	Mirtazapine Treatment of Anxiety in Children and Adolescents With Pervasive Developmental Disorders
NCT01706523	Phase 3	TERMINATED	Open Label Extension Study of STX209 (Arbaclofen) in Autism Spectrum Disorders
NCT01825798	Phase 3	COMPLETED	Treatment of Overweight Induced by Antipsychotic Medication in Young People With Autism Spectrum Disorders (ASD)
NCT01972074	Phase 3	COMPLETED	Behavioral and Neural Response to Memantine in Adolescents With Autism Spectrum Disorder
NCT02985749	Phase 3	COMPLETED	A Study of Oxytocin for the Treatment of Social Impairment in Individuals With High Functioning Autism Spectrum Disorder
NCT03197922	Phase 3	COMPLETED	Treatment of Encopresis in Children With Autism Spectrum Disorders
NCT03504917	Phase 3	TERMINATED	A Study of Balovaptan in Adults With Autism Spectrum Disorder With a 2-Year Open-Label Extension
NCT03553875	Phase 3	TERMINATED	Memantine for the Treatment of Social Deficits in Youth With Disorders of Impaired Social Interactions
NCT03640156	Phase 3	COMPLETED	Modulating Socially Adaptive Mirror System Functioning in Autism by Oxytocin
NCT03715153	Phase 3	TERMINATED	Efficacy and Safety of Bumetanide Oral Liquid Formulation in Children Aged From 2 to Less Than 7 Years Old With Autism Spectrum Disorder.
NCT03715166	Phase 3	TERMINATED	Efficacy and Safety of Bumetanide Oral Liquid Formulation in Children and Adolescents Aged From 7 to Less Than 18 Years Old With Autism Spectrum Disorder
NCT04233502	Phase 3	WITHDRAWN	Efficacy and Safety of Slenyto for Insomnia in Children With ASD
NCT04578756	Phase 3	COMPLETED	Open-Label, Flexible-dose Study to Evaluate the Long-Term Safety and Tolerability of Cariprazine in the Treatment of Pediatric Participants With Schizophrenia, Bipolar I Disorder, or Autism Spectrum Disorder
NCT04623398	Phase 3	COMPLETED	Effect of Lithium in Patients With Autism Spectrum Disorder and Phelan-McDermid Syndrome (SHANK3 Haploinsufficiency)
NCT04725383	Phase 3	TERMINATED	Amitriptyline for Repetitive Behaviors in Autism Spectrum Disorders
NCT05212493	Phase 3	COMPLETED	The Effects of Medical Cannabis in Children With Autistic Spectrum Disorder
NCT05361707	Phase 3	UNKNOWN	Evaluating the Effects of Tasimelteon in Individuals With Autism Spectrum Disorder (ASD) and Sleep Disturbances
NCT05439616	Phase 3	COMPLETED	Study of Cariprazine Oral Capsules or Solution to Assess Adverse Events and Change in Irritability Due to Autism Spectrum Disorder (ASD) in Participants Aged 5-17 Years With ASD
NCT06229210	Phase 3	RECRUITING	Safety and Tolerability Trial of Lumateperone in Pediatric Patients With Schizophrenia, Bipolar Disorder or Autism Spectrum Disorder
NCT06333964	Phase 3	COMPLETED	A Study to Evaluate the Efficacy and Safety of AST-001 in ASD Children
NCT07257939	Phase 3	NOT_YET_RECRUITING	NTI164 in Autism Spectrum Disorder
NCT07655115	Phase 3	RECRUITING	Single Dose Double-blind, Placebo-controlled Cross-over (SDDBPCCO) Shiftability Study, Will be Followed by a 10-week Open-label Study With Arbaclofen (4 Weeks of Titration and Then 6 Weeks of Active/Stable Treatment). The Effects of Arbaclofen on Target EEG and ERG Metrics Will be Associated With th
NCT00251303	Phase 2	COMPLETED	Riluzole to Treat Child and Adolescent Obsessive-Compulsive Disorder With or Without Autism Spectrum Disorders
NCT00614198	Phase 2	COMPLETED	ScanBrit Dietary Intervention in Autism
NCT00619190	Phase 2	COMPLETED	Study of Aripiprazole to Treat Children and Adolescents With Autism
NCT00709202	Phase 2	COMPLETED	Efficacy and Tolerability Study of Betahistine to Ameliorate Antipsychotic Associated Weight Gain
NCT00846547	Phase 2	COMPLETED	Open-Label Study of the Safety and Tolerability of STX209 in Subjects With Autism Spectrum Disorders
NCT01064973	Phase 2	TERMINATED	An Open Label Extension Study of STX209 in Subjects With Autism Spectrum Disorders
NCT01170325	Phase 2	WITHDRAWN	A Study of Divalproex Sodium in Children With ASD and Epileptiform EEG
NCT01205282	Phase 2	COMPLETED	Dose Finding Study of Pioglitazone in Children With Autism Spectrum Disorders (ASD) (PIO)
NCT01248130	Phase 2	TERMINATED	Omega-3 Fatty Acids Monotherapy in Children and Adolescents With Autism Spectrum Disorders
NCT01248728	Phase 2	COMPLETED	Omega-3 Fatty Acids For Treatment Of Young Children With Autism (OMG)
NCT01256060	Phase 2	COMPLETED	Intranasal Oxytocin for the Treatment of Children and Adolescents With ASD (OXY)
NCT01288716	Phase 2	COMPLETED	Study of Arbaclofen for the Treatment of Social Withdrawal in Subjects With Autism Spectrum Disorders
NCT01300923	Phase 2	COMPLETED	Acamprosate in Youth With Fragile X Syndrome
NCT01366859	Phase 2	COMPLETED	Nutritional Intervention in Children With Autism Using Whey Protein (Immunocal): Impact on Core Areas of Behavior
NCT01372449	Phase 2	COMPLETED	A Multi-site Double-blind Placebo-controlled Trial of Memantine Versus Placebo in Children With Autism (MEM)
NCT01395953	Phase 2	WITHDRAWN	Double-blind Trial of Buspirone for the Treatment of Anxiety in Youth With Autism Spectrum Disorders