DPF3

Summary

DPF3 (double PHD fingers 3, HGNC:17427) is a protein-coding gene on chromosome 14q24.2, encoding Zinc finger protein DPF3 (Q92784). Belongs to the neuron-specific chromatin remodeling complex (nBAF complex).

This gene encodes a member of the D4 protein family. The encoded protein is a transcription regulator that binds acetylated histones and is a component of the BAF chromatin remodeling complex. Alternate splicing results in multiple transcript variants encoding different isoforms.

Source: NCBI Gene 8110 — RefSeq curated summary.

At a glance

• GWAS associations: 18
• Clinical variants (ClinVar): 64 total
• MANE Select transcript: NM_001280542

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17427
Approved symbol	DPF3
Name	double PHD fingers 3
Location	14q24.2
Locus type	gene with protein product
Status	Approved
Aliases	cer-d4, Cerd4, FLJ14079, BAF45c, SMARCG3
Ensembl gene	ENSG00000205683
Ensembl biotype	protein_coding
OMIM	601672
Entrez	8110

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 10 protein_coding_CDS_not_defined, 3 nonsense_mediated_decay, 1 protein_coding

ENST00000366353, ENST00000381216, ENST00000546183, ENST00000553608, ENST00000554594, ENST00000555469, ENST00000555781, ENST00000556238, ENST00000556509, ENST00000556891, ENST00000556902, ENST00000556997, ENST00000557704, ENST00000614862

RefSeq mRNA: 4 — MANE Select: NM_001280542 NM_001280542, NM_001280543, NM_001280544, NM_012074

CCDS: CCDS45133, CCDS61495, CCDS61496, CCDS61497

Canonical transcript exons

ENST00000556509 — 11 exons

Exon	Start	End
ENSE00001487853	72753264	72753371
ENSE00001487854	72771733	72771893
ENSE00001632935	72619903	72619984
ENSE00001637932	72609034	72619367
ENSE00001691816	72629624	72629736
ENSE00002460750	72894057	72894101
ENSE00003511037	72714423	72714501
ENSE00003528883	72731807	72731934
ENSE00003597719	72674240	72674368
ENSE00003628504	72723633	72723728
ENSE00003675035	72693076	72693213

Expression profiles

Bgee: expression breadth ubiquitous, 217 present calls, max score 90.59.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.3879 / max 420.4023, expressed in 1167 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
143944	6.3704	1167
143942	0.0174	7

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left ventricle myocardium	UBERON:0006566	90.59	gold quality
quadriceps femoris	UBERON:0001377	89.36	gold quality
vastus lateralis	UBERON:0001379	89.13	gold quality
deltoid	UBERON:0001476	88.94	gold quality
cardiac muscle of right atrium	UBERON:0003379	87.93	silver quality
skeletal muscle tissue	UBERON:0001134	87.57	gold quality
gastrocnemius	UBERON:0001388	87.46	gold quality
muscle of leg	UBERON:0001383	87.22	gold quality
hindlimb stylopod muscle	UBERON:0004252	87.18	gold quality
cerebellar vermis	UBERON:0004720	87.12	gold quality
cerebellum	UBERON:0002037	87.01	gold quality
cerebellar cortex	UBERON:0002129	86.67	gold quality
cerebellar hemisphere	UBERON:0002245	86.64	gold quality
tibialis anterior	UBERON:0001385	86.06	silver quality
right hemisphere of cerebellum	UBERON:0014890	85.80	gold quality
myocardium	UBERON:0002349	85.64	gold quality
biceps brachii	UBERON:0001507	85.46	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	85.40	gold quality
buccal mucosa cell	CL:0002336	85.37	gold quality
muscle tissue	UBERON:0002385	85.25	gold quality
cardiac ventricle	UBERON:0002082	84.04	gold quality
heart left ventricle	UBERON:0002084	84.02	gold quality
heart right ventricle	UBERON:0002080	83.56	gold quality
left testis	UBERON:0004533	83.50	gold quality
endothelial cell	CL:0000115	83.23	gold quality
right testis	UBERON:0004534	83.19	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	82.77	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.60	gold quality
testis	UBERON:0000473	82.10	gold quality
apex of heart	UBERON:0002098	81.96	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.35

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

Target	Regulation
DPF3

Upstream regulators (CollecTRI, top): DPF3, NR1I2, STAT5A, STAT5B

Literature-anchored findings (GeneRIF, showing 16)

• DPF3 adds a further layer of complexity to the BAF complex by representing a tissue-specific anchor between histone acetylations as well as methylations and chromatin remodeling. (PMID:18765789)
• three-dimensional solution structures and biochemical analysis of DPF3b highlight the molecular basis of the integrated tandem PHD finger, which acts as one functional unit in the sequence-specific recognition of lysine-14-acetylated histone H3 (PMID:20613843)
• by linking RelA and p50 to the SWI/SNF complex, DPF3a/b induces the transactivation of NF-kappaB target gene promoters in relatively inactive chromatin contexts. (PMID:22334708)
• These findings provide insights in the STAT5 dependent transcriptional regulation of Dpf3. (PMID:24155890)
• DFP3 protein rs10129954 SNP is associated with poor sperm morphology. (PMID:24271036)
• Immunohistochemical staining showed that intensive DPF3 staining occurred in proximal anastomosis and the positive staining was hardly observed in stenotic segment in colon specimens from patients with Hirschsprung’s disease (PMID:25120773)
• Activation of DPF3a upon hypertrophic stimuli in cardiac hypertrophy switches cardiac fetal gene expression from being silenced by HEY to being activated by BRG1. (PMID:26582913)
• SLC1A1 and DPF3 were strongly associated with idiopathic male infertility and were significantly correlated with semen quality alterations (PMID:27232852)
• the high resolution crystal structure of the tandem PHD fingers of DPF3b in complex with an H3K14ac peptide. (PMID:27402533)
• DPF3 single nucleotide polymorphisms were significantly correlated with male infertility in a Japanese population. (PMID:28975488)
• downregulation of DPF3 plays an indispensable function in the progression of breast cancer (PMID:31076105)
• Altered regulation of DPF3, a member of the SWI/SNF complexes, underlies the 14q24 renal cancer susceptibility locus. (PMID:34390653)
• The renal cancer risk allele at 14q24.2 activates a novel hypoxia-inducible transcription factor-binding enhancer of DPF3 expression. (PMID:35148991)
• The SWI/SNF chromatin remodeling factor DPF3 regulates metastasis of ccRCC by modulating TGF-beta signaling. (PMID:35945219)
• Non-canonical role for the BAF complex subunit DPF3 in mitosis and ciliogenesis. (PMID:38661008)
• DPF3 polymorphisms increased the risk of pulmonary tuberculosis in the Northwest Chinese Han population. (PMID:38795855)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	dpf3	ENSDARG00000025309
mus_musculus	Dpf3	ENSMUSG00000021221
rattus_norvegicus	Dpf3	ENSRNOG00000008086
drosophila_melanogaster	tth	FBGN0030502
drosophila_melanogaster	d4	FBGN0033015
caenorhabditis_elegans		WBGENE00016200

Paralogs (9): DPF1 (ENSG00000011332), RSF1 (ENSG00000048649), KAT6A (ENSG00000083168), KAT8 (ENSG00000103510), PHF10 (ENSG00000130024), DPF2 (ENSG00000133884), KAT7 (ENSG00000136504), KAT6B (ENSG00000156650), KAT5 (ENSG00000172977)

Protein

Protein identifiers

Zinc finger protein DPF3 — Q92784 (reviewed: Q92784)

Alternative names: BRG1-associated factor 45C, Zinc finger protein cer-d4

All UniProt accessions (2): Q92784, F8W7T1

UniProt curated annotations — full annotation on UniProt →

Function. Belongs to the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic 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 post-mitotic 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. Muscle-specific component of the BAF complex, a multiprotein complex involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Specifically binds acetylated lysines on histone 3 and 4 (H3K14ac, H3K9ac, H4K5ac, H4K8ac, H4K12ac, H4K16ac). In the complex, it acts as a tissue-specific anchor between histone acetylations and methylations and chromatin remodeling. It thereby probably plays an essential role in heart and skeletal muscle development. Acts as a regulator of myogenesis in cooperation with HDGFL2. Mediates the interaction of HDGFL2 with the BAF complex. HDGFL2-DPF3a activate myogenic genes by increasing chromatin accessibility through recruitment of SMARCA4/BRG1/BAF190A (ATPase subunit of the BAF complex) to myogenic gene promoters.

Subunit / interactions. Component of the BAF complex, which includes at least actin (ACTB), ARID1A, ARID1B/BAF250, SMARCA2, SMARCA4/BRG1/BAF190A, ACTL6A/BAF53, ACTL6B/BAF53B, SMARCE1/BAF57, SMARCC1/BAF155, SMARCC2/BAF170, SMARCB1/SNF5/INI1, and one or more of SMARCD1/BAF60A, SMARCD2/BAF60B, or SMARCD3/BAF60C. In muscle cells, the BAF complex also contains DPF3. Interacts with acetylated histones H3 and H4. 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. Interacts with HDGFL2, SMARCA4/BRG1/BAF190A, SMARCC1/BAF155 and SMARCD1/BAF60A.

Subcellular location. Nucleus.

Post-translational modifications. Phosphorylation at Ser-323 enhances its interaction with HDGFL2.

Domain organisation. The PHD-type zinc fingers mediate the binding to acetylated histones.

Miscellaneous. Lacks PHD-type zinc fingers and does not bind to acetylated histones H3 and H4.

Similarity. Belongs to the requiem/DPF family.

Isoforms (5)

UniProt ID	Names	Canonical?
Q92784-1	1, DPF3b	yes
Q92784-2	2, DPF3a
Q92784-3	3
Q92784-4	4
Q92784-5	5

RefSeq proteins (4): NP_001267471, NP_001267472, NP_001267473, NP_036206 (=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 (48 total): turn 9, mutagenesis site 7, sequence conflict 7, strand 5, splice variant 4, zinc finger region 3, helix 3, region of interest 3, sequence variant 2, compositionally biased region 2, chain 1, modified residue 1, cross-link 1

Structure

Experimental structures (PDB)

8 structures.

PDB	Method	Resolution (Å)
5SZC	X-RAY DIFFRACTION	1.19
5SZB	X-RAY DIFFRACTION	1.2
5I3L	X-RAY DIFFRACTION	1.85
9UTH	X-RAY DIFFRACTION	2.69
2KWJ	SOLUTION NMR
2KWK	SOLUTION NMR
2KWN	SOLUTION NMR
2KWO	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q92784-F1	73.58	0.43

Functional residue map

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

Post-translational modifications (2): 323, 99

Mutagenesis-validated functional residues (7):

Position	Phenotype
358	abolishes binding to acetylated histones h3 and h4.
360	abolishes binding to acetylated histones h3 and h4; when associated with r-363.
363	abolishes binding to acetylated histones h3 and h4; when associated with r-360.
323	phosphorylation-null mutant. loss of interaction with hdgfl2.
323	phosphomimetic mutant. increased interaction with hdgfl2.
325	loss of interaction with hdgfl2. no effect on interaction with smarca4, smarcc1 and smarcd1.
328	loss of interaction with hdgfl2. no effect on interaction with smarca4, smarcc1 and smarcd1.

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: 219 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_DN, GSE45365_NK_CELL_VS_CD11B_DC_UP, GOBP_REGULATION_OF_DOUBLE_STRAND_BREAK_REPAIR, GOBP_CHROMOSOME_ORGANIZATION, BENPORATH_ES_WITH_H3K27ME3, MYOGENIN_Q6, NKX25_02, GCANCTGNY_MYOD_Q6, GOZGIT_ESR1_TARGETS_DN, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_UP, GOBP_CELL_CYCLE_PHASE_TRANSITION, TGACCTY_ERR1_Q2, GOBP_REGULATION_OF_DNA_REPAIR, COUP_01

GO Biological Process (12): chromatin remodeling (GO:0006338), regulation of transcription by RNA polymerase II (GO:0006357), nervous system development (GO:0007399), muscle organ development (GO:0007517), regulation of mitotic metaphase/anaphase transition (GO:0030071), positive regulation of cell differentiation (GO:0045597), positive regulation of myoblast differentiation (GO:0045663), 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), chromatin organization (GO:0006325)

GO Molecular Function (3): zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (6): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), SWI/SNF complex (GO:0016514), brahma complex (GO:0035060), nBAF complex (GO:0071565)

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
SWI/SNF superfamily-type complex	3
regulation of mitotic cell cycle phase transition	2
cellular anatomical structure	2
chromatin organization	1
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
system development	1
animal organ development	1
muscle structure 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
myoblast differentiation	1
positive regulation of cell differentiation	1
regulation of myoblast differentiation	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
cellular component organization	1
transition metal ion binding	1
binding	1
cation binding	1
chromosome	1
intracellular membrane-bounded organelle	1
nuclear lumen	1

Protein interactions and networks

STRING

656 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DPF3	ACTL6B	O94805	989
DPF3	DPF1	Q92782	982
DPF3	SMARCD3	Q6STE5	936
DPF3	PHF10	Q8WUB8	928
DPF3	DPF2	Q92785	847
DPF3	PBRM1	Q86U86	819
DPF3	ARID1B	Q8NFD5	818
DPF3	ACTL6A	O96019	791
DPF3	ARID1A	O14497	789
DPF3	SS18L1	O75177	768
DPF3	SMARCC1	Q92922	759
DPF3	SMARCD2	Q92925	758
DPF3	SMARCE1	Q969G3	752
DPF3	SMARCD1	Q96GM5	747
DPF3	SMARCC2	Q8TAQ2	746

IntAct

41 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
SMARCE1	SMARCA2	psi-mi:“MI:0914”(association)	0.730
SMARCD3	ARID1A	psi-mi:“MI:0914”(association)	0.640
BCL7C	ARID1A	psi-mi:“MI:0914”(association)	0.640
BCL7A	ARID1A	psi-mi:“MI:0914”(association)	0.640
DPF3	ARID1A	psi-mi:“MI:0914”(association)	0.530
DPF1	ARID1A	psi-mi:“MI:0914”(association)	0.530
NEUROD1	TCF4	psi-mi:“MI:0914”(association)	0.530
SS18L2	ARID1A	psi-mi:“MI:0914”(association)	0.480
ETV7	NFIB	psi-mi:“MI:2364”(proximity)	0.470
DPF3	H3C1	psi-mi:“MI:0407”(direct interaction)	0.440
CFTR	DPF3	psi-mi:“MI:0915”(physical association)	0.370
DPF3	IL6	psi-mi:“MI:0914”(association)	0.350
DPF3	RELA	psi-mi:“MI:0914”(association)	0.350
DPF3	ARID1A	psi-mi:“MI:0914”(association)	0.350
SMARCB1		psi-mi:“MI:0914”(association)	0.350
NUDCD1	DNAJB2	psi-mi:“MI:0914”(association)	0.350
ARID1B	RTCA	psi-mi:“MI:0914”(association)	0.350

BioGRID (214): ARID1A (Affinity Capture-MS), ARID1B (Affinity Capture-MS), SMARCC2 (Affinity Capture-MS), SMARCC1 (Affinity Capture-MS), SMARCA2 (Affinity Capture-MS), SMARCA4 (Affinity Capture-MS), SMARCD3 (Affinity Capture-MS), SMARCD2 (Affinity Capture-MS), SMARCD1 (Affinity Capture-MS), ARID2 (Affinity Capture-MS), PBRM1 (Affinity Capture-MS), SMARCB1 (Affinity Capture-MS), BRD7 (Affinity Capture-MS), SMARCE1 (Affinity Capture-MS), BCL7A (Affinity Capture-MS)

ESM2 similar proteins: A0A0K3AXH1, A2WXR5, A2XTW9, A2Y0Q2, A2Y4R8, A9LMC0, B8ADZ3, B8AMA8, B8B8C5, B8B8I3, B8BJV8, F4I2J8, O81488, P13864, P15130, P26358, P58268, P58269, P58270, P69596, P69597, P69598, Q12830, Q24K09, Q2R837, Q40359, Q5XEM9, Q60DW3, Q61103, Q6BER5, Q6YTY3, Q6Z7F4, Q75IR6, Q7F2Z1, Q7T2A3, Q7XUW3, Q84TV4, Q8H383, Q8LA16, Q8S8M9

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

3 interactions.

A	Effect	B	Mechanism
DPF3	“form complex”	“Muscle cell-specific SWI/SNF ARID1A variant”	binding
DPF3	“form complex”	“Muscle cell-specific SWI/SNF ARID1B variant”	binding
DPF3	“form complex”	“Muscle cell-specific SWI/SNF SMARCA4 variant”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 36 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	258.5×	5e-24
Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF)	13	219.9×	3e-27
Formation of the polybromo-BAF (pBAF) complex	9	211.5×	9e-19
Formation of the embryonic stem cell BAF (esBAF) complex	9	200.3×	1e-18
Formation of the non-canonical BAF (ncBAF) complex	8	199.0×	2e-16
Regulation of endogenous retroelements	11	150.1×	5e-21
Regulation of MITF-M-dependent genes involved in pigmentation	13	127.9×	6e-24
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known	9	100.2×	2e-15

GO biological processes:

GO term	Partners	Fold	FDR
regulation of G0 to G1 transition	12	237.9×	1e-24
regulation of nucleotide-excision repair	12	212.4×	3e-24
regulation of mitotic metaphase/anaphase transition	12	174.9×	3e-23
nucleosome disassembly	7	165.2×	3e-13
positive regulation of double-strand break repair	12	121.4×	4e-21
positive regulation of T cell differentiation	9	120.6×	1e-15
regulation of G1/S transition of mitotic cell cycle	12	108.1×	2e-20
positive regulation of myoblast differentiation	9	97.0×	9e-15

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	59
Likely benign	0
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

4446 predictions. Top by Δscore:

Variant	Effect	Δscore
14:72629617:AACTC:A	donor_loss	1.0000
14:72629618:ACTCA:A	donor_loss	1.0000
14:72629619:CTC:C	donor_loss	1.0000
14:72629620:TCA:T	donor_loss	1.0000
14:72629621:CAC:C	donor_loss	1.0000
14:72629622:A:AC	donor_gain	1.0000
14:72629622:ACATC:A	donor_loss	1.0000
14:72629623:C:CC	donor_gain	1.0000
14:72629623:CA:C	donor_gain	1.0000
14:72629623:CAT:C	donor_gain	1.0000
14:72629734:GACC:G	acceptor_loss	1.0000
14:72629735:ACCT:A	acceptor_loss	1.0000
14:72629736:CCTGG:C	acceptor_loss	1.0000
14:72629737:C:CC	acceptor_gain	1.0000
14:72629738:T:A	acceptor_loss	1.0000
14:72693071:CTCA:C	donor_loss	1.0000
14:72693073:CA:C	donor_loss	1.0000
14:72693074:A:AC	donor_gain	1.0000
14:72693074:ACGC:A	donor_gain	1.0000
14:72693075:C:CC	donor_gain	1.0000
14:72693075:CG:C	donor_gain	1.0000
14:72693075:CGCC:C	donor_gain	1.0000
14:72693075:CGCCT:C	donor_gain	1.0000
14:72693209:ACAGA:A	acceptor_gain	1.0000
14:72693210:CAGA:C	acceptor_gain	1.0000
14:72693210:CAGAC:C	acceptor_gain	1.0000
14:72693211:AGA:A	acceptor_gain	1.0000
14:72693211:AGAC:A	acceptor_loss	1.0000
14:72693212:GA:G	acceptor_gain	1.0000
14:72693212:GAC:G	acceptor_loss	1.0000

AlphaMissense

2491 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:72619345:G:C	C363W	1.000
14:72619346:C:G	C363S	1.000
14:72619346:C:T	C363Y	1.000
14:72619347:A:G	C363R	1.000
14:72619347:A:T	C363S	1.000
14:72619354:G:C	C360W	1.000
14:72619355:C:A	C360F	1.000
14:72619355:C:G	C360S	1.000
14:72619355:C:T	C360Y	1.000
14:72619356:A:G	C360R	1.000
14:72619356:A:T	C360S	1.000
14:72619360:C:A	W358C	1.000
14:72619360:C:G	W358C	1.000
14:72619362:A:G	W358R	1.000
14:72619362:A:T	W358R	1.000
14:72619934:A:C	C345W	1.000
14:72619935:C:A	C345F	1.000
14:72619935:C:G	C345S	1.000
14:72619935:C:T	C345Y	1.000
14:72619936:A:G	C345R	1.000
14:72619936:A:T	C345S	1.000
14:72619943:G:C	H342Q	1.000
14:72619943:G:T	H342Q	1.000
14:72619944:T:A	H342L	1.000
14:72619944:T:C	H342R	1.000
14:72619945:G:A	H342Y	1.000
14:72619945:G:C	H342D	1.000
14:72619945:G:T	H342N	1.000
14:72619948:A:C	Y341D	1.000
14:72619950:C:T	G340D	1.000

dbSNP variants (sampled 300 via entrez): RS1000026477 (14:72850334 T>C), RS1000046776 (14:72755771 G>C), RS1000051360 (14:72677658 G>C), RS1000054329 (14:72609180 A>T), RS1000060532 (14:72877875 A>G), RS1000060919 (14:72834601 C>A), RS1000069062 (14:72808342 GGAA>G), RS1000075770 (14:72652617 C>T), RS1000082257 (14:72755522 A>C), RS1000082503 (14:72892851 T>C), RS1000100587 (14:72795256 T>C), RS1000101410 (14:72647556 A>G), RS1000104593 (14:72715502 G>C), RS1000105461 (14:72640994 A>C), RS1000132174 (14:72876301 A>G)

Disease associations

OMIM: gene MIM:601672 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

18 associations (top):

Study	Trait	p-value
GCST004710_8	Renal cell carcinoma	2.000000e-24
GCST005359_22	Disease progression in age-related macular degeneration	3.000000e-07
GCST005580_186	Intraocular pressure	2.000000e-08
GCST005752_139	Systemic lupus erythematosus	2.000000e-06
GCST005790_29	Rosacea symptom severity	3.000000e-06
GCST006061_64	Atrial fibrillation	7.000000e-08
GCST006414_23	Atrial fibrillation	3.000000e-10
GCST007096_98	Pulse pressure	2.000000e-08
GCST007231_11	Tuberculosis	2.000000e-06
GCST007324_141	Adventurousness	3.000000e-10
GCST008225_1	Renal cell carcinoma	2.000000e-14
GCST008762_11	Intake of sweets	4.000000e-06
GCST009391_2034	Metabolite levels	2.000000e-06
GCST010002_156	Refractive error	7.000000e-25
GCST010988_540	Adult body size	1.000000e-08
GCST90000025_542	Appendicular lean mass	6.000000e-12
GCST90000654_55	Central corneal thickness	5.000000e-11
GCST90002383_261	Hematocrit	4.000000e-14

EFO canonical traits (9, from GWAS)

EFO ID	Trait name
EFO:0008336	disease progression measurement
EFO:0004695	intraocular pressure measurement
EFO:0009180	rosacea severity measurement
EFO:0005763	pulse pressure measurement
EFO:0008579	risk-taking behaviour
EFO:0010158	sugar consumption measurement
EFO:0004980	appendicular lean mass
EFO:0005213	central corneal thickness
EFO:0004348	hematocrit

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression, decreases methylation, increases methylation	6
Valproic Acid	affects cotreatment, increases expression	5
Smoke	increases abundance, increases expression, decreases expression	3
Cadmium	decreases expression, increases abundance	2
Nickel	decreases expression	2
GSK-J4	decreases expression	1
FR900359	increases phosphorylation	1
methyleugenol	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, increases methylation, decreases methylation	1
2,5,2’,5’-tetrachlorobiphenyl	decreases expression	1
sodium arsenite	affects methylation	1
butyraldehyde	increases expression	1
benzo(e)pyrene	affects methylation	1
aflatoxin B2	increases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment, decreases expression	1
2-palmitoylglycerol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	increases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
jinfukang	affects cotreatment, decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Air Pollutants	increases abundance, increases expression	1
Catechin	affects cotreatment, increases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Coal	increases abundance, increases expression	1
Doxorubicin	decreases expression	1
Lipopolysaccharides	increases expression, affects cotreatment, decreases expression, affects response to substance	1
Methapyrilene	affects methylation	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_SL12	HAP1 DPF3 (-) 1	Cancer cell line	Male
CVCL_SL13	HAP1 DPF3 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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