EMSY

Summary

EMSY (EMSY transcriptional repressor, BRCA2 interacting, HGNC:18071) is a protein-coding gene on chromosome 11q13.5, encoding BRCA2-interacting transcriptional repressor EMSY (Q7Z589). Regulator which is able to repress transcription, possibly via its interaction with a multiprotein chromatin remodeling complex that modifies the chromatin.

Predicted to enable identical protein binding activity. Predicted to be involved in DNA repair; chromatin organization; and regulation of DNA-templated transcription. Located in nucleoplasm.

Source: NCBI Gene 56946 — RefSeq curated summary.

At a glance

• GWAS associations: 69
• Clinical variants (ClinVar): 42 total
• MANE Select transcript: NM_001300942

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18071
Approved symbol	EMSY
Name	EMSY transcriptional repressor, BRCA2 interacting
Location	11q13.5
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000158636
Ensembl biotype	protein_coding
OMIM	608574
Entrez	56946

Gene structure

Transcript identifiers

Ensembl transcripts: 42 — 37 protein_coding, 4 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000334736, ENST00000427574, ENST00000524451, ENST00000524490, ENST00000524767, ENST00000525038, ENST00000525919, ENST00000525959, ENST00000528826, ENST00000529032, ENST00000531641, ENST00000531793, ENST00000531998, ENST00000532719, ENST00000533248, ENST00000533972, ENST00000533988, ENST00000534573, ENST00000695367, ENST00000884895, ENST00000884896, ENST00000884897, ENST00000884898, ENST00000884899, ENST00000884900, ENST00000884901, ENST00000884902, ENST00000884903, ENST00000884904, ENST00000884905, ENST00000884906, ENST00000884907, ENST00000884908, ENST00000884909, ENST00000884910, ENST00000884911, ENST00000884912, ENST00000884913, ENST00000884914, ENST00000884915, ENST00000916764, ENST00000949750

RefSeq mRNA: 4 — MANE Select: NM_001300942 NM_001300942, NM_001300943, NM_001300944, NM_020193

CCDS: CCDS73349, CCDS73350, CCDS73351, CCDS8244

Canonical transcript exons

ENST00000695367 — 22 exons

Exon	Start	End
ENSE00001040001	76545797	76546297
ENSE00001040003	76544259	76544822
ENSE00001102384	76526462	76526635
ENSE00001102392	76516142	76516312
ENSE00001102425	76513386	76513535
ENSE00001102435	76523155	76523291
ENSE00001102458	76459933	76460085
ENSE00001152894	76539599	76539640
ENSE00001152940	76496215	76496469
ENSE00002167218	76446900	76447008
ENSE00002200641	76549952	76553031
ENSE00003477618	76537795	76537950
ENSE00003494287	76528268	76528466
ENSE00003510420	76463821	76464080
ENSE00003528121	76542216	76542367
ENSE00003535059	76535895	76536059
ENSE00003567437	76451858	76451957
ENSE00003592745	76472564	76472840
ENSE00003618438	76458183	76458358
ENSE00003628634	76453314	76453388
ENSE00003963535	76445018	76445128
ENSE00003963537	76454749	76454790

Expression profiles

Bgee: expression breadth ubiquitous, 260 present calls, max score 90.48.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.4802 / max 523.7721, expressed in 1805 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
115940	22.9787	1804
115941	1.3060	745
115942	0.1955	92

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	90.48	gold quality
calcaneal tendon	UBERON:0003701	89.84	gold quality
cortical plate	UBERON:0005343	89.22	gold quality
ganglionic eminence	UBERON:0004023	88.84	gold quality
corpus callosum	UBERON:0002336	87.90	gold quality
cartilage tissue	UBERON:0002418	87.39	gold quality
colonic epithelium	UBERON:0000397	87.21	gold quality
right uterine tube	UBERON:0001302	86.29	gold quality
endothelial cell	CL:0000115	86.21	gold quality
right hemisphere of cerebellum	UBERON:0014890	85.78	gold quality
left ovary	UBERON:0002119	85.73	gold quality
adrenal tissue	UBERON:0018303	85.62	gold quality
popliteal artery	UBERON:0002250	85.58	gold quality
tibial artery	UBERON:0007610	85.57	gold quality
cerebellar cortex	UBERON:0002129	85.49	gold quality
cerebellar hemisphere	UBERON:0002245	85.49	gold quality
hindlimb stylopod muscle	UBERON:0004252	85.41	gold quality
right ovary	UBERON:0002118	84.92	gold quality
aorta	UBERON:0000947	84.89	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.85	gold quality
ovary	UBERON:0000992	84.80	gold quality
endocervix	UBERON:0000458	84.76	gold quality
body of uterus	UBERON:0009853	84.75	gold quality
secondary oocyte	CL:0000655	84.67	gold quality
ectocervix	UBERON:0012249	84.67	gold quality
cerebellum	UBERON:0002037	84.61	gold quality
right lung	UBERON:0002167	84.51	gold quality
germinal epithelium of ovary	UBERON:0001304	84.46	gold quality
sural nerve	UBERON:0015488	84.37	gold quality
monocyte	CL:0000576	84.18	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-100618	yes	163.88
E-ANND-3	yes	5.86

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ETS1

miRNA regulators (miRDB)

131 targeting EMSY, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-302E	99.96	70.74	2669
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-335-3P	99.93	73.36	4958

Literature-anchored findings (GeneRIF, showing 35)

• The remarkable clinical overlap between sporadic EMSY amplification and familial BRCA2 deletion implicates a BRCA2 pathway in sporadic breast and ovarian cancer. (PMID:14651845)
• The crystal structure of residues 1-108 of EMSY at 2.0 A resolution is reported; the structure contains both the ENT domain and the HP1beta/BS69-binding motif. (PMID:15947784)
• report the crystal structure of the ENT domain of EMSY; dimerisation of EMSY mediated by the ENT domain could provide flexibility for it to bind two or more different substrates simultaneously (PMID:15978617)
• common genetic variation in EMSY does not appear to have a role in development of breast or ovarian cancer (PMID:16029503)
• These results support the hypothesis that EMSY overexpression can play a role in the genesis of human breast cancer. (PMID:16145051)
• Findings support the role of EMSY as a key oncogene within the 11q13 amplicon in ovarian cancer. (PMID:16236351)
• In an ovarian carcinoma cohort, RSF1 was amplified in 16% of the cases. It was correlated with serous histology and a worse prognosis. The 11q13 amplicon in ovarian cancer is likely driven by a cassette of genes rather than by a single oncogene. (PMID:18314909)
• gene copy numbers of EMSY in breast cancers (PMID:18393977)
• Data examine possible allelic imbalance in papillary thyroid cancer at EMSY, CAPN5, and PAK1, as candidate genes within 11q13.5-q14 region using a single nucleotide polymorphism-based analysis. (PMID:18787380)
• The identified components revealed factors involved in histone methylation and cell cycle control and include Ash2L, RbBP5, WDR5, HCF-1, DBC-1, and EMSY. (PMID:19131338)
• co-amplification of CCND1 and EMSY identified a poor prognostic subset of ER-positive tamoxifen-treated patients (PMID:19636701)
• Sporadic ovarian cancer shows overexpression of EMSY at a prevalence similar to that found in breast cancer and the overexpression is correlated with the protein level. (PMID:20349280)
• EMSY amplification does occur independently of CCND1 amplification in a minority of familial breast cancers, supporting its role as a possible breast cancer oncogene (PMID:21327470)
• EMSY amplification may mimic BRCA2 deficiency, at least by overriding RPA and PALB2, crippling the BRCA2/RAD51 complex at DNA-damage and replication/transcription sites (PMID:21409565)
• There are 2 independent signals, one in C11orf30 and the other in LRRC32, that are strongly associated with serum IgE levels. C11orf30-LRRC32 region may represent a common locus for atopic diseases via pathways involved in regulation of serum IgE levels (PMID:22070912)
• Akt1 regulates the interferon response through phosphorylation of the transcriptional repressor EMSY (PMID:22315412)
• EMSY is recruited to the miR-31 promoter by the DNA binding factor ETS-1, and it represses miR-31 transcription by delivering the H3K4me3 demethylase JARID1b/PLU-1/KDM5B (PMID:24582497)
• Univariate analysis revealed a significant positive association between EMSY expression and lymph node metastasis, larger tumor size, as well as a non-significant relation with increased risk of recurrence. (PMID:24641409)
• Eosinophilic esophagitis was associate with increased expression of C11orf30. (PMID:25407941)
• Our study demonstrated that EMSY played an oncogenic role in the progression of ovarian cancer cells and EMSY might be a promising target for the treatment (PMID:25510665)
• The association of higher levels of expression of C11orf30 may be involved in transcription repression of interferon-stimulated genes, and its association with sensitization to multiple allergens suggest that this locus is highly relevant for atopy. (PMID:25546184)
• The rs2155219 single nucleotide polymorphism was significantly associated with atopic dermatitis. (PMID:26464032)
• identify a novel substoichiometric interactor of the complex, transcription factor ZNF131, which recruits EMSY to a large number of active, H3K4me3 marked promoters. (PMID:26841866)
• Our results show a high frequency of EMSY amplification in MBC, thus pointing to a role of EMSY in the pathogenesis of this disease. EMSY amplification may be a new feature that might uncover underlying molecular pathways of MBCs and may allow for the identification of MBC subgroups with potential clinical implication for targeted therapeutic approaches. (PMID:27628328)
• EMSY overexpression impairs the repair of damaged DNA, suggesting that EMSY belongs to the family of BRCAness proteins (PMID:28099152)
• Altogether, 12 germline EMSY variants were observed in hereditary breast cancer and ovarian cancer families. Two alterations were located in the coding region, five alterations were intronic, and five alterations were located in the 3’untranslated region (UTR). Variant frequencies did not differ between cases and controls. These results suggest that the identified EMSY variants are likely neutral at the population level. (PMID:28738860)
• We conclude that EMSY and CCND1 work in collaboration and contribute to the pathogenesis of lung cancer. (PMID:28824300)
• This study identifies multiple novel loci as risk factors for PA and food allergy and establishes C11orf30 as a risk locus for both PA and food allergy. Multiple genes (C11orf30/EMSY, SKAP1, and CTNNA3) identified by this study are involved in epigenetic regulation of gene expression. (PMID:29030101)
• this study shows that EMSY is increased and activates TSLP & CCL5 expression in eosinophilic esophagitis (PMID:29663593)
• EMSY involvement in the DNA repair in ovarian cancer [review] (PMID:31154666)
• High EMSY expression was associated with superior survival in the high-grade serous ovarian carcinoma. (PMID:31154673)
• biopsy samples from patients with AD show greater EMSY staining in the nucleus, which is consistent with an increased functional effect of this transcriptional control protein. (PMID:31158401)
• Genetic variants of the C11orf30-LRRC32 region are associated with childhood asthma in the Chinese population. (PMID:31812328)
• Polymorphisms in the airway epithelium related genes CDHR3 and EMSY are associated with asthma susceptibility. (PMID:33213402)
• EMSY inhibits homologous recombination repair and the interferon response, promoting lung cancer immune evasion. (PMID:34963055)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	emsy	ENSDARG00000059059
mus_musculus	Emsy	ENSMUSG00000035401
rattus_norvegicus	Emsy	ENSRNOG00000015560
drosophila_melanogaster	CG15356	FBGN0031377

Protein

Protein identifiers

BRCA2-interacting transcriptional repressor EMSY — Q7Z589 (reviewed: Q7Z589)

All UniProt accessions (7): E9PMC9, E9PPE6, Q7Z589, H0YCS3, H0YDI4, H0YEP9, H0YET8

UniProt curated annotations — full annotation on UniProt →

Function. Regulator which is able to repress transcription, possibly via its interaction with a multiprotein chromatin remodeling complex that modifies the chromatin. Its interaction with BRCA2 suggests that it may play a central role in the DNA repair function of BRCA2. Mediates ligand-dependent transcriptional activation by nuclear hormone receptors.

Subunit / interactions. Homodimer. Interacts with the transactivation domain of BRCA2. Interacts with CBX1 (via chromoshadow domain). Interacts with ZMYND11. Does not interact with CBX3 or CBX5. Component of a nuclear receptor-mediated transcription complex composed of at least ZNF335, CCAR2 and EMSY; the complex stimulates the transcription of nuclear receptor target genes such as SOX9 and HOXA1. Within the complex interacts with CCAR2 and ZNF335. Components of this complex may associate with components of a histone methylation complex to form a complex at least composed of ZNF335, HCFC1, CCAR2, EMSY, MKI67, RBBP5, ASH2L and WDR5. Within this complex, interacts with ASH2L and RBBP5.

Subcellular location. Nucleus.

Post-translational modifications. O-glycosylated during cytokinesis at sites identical or close to phosphorylation sites, this interferes with the phosphorylation status.

Miscellaneous. Defects in EMSY may be a cause of sporadic breast cancer and higher-grade ovarian cancers. Overexpressed through amplification almost exclusively in sporadic breast cancer (13%) and higher-grade ovarian cancer (17%). Amplification is associated with worse survival, particularly in node-negative breast cancer, suggesting that it may be of prognostic value. Was named EMSY by PubMed:14651845 because the protein sequence contains the word ‘SISTER’, after the first author’s sister, who is a breast cancer nurse.

Isoforms (7)

UniProt ID	Names	Canonical?
Q7Z589-1	1	yes
Q7Z589-2	2
Q7Z589-3	3
Q7Z589-4	4
Q7Z589-5	5
Q7Z589-6	6
Q7Z589-7	7

RefSeq proteins (4): NP_001287871, NP_001287872, NP_001287873, NP_064578 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005491	ENT_dom	Domain
IPR033482	EMSY	Family
IPR036142	ENT_dom-like_sf	Homologous_superfamily

Pfam: PF03735

UniProt features (51 total): region of interest 8, splice variant 8, compositionally biased region 7, modified residue 7, glycosylation site 7, helix 7, strand 3, mutagenesis site 2, chain 1, domain 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
1UZ3	X-RAY DIFFRACTION	1.1
2FMM	X-RAY DIFFRACTION	1.8
1UTU	X-RAY DIFFRACTION	2

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7Z589-F1	42.40	0.07

Functional residue map

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

Post-translational modifications (7): 207, 209, 213, 238, 818, 821, 1136

Glycosylation sites (7): 228, 236, 271, 501, 506, 557, 1120

Mutagenesis-validated functional residues (2):

Position	Phenotype
100–102	abolishes interaction with cbx1.
106	abolishes interaction with zmynd11.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 171 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, E2F_Q4, MYOGENIN_Q6, E2F4DP1_01, TGCACTT_MIR519C_MIR519B_MIR519A, GGGTGGRR_PAX4_03, chr11q13, YY1_Q6, SP1_Q2_01, E2F1DP1_01, E2F1DP2_01, TCF11_01, HFH4_01, GOBP_DNA_DAMAGE_RESPONSE, TGACATY_UNKNOWN

GO Biological Process (4): DNA repair (GO:0006281), chromatin organization (GO:0006325), regulation of DNA-templated transcription (GO:0006355), DNA damage response (GO:0006974)

GO Molecular Function (2): identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (2): nucleoplasm (GO:0005654), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA metabolic process	1
DNA damage response	1
cellular component organization	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
cellular response to stress	1
protein binding	1
binding	1
nuclear lumen	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1494 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
EMSY	BRCA2	P51587	997
EMSY	ZMYND11	Q15326	890
EMSY	CBX1	P23197	808
EMSY	PHF12	Q96QT6	785
EMSY	LRRC32	Q14392	725
EMSY	SIN3A	Q96ST3	717
EMSY	KDM5A	P29375	717
EMSY	MORF4L1	Q9UBU8	709
EMSY	ZBTB35	P52739	699
EMSY	BRCA1	P38398	691
EMSY	PALB2	Q86YC2	662
EMSY	CAPN14	A8MX76	600
EMSY	SUDS3	Q9H7L9	566
EMSY	WDR36	Q8NI36	542
EMSY	GATAD1	Q8WUU5	525

IntAct

150 interactions, top by confidence:

A	B	Type	Score
HDAC1	CDK2AP1	psi-mi:“MI:0914”(association)	0.840
HDAC1	TNRC18	psi-mi:“MI:0914”(association)	0.790
RBBP4	CDK2AP1	psi-mi:“MI:0914”(association)	0.790
MORF4L1	SIN3B	psi-mi:“MI:0914”(association)	0.730
HDAC1	ZNF609	psi-mi:“MI:0914”(association)	0.730
RBBP7	HAT1	psi-mi:“MI:0914”(association)	0.730
KDM5A	SIN3B	psi-mi:“MI:0914”(association)	0.640
USP20	HIF1A	psi-mi:“MI:0914”(association)	0.630
CBX1	EMSY	psi-mi:“MI:0407”(direct interaction)	0.620
ZNF335	EMSY	psi-mi:“MI:0914”(association)	0.580
EMSY	ZNF646	psi-mi:“MI:0915”(physical association)	0.560
DDIT3	EMSY	psi-mi:“MI:0915”(physical association)	0.560
ZNF646	EMSY	psi-mi:“MI:0915”(physical association)	0.560
EMSY	BRAF	psi-mi:“MI:0915”(physical association)	0.550
EMSY	BRAF	psi-mi:“MI:2364”(proximity)	0.550
SIN3B	TNRC18	psi-mi:“MI:0914”(association)	0.530
BCOR	CBX4	psi-mi:“MI:0914”(association)	0.530
TMEM171	THAP12	psi-mi:“MI:0914”(association)	0.530

BioGRID (217): C11orf30 (Two-hybrid), C11orf30 (Two-hybrid), C11orf30 (Affinity Capture-RNA), C11orf30 (Affinity Capture-RNA), C11orf30 (Protein-peptide), C11orf30 (Affinity Capture-MS), C11orf30 (Affinity Capture-MS), C11orf30 (Affinity Capture-MS), C11orf30 (Proximity Label-MS), C11orf30 (Affinity Capture-MS), C11orf30 (Affinity Capture-MS), C11orf30 (Affinity Capture-MS), C11orf30 (Affinity Capture-MS), C11orf30 (Affinity Capture-MS), C11orf30 (Affinity Capture-MS)

ESM2 similar proteins: A1Z9E2, B0R0I6, B5DE69, G5ED89, O94842, P25425, P32519, P34333, P34447, Q02086, Q08CM4, Q09XV5, Q0IHV2, Q0P5K4, Q0V9U1, Q15723, Q28BL7, Q3TUF7, Q571G4, Q5E9U0, Q5F3U0, Q5R6A9, Q5RBN8, Q5RCV7, Q60775, Q641Z1, Q6DJM6, Q6IQU7, Q6MZP7, Q7Z589, Q7ZUV7, Q7ZX03, Q86NP2, Q8AYC1, Q8BIH0, Q8BMB0, Q8BU11, Q8CHI8, Q8IRW8, Q8WNV2

Diamond homologs: F4K2F0, Q08A72, Q7Z589, Q8BMB0, Q9C7C4, Q9FG29, Q7ZUV7

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
EMSY	“down-regulates activity”	BRCA2	binding
EMSY	“up-regulates activity”	ZMYND11	binding
EMSY	“up-regulates activity”	CBX1	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 167 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
Regulation of TP53 Activity through Acetylation	5	19.5×	8e-04
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known	5	12.8×	3e-03
Formation of WDR5-containing histone-modifying complexes	5	11.3×	4e-03
NOTCH1 Intracellular Domain Regulates Transcription	5	10.2×	7e-03
Transcriptional regulation by RUNX1	8	10.0×	3e-04
Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells)	8	10.0×	3e-04
Deactivation of the beta-catenin transactivating complex	5	10.0×	7e-03
Regulation of PTEN gene transcription	6	9.2×	3e-03

GO biological processes:

GO term	Partners	Fold	FDR
positive regulation of stem cell population maintenance	6	13.6×	6e-04
positive regulation of miRNA transcription	6	11.5×	1e-03
heterochromatin formation	6	10.1×	2e-03
chromatin remodeling	18	8.6×	1e-09
chromatin organization	9	5.9×	2e-03
DNA damage response	14	4.9×	2e-04

Disease & clinical

Cancer significance

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	11
Likely benign	2
Benign	7

Top pathogenic / likely-pathogenic (0)

SpliceAI

4850 predictions. Top by Δscore:

Variant	Effect	Δscore
11:76446898:AG:A	acceptor_gain	1.0000
11:76446899:GG:G	acceptor_gain	1.0000
11:76446978:G:T	donor_gain	1.0000
11:76447005:TTGG:T	donor_loss	1.0000
11:76447007:GG:G	donor_gain	1.0000
11:76447007:GGGTA:G	donor_loss	1.0000
11:76447008:GG:G	donor_gain	1.0000
11:76447009:G:GA	donor_loss	1.0000
11:76447009:G:GG	donor_gain	1.0000
11:76447010:T:G	donor_loss	1.0000
11:76447422:G:GT	donor_gain	1.0000
11:76451856:A:AG	acceptor_gain	1.0000
11:76451857:G:GA	acceptor_gain	1.0000
11:76451857:GA:G	acceptor_gain	1.0000
11:76451950:GTTCT:G	donor_gain	1.0000
11:76451951:TTCTT:T	donor_gain	1.0000
11:76451958:GTAA:G	donor_loss	1.0000
11:76453312:A:AG	acceptor_gain	1.0000
11:76453313:G:GG	acceptor_gain	1.0000
11:76453313:GC:G	acceptor_gain	1.0000
11:76453381:GCACA:G	donor_gain	1.0000
11:76453385:A:AG	donor_gain	1.0000
11:76453385:A:G	donor_gain	1.0000
11:76453389:G:GG	donor_gain	1.0000
11:76458179:TTA:T	acceptor_loss	1.0000
11:76458180:TA:T	acceptor_loss	1.0000
11:76458181:A:AG	acceptor_gain	1.0000
11:76458181:AG:A	acceptor_loss	1.0000
11:76458182:G:GT	acceptor_gain	1.0000
11:76458182:GT:G	acceptor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000042123 (11:76551221 C>T), RS1000065390 (11:76477588 T>G), RS1000073454 (11:76456962 G>A), RS1000119090 (11:76500733 G>A,C), RS1000127803 (11:76450731 A>G), RS1000152216 (11:76551716 C>G), RS1000181347 (11:76495470 C>T), RS1000210394 (11:76522548 T>G), RS1000263958 (11:76450938 T>C), RS1000283812 (11:76443511 C>G), RS1000307427 (11:76483695 C>G), RS1000362544 (11:76468220 C>G), RS1000385734 (11:76443333 T>C), RS1000419380 (11:76537702 C>A,T), RS1000439362 (11:76483342 C>A)

Disease associations

OMIM: gene MIM:608574 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

69 associations (top):

Study	Trait	p-value
GCST000207_24	Crohn’s disease	1.000000e-09
GCST000374_1	Atopic dermatitis	8.000000e-10
GCST000879_65	Crohn’s disease	6.000000e-13
GCST001303_1	IgE grass sensitization	1.000000e-08
GCST001310_4	Allergic rhinitis	4.000000e-08
GCST001709_3	Atopic dermatitis	3.000000e-06
GCST002083_26	Self-reported allergy	2.000000e-19
GCST002084_9	Allergic sensitization	1.000000e-18
GCST002100_4	Atopic dermatitis	4.000000e-13
GCST002527_8	Eosinophilic esophagitis	4.000000e-07
GCST002697_3	Eosinophilic esophagitis	4.000000e-11
GCST002740_2	Inflammatory skin disease	3.000000e-12
GCST003180_6	Atopic march	2.000000e-15
GCST003184_23	Atopic dermatitis	3.000000e-09
GCST003184_34	Atopic dermatitis	5.000000e-13
GCST003854_11	Gut microbiota (functional units)	1.000000e-07
GCST003854_14	Gut microbiota (functional units)	5.000000e-07
GCST003854_48	Gut microbiota (functional units)	3.000000e-06
GCST003854_50	Gut microbiota (functional units)	3.000000e-06
GCST003987_7	Asthma	1.000000e-16
GCST003990_6	Allergy	1.000000e-14
GCST004600_98	Eosinophil percentage of white cells	3.000000e-23
GCST004606_205	Eosinophil count	7.000000e-26
GCST004617_137	Eosinophil percentage of granulocytes	4.000000e-21
GCST004861_1	Itch intensity from mosquito bite	2.000000e-09
GCST004979_1	Food allergy	9.000000e-11
GCST005212_17	Asthma	2.000000e-14
GCST005975_19	Eosinophil count	1.000000e-08
GCST006038_1	Food allergy	8.000000e-11
GCST006038_3	Food allergy	6.000000e-11

EFO canonical traits (16, from GWAS)

EFO ID	Trait name
EFO:0005298	allergic sensitization measurement
EFO:0007755	atopic march
EFO:0007874	gut microbiome measurement
EFO:0007991	eosinophil percentage of leukocytes
EFO:0004842	eosinophil count
EFO:0007996	eosinophil percentage of granulocytes
EFO:0008377	mosquito bite reaction itch intensity measurement
EFO:0007016	food allergy measurement
EFO:0007017	peanut allergy measurement
EFO:0006335	systolic blood pressure
EFO:0005763	pulse pressure measurement
EFO:0009941	Inhalant adrenergic use measurement
EFO:0009942	Glucocorticoid use measurement
EFO:0009943	Antihistamine use measurement
EFO:1002011	adult onset asthma
EFO:0004612	high density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs7927894	EMSY		0.00	0

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, decreases methylation, increases expression	8
trichostatin A	affects cotreatment, decreases expression	3
entinostat	decreases expression, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
TAK-243	increases sumoylation	1
methylmercuric chloride	decreases expression	1
arsenite	decreases reaction, affects binding	1
butyraldehyde	decreases expression	1
coumarin	affects phosphorylation	1
pentanal	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	increases methylation	1
jinfukang	decreases expression	1
(+)-JQ1 compound	increases expression	1
Vorinostat	increases expression	1
Atrazine	increases expression	1
Cadmium	decreases expression, increases abundance	1
Caffeine	decreases phosphorylation	1
Diazinon	increases methylation	1
Doxorubicin	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	decreases expression	1
Gallic Acid	decreases expression	1
Methyl Methanesulfonate	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_SF98	HAP1 C11orf30 (-) 1	Cancer cell line	Male
CVCL_SF99	HAP1 C11orf30 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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