SOX1

Summary

SOX1 (SRY-box transcription factor 1, HGNC:11189) is a protein-coding gene on chromosome 13q34, encoding Transcription factor SOX-1 (O00570). Transcriptional activator.

This intronless gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional activator after forming a protein complex with other proteins. In mice, a similar protein regulates the gamma-crystallin genes and is essential for lens development.

Source: NCBI Gene 6656 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 87 total
• MANE Select transcript: NM_005986

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11189
Approved symbol	SOX1
Name	SRY-box transcription factor 1
Location	13q34
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000182968
Ensembl biotype	protein_coding
OMIM	602148
Entrez	6656

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000330949

RefSeq mRNA: 1 — MANE Select: NM_005986 NM_005986

CCDS: CCDS9523

Canonical transcript exons

ENST00000330949 — 1 exons

Exon	Start	End
ENSE00001329627	112067149	112071706

Expression profiles

Bgee: expression breadth broad, 59 present calls, max score 95.70.

FANTOM5 (CAGE): breadth broad, TPM avg 4.4767 / max 361.4598, expressed in 246 samples.

FANTOM5 promoters (11 alternative TSS)

Promoter ID	TPM avg	Samples expressed
136130	3.1603	230
136133	0.5473	139
136134	0.2729	110
136138	0.0940	44
136131	0.0780	50
136139	0.0643	34
136137	0.0593	36
136135	0.0578	33
136136	0.0514	17
136132	0.0485	26

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	95.70	gold quality
ganglionic eminence	UBERON:0004023	89.99	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.23	gold quality
secondary oocyte	CL:0000655	80.69	gold quality
buccal mucosa cell	CL:0002336	77.66	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	76.91	gold quality
endothelial cell	CL:0000115	68.62	silver quality
ileal mucosa	UBERON:0000331	68.22	silver quality
hypothalamus	UBERON:0001898	67.04	gold quality
cortical plate	UBERON:0005343	66.85	gold quality
amygdala	UBERON:0001876	66.77	gold quality
Brodmann (1909) area 46	UBERON:0006483	66.61	gold quality
entorhinal cortex	UBERON:0002728	66.37	silver quality
nucleus accumbens	UBERON:0001882	65.73	gold quality
temporal lobe	UBERON:0001871	65.70	gold quality
prefrontal cortex	UBERON:0000451	65.32	gold quality
primary visual cortex	UBERON:0002436	65.28	gold quality
neocortex	UBERON:0001950	65.09	gold quality
caudate nucleus	UBERON:0001873	65.01	gold quality
middle temporal gyrus	UBERON:0002771	64.74	silver quality
cerebral cortex	UBERON:0000956	64.66	gold quality
postcentral gyrus	UBERON:0002581	64.61	silver quality
frontal cortex	UBERON:0001870	64.50	gold quality
anterior cingulate cortex	UBERON:0009835	64.49	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	64.23	gold quality
superior frontal gyrus	UBERON:0002661	63.88	gold quality
Brodmann (1909) area 9	UBERON:0013540	63.34	gold quality
Brodmann (1909) area 23	UBERON:0013554	63.19	silver quality
pancreatic ductal cell	CL:0002079	62.23	silver quality
putamen	UBERON:0001874	62.02	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.81

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

3 targets.

Target	Regulation
HES1	Repression
NEUROG1	Activation
PAX6	Unknown

Upstream regulators (CollecTRI, top): NANOG

miRNA regulators (miRDB)

79 targeting SOX1, 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-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-570-3P	99.96	72.41	4910
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-4753-3P	99.90	71.03	3786

Literature-anchored findings (GeneRIF, showing 37)

• Sox1 works through multiple independent pathways to promote neuronal cell fate determination and differentiation. (PMID:15110721)
• The detection of SOX1 antibodies in patients with Lambert-Eaton myasthenic syndrome (LEMS) predicts the presence of small cell lung cancer and may be used to follow more closely those LEMS patients with no evidence of cancer at the initial workup. (PMID:18032743)
• expression of Sox1, Sox2 and Sox9 was detected at the mRNA level in both foetal and adult cerebellum samples; Sox1, Sox2 and Sox9 expression was detected in the Purkinje cell layer of the adult cerebellum (PMID:19061938)
• Data show that SOX antibodies have diagnostic value in discriminating SCLC-LEMS from nontumor LEMS, but have no relation to survival in patients with SCLC. (PMID:19667272)
• Supratentorial PNETs expressed significantly higher levels of SOX2, NOTCH1, ID1, and ASCL-1 transcripts. (PMID:20515335)
• Transgenic interneuron diversification in the p2 domain is more complex than previously thought and directly implicates Sox1 in this process. (PMID:20844123)
• These findings suggest that SOX1 might function as an important tumor suppressor during the development of hepatocellular carcinoma. (PMID:22767186)
• The level and timing of SOX1 expression affects neural induction as well as neural lineage. (PMID:22860217)
• Concomitant epigenetic silencing of SOX1 and SFRPs through promoter hypermethylation is frequent in hepatocellular carcinoma, and this might contribute to abnormal activation of canonical Wnt signal pathway. (PMID:23215838)
• SOX1 antibodies are a specific marker for SCLC-LEMS but they are also found in SCLC patients without paraneoplastic neurological syndromes (PMID:23278580)
• Taken together, these data suggest that SOX1 can function as a tumor suppressor partly by interfering with Wnt/beta-catenin signaling in cervical cancer. (PMID:23927962)
• Inactivation of SOX1 gene is associated with cisplatin resistance in human non-small cell lung cancer cell. (PMID:23994634)
• we successfully established a three-step inducing protocol to derive Neural stem cells from adipose-derived mesenchymal stem cells with high purity by Sox1 activation (PMID:24138016)
• The methylation index of SOX1 recovered from scrapings of uterine cervix adenocarcinomas is significantly higher than in normal controls. (PMID:24407576)
• PAX1 and SOX1 DNA methylation correlate with a cervical intraepithelial neoplasia diagnosis. (PMID:24799352)
• SOX1 decreases the expression of beta-catenin in a proteasome-independent manner. (PMID:25427424)
• Our results suggest that SOX1 is epigenetically silenced in the majority of NSCLC and restoration of SOX1 inhibited cell migration by regulating actin cytoskeletal remodeling in NSCLC. (PMID:25613070)
• SOX 1 suppressed cell growth and invasion in Tu212 cells by inhibiting Wnt pathway, and the anti-tumor effect of SOX 1 could be weakened by SOX 2, which may be a potential molecular basis for clinical treatment of laryngeal squamous cell carcinoma . (PMID:26040764)
• downregulation of SOX-1 was correlated with poor prognosis and tumor development in hepatocellular carcinoma. (PMID:26191244)
• The analysis identified a signaling axis between FGF signaling and the transcription factor Sox1, which is preferentially expressed in stem- and mesenchymal-like breast cancers. (PMID:26365194)
• The results of the SRY gene amplification of plasma DNA from pregnant women was the same as that of the amniocyte DNA (PMID:26782455)
• Taken together, these data suggest that SOX1 can function as a tumor suppressor partly by interfering with Wnt/beta-catenin signaling in breast cancer. (PMID:27206213)
• The sensitivity was found to be 62% and 83% for DAPK1 and SOX1, respectively, when analyzed separately in the singleplex assay, but increased to 90% in the multiplex assay when either or both of the SOX1 and the DAPK1 gene promoters showed methylation. (PMID:27452040)
• the under-expression of SOX1 was associated significantly with SALL4 overexpression. This study was the first to evaluate SOX1 underexpression and its association with poor prognosis in esophageal squamous cell carcinoma. (PMID:27576349)
• Data show that high levels of SRY-box transcription factor 1 (SOX1) observed in a subset of patients correlate with lower overall survival, and suggest SOX1 as a potential target in the glioma stem cells (GSCs) population in glioblastoma. (PMID:28425506)
• aberrant methylation of SOX1 and VIM promoters may be potential biomarkers for noninvasive detection of hepatocellular carcinoma and metastasis (PMID:28592127)
• SOX1 overlapping transcript was found to be highly expressed in differentiated neural stem cells across different time points of differentiation, and its expression correlated with SOX1 gene expression. (PMID:28674729)
• a methylation-specific expression gene of cervical adenocarcinoma (PMID:31567982)
• The methylation levels ofPAX1, SOX1 and ZNF582 genes were all higher in cancer tissues. (PMID:31629253)
• SOX1 promotes differentiation of nasopharyngeal carcinoma cells by activating retinoid metabolic pathway. (PMID:32382038)
• In Silico Identification of SOX1 Post-Translational Modifications Highlights a Shared Protein Motif. (PMID:33202879)
• SOX1 and PAX1 Are Hypermethylated in Cervical Adenocarcinoma and Associated with Better Prognosis. (PMID:33376722)
• Discordant SOX-1 antibodies results in paraneoplastic Lambert-Eaton syndrome diagnosis by the clinical laboratory. (PMID:34450126)
• Study of the influence of NGF-beta gene overexpression in human mesenchymal stem cells on the expression level of SOX1 and neural pathway genes. (PMID:35348963)
• Transcriptional Circuitry of NKX2-1 and SOX1 Defines an Unrecognized Lineage Subtype of Small-Cell Lung Cancer. (PMID:35848993)
• Is hypermethylation of SOX1 gene an independent prognostic marker in surgically resected non-small cell lung cancer? (PMID:36412431)
• A similar protein directly regulates the gamma-crystallin genes and is essential for lens development in mice. (PMID:9512512)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	sox1b	ENSDARG00000008131
danio_rerio	sox1a	ENSDARG00000069866
mus_musculus	Sox1	ENSMUSG00000096014
rattus_norvegicus	Sox1	ENSRNOG00000064976
drosophila_melanogaster	SoxN	FBGN0029123

Paralogs (20): SOX8 (ENSG00000005513), SOX30 (ENSG00000039600), SOX10 (ENSG00000100146), SOX6 (ENSG00000110693), SOX4 (ENSG00000124766), SOX21 (ENSG00000125285), SOX9 (ENSG00000125398), SOX15 (ENSG00000129194), SOX5 (ENSG00000134532), SOX3 (ENSG00000134595), SOX13 (ENSG00000143842), SOX17 (ENSG00000164736), SOX14 (ENSG00000168875), SOX7 (ENSG00000171056), SOX11 (ENSG00000176887), SOX12 (ENSG00000177732), CFAP65 (ENSG00000181378), SOX2 (ENSG00000181449), SRY (ENSG00000184895), SOX18 (ENSG00000203883)

Protein

Protein identifiers

Transcription factor SOX-1 — O00570 (reviewed: O00570)

All UniProt accessions (1): O00570

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional activator. May function as a switch in neuronal development. Keeps neural cells undifferentiated by counteracting the activity of proneural proteins and suppresses neuronal differentiation.

Subcellular location. Nucleus.

Tissue specificity. Mainly expressed in the developing central nervous system.

Domain organisation. The 9aaTAD motif is a transactivation domain present in a large number of yeast and animal transcription factors.

RefSeq proteins (1): NP_005977* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009071	HMG_box_dom	Domain
IPR022097	SOX_fam	Family
IPR036910	HMG_box_dom_sf	Homologous_superfamily
IPR050140	SRY-related_HMG-box_TF-like	Family

Pfam: PF00505, PF12336

UniProt features (11 total): sequence conflict 4, region of interest 2, compositionally biased region 2, chain 1, DNA-binding region 1, short sequence motif 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O00570-F1	59.29	0.23

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-9823739	Formation of the anterior neural plate
R-HSA-9832991	Formation of the posterior neural plate
R-HSA-1266738	Developmental Biology
R-HSA-9758941	Gastrulation

MSigDB gene sets: 140 (showing top): GOBP_SPINAL_CORD_DEVELOPMENT, GOBP_FOREBRAIN_NEURON_DEVELOPMENT, GOBP_RESPONSE_TO_PEPTIDE, TTTGTAG_MIR520D, GOBP_NEUROGENESIS, GOBP_CELL_DIFFERENTIATION_IN_SPINAL_CORD, GOBP_DORSAL_VENTRAL_PATTERN_FORMATION, GOBP_FOREBRAIN_DEVELOPMENT, GOBP_FOREBRAIN_GENERATION_OF_NEURONS, GOBP_VENTRAL_SPINAL_CORD_DEVELOPMENT, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, DAWSON_METHYLATED_IN_LYMPHOMA_TCL1, chr13q34, GOBP_NEURON_FATE_SPECIFICATION, GOBP_CENTRAL_NERVOUS_SYSTEM_NEURON_DIFFERENTIATION

GO Biological Process (15): negative regulation of transcription by RNA polymerase II (GO:0000122), lens morphogenesis in camera-type eye (GO:0002089), chromatin organization (GO:0006325), regulation of DNA-templated transcription (GO:0006355), brain development (GO:0007420), ventral spinal cord interneuron specification (GO:0021521), forebrain neuron development (GO:0021884), neuron differentiation (GO:0030182), positive regulation of transcription by RNA polymerase II (GO:0045944), regulation of oligodendrocyte differentiation (GO:0048713), interneuron migration (GO:1904936), cellular response to leukemia inhibitory factor (GO:1990830), neuron migration (GO:0001764), forebrain neuron differentiation (GO:0021879), forebrain development (GO:0030900)

GO Molecular Function (7): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), protein binding (GO:0005515), sequence-specific DNA binding (GO:0043565)

GO Cellular Component (2): chromatin (GO:0000785), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Gastrulation	2
Developmental Biology	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of transcription by RNA polymerase II	3
RNA polymerase II transcription regulatory region sequence-specific DNA binding	3
transcription by RNA polymerase II	2
generation of neurons	2
negative regulation of DNA-templated transcription	1
lens development in camera-type eye	1
anatomical structure morphogenesis	1
camera-type eye morphogenesis	1
cellular component organization	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
central nervous system development	1
animal organ development	1
head development	1
neuron fate specification	1
cell fate specification involved in pattern specification	1
ventral spinal cord interneuron fate commitment	1
forebrain neuron differentiation	1
central nervous system neuron development	1
cell differentiation	1
positive regulation of DNA-templated transcription	1
regulation of glial cell differentiation	1
oligodendrocyte differentiation	1
neuron migration	1
cellular response to cytokine stimulus	1
response to leukemia inhibitory factor	1
cell migration	1
forebrain generation of neurons	1
central nervous system neuron differentiation	1
brain development	1
anatomical structure development	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription activator activity	1
positive regulation of transcription by RNA polymerase II	1
nucleic acid binding	1
transcription cis-regulatory region binding	1

Protein interactions and networks

STRING

2098 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SOX1	PAX6	P26367	884
SOX1	NEUROG2	Q9H2A3	862
SOX1	NES	P48681	791
SOX1	OTX2	P32243	786
SOX1	LGI1	O95970	760
SOX1	NANOG	Q9H9S0	735
SOX1	ZIC4	Q8N9L1	734
SOX1	POU5F1	P31359	733
SOX1	KLF4	P78338	732
SOX1	AMPH	P49418	723
SOX1	PNMA2	Q9UL42	720
SOX1	DPYSL5	Q9BPU6	694
SOX1	FOXA2	Q9Y261	689
SOX1	BIN1	O00499	667
SOX1	RCVRN	P35243	663

IntAct

8 interactions, top by confidence:

A	B	Type	Score
SOX5	SOX1	psi-mi:“MI:0914”(association)	0.530
SOX1	STAT3	psi-mi:“MI:0915”(physical association)	0.400
STAT3	SOX1	psi-mi:“MI:0915”(physical association)	0.400
CIAO1	SOX1	psi-mi:“MI:0914”(association)	0.350
SFMBT1	SOX1	psi-mi:“MI:0914”(association)	0.350
LIN28A	MEX3A	psi-mi:“MI:0914”(association)	0.350

BioGRID (9): CTNNB1 (Affinity Capture-Western), SOX1 (Affinity Capture-Western), SOX1 (Affinity Capture-MS), SOX1 (Affinity Capture-MS), CIAO1 (Affinity Capture-MS), SFMBT1 (Affinity Capture-MS), SOX1 (Affinity Capture-MS), SOX1 (Affinity Capture-MS), SOX1 (Affinity Capture-MS)

ESM2 similar proteins: A2TED3, O00570, O57401, O95409, P06602, P07548, P09085, P14734, P16241, P20264, P22544, P23441, P23757, P31361, P32027, P32182, P32242, P35583, P39768, P40764, P41225, P43241, P43698, P43699, P48430, P48431, P48432, P50220, P53783, P53784, P54231, P54269, P56224, P80205, Q04649, Q07687, Q24255, Q24533, Q2PG84, Q2Z1R2

Diamond homologs: A2TED3, A4QNG3, B0ZTE1, B0ZTE2, O00570, O42569, O57401, O60248, O95416, P36389, P36390, P36393, P36395, P36396, P41225, P43267, P47792, P48046, P48430, P48431, P48432, P48433, P51501, P53783, P53784, P54231, P55863, P61259, Q04892, Q05066, Q20201, Q21305, Q24533, Q28447, Q28778, Q28783, Q28798, Q2PG84, Q2Z1R2, Q32PP9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	74
Likely benign	9
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

24 predictions. Top by Δscore:

Variant	Effect	Δscore
13:112069077:TGAGA:T	acceptor_gain	0.5100
13:112068060:G:GG	donor_gain	0.4900
13:112068051:G:GT	donor_gain	0.4800
13:112068055:G:GT	donor_gain	0.4800
13:112068280:G:GT	donor_gain	0.4700
13:112068059:A:AG	donor_gain	0.4500
13:112069078:GAGAC:G	acceptor_gain	0.4400
13:112069079:AGAC:A	acceptor_gain	0.3500
13:112069078:G:GC	acceptor_gain	0.3400
13:112069076:TTGAG:T	acceptor_gain	0.3300
13:112068015:G:GG	donor_gain	0.3000
13:112068014:A:AG	donor_gain	0.2900
13:112069296:TCC:T	donor_gain	0.2700
13:112068954:A:C	acceptor_gain	0.2600
13:112069011:G:C	acceptor_gain	0.2600
13:112069107:C:CA	acceptor_gain	0.2600
13:112069075:CTTGA:C	acceptor_gain	0.2500
13:112069080:G:T	acceptor_gain	0.2500
13:112068448:GGC:G	donor_gain	0.2300
13:112067932:A:AG	donor_gain	0.2100
13:112069009:C:A	acceptor_gain	0.2100
13:112069107:CGG:C	acceptor_gain	0.2000
13:112069884:ACTGC:A	acceptor_gain	0.2000
13:112069888:C:CA	acceptor_gain	0.2000

AlphaMissense

2508 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:112067810:T:A	V51D	1.000
13:112067812:A:G	K52E	1.000
13:112067813:A:T	K52I	1.000
13:112067814:A:C	K52N	1.000
13:112067814:A:T	K52N	1.000
13:112067815:C:G	R53G	1.000
13:112067815:C:T	R53W	1.000
13:112067816:G:A	R53Q	1.000
13:112067816:G:T	R53L	1.000
13:112067818:C:A	P54T	1.000
13:112067818:C:G	P54A	1.000
13:112067818:C:T	P54S	1.000
13:112067819:C:A	P54H	1.000
13:112067819:C:G	P54R	1.000
13:112067819:C:T	P54L	1.000
13:112067822:T:A	M55K	1.000
13:112067822:T:C	M55T	1.000
13:112067822:T:G	M55R	1.000
13:112067823:G:A	M55I	1.000
13:112067823:G:C	M55I	1.000
13:112067823:G:T	M55I	1.000
13:112067824:A:C	N56H	1.000
13:112067824:A:G	N56D	1.000
13:112067824:A:T	N56Y	1.000
13:112067825:A:C	N56T	1.000
13:112067825:A:G	N56S	1.000
13:112067825:A:T	N56I	1.000
13:112067826:C:A	N56K	1.000
13:112067826:C:G	N56K	1.000
13:112067827:G:A	A57T	1.000

dbSNP variants (sampled 300 via entrez): RS1000152600 (13:112065753 A>C,G), RS1000181398 (13:112069014 A>G), RS1000380437 (13:112066969 G>A,C), RS1001138683 (13:112067770 G>A,T), RS1001554326 (13:112066933 G>A), RS1001735491 (13:112071030 A>ATAATGC), RS1001889852 (13:112067754 GGGCGGA>G,GGGCGGAGGCGGA), RS1002026780 (13:112070572 A>T), RS1002092970 (13:112071763 G>A), RS1002187939 (13:112071254 GCA>G), RS1002547585 (13:112069086 T>G), RS1002562111 (13:112066079 T>C), RS1002784606 (13:112070101 C>G), RS1003649075 (13:112069289 A>C), RS1004349200 (13:112067552 C>A,T)

Disease associations

OMIM: gene MIM:602148 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): epilepsy (MONDO:0005027)

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST002613_4	Chronic mucus hypersecretion	8.000000e-06
GCST002875_141	Diisocyanate-induced asthma	6.000000e-06
GCST002935_27	Lead levels	9.000000e-06
GCST003993_3	Menarche (age at onset)	1.000000e-08
GCST007576_68	Chronotype	4.000000e-09

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0005673	chronic mucus hypersecretion
EFO:0006995	response to diisocyanate
EFO:0004703	age at menarche
EFO:0008328	chronotype measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D004827	Epilepsy	C10.228.140.490

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, decreases expression, increases methylation	7
trichostatin A	affects cotreatment, decreases expression, affects expression	5
Paraquat	affects expression, affects reaction, decreases expression, increases expression	4
bisphenol A	decreases expression, increases methylation, decreases reaction, affects expression, affects reaction	3
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression, decreases expression	3
Tretinoin	decreases expression	3
mercuric bromide	decreases expression, affects cotreatment	2
LDN 193189	affects cotreatment, increases expression	2
Vorinostat	affects cotreatment, decreases expression	2
Arsenic	affects expression, increases methylation	2
Benzo(a)pyrene	affects methylation, increases expression	2
Diethylhexyl Phthalate	increases abundance, increases methylation, decreases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
methylmercuric chloride	decreases expression	1
decabromobiphenyl ether	increases expression	1
ascorbate-2-phosphate	affects binding, affects cotreatment, decreases expression	1
mono-(2-ethylhexyl)phthalate	increases abundance, increases methylation	1
sodium arsenite	increases expression	1
tetrabromobisphenol A	increases expression	1
4-(2-(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-naphthalenyl)-1-propenyl)benzoic acid	affects cotreatment, decreases expression	1
entinostat	decreases expression	1
Chir 99021	affects cotreatment, decreases expression, affects binding	1
2,2’,4,4’-tetrabromodiphenyl ether	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
XAV939	affects binding, affects cotreatment, decreases expression	1
3-(4-pyridyl)-1H-indole	affects cotreatment, decreases expression	1
Arsenic Trioxide	decreases expression	1
Alitretinoin	decreases expression	1
Ascorbic Acid	decreases expression, affects binding, affects cotreatment	1
Dexamethasone	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00004637	PHASE4	COMPLETED	Double-Blind, Placebo-Controlled Trial of Vitamin E as Add-on Therapy for Children With Epilepsy
NCT00043914	PHASE4	COMPLETED	Measurement Of Serum Levels Of Two Antiepileptic Drugs During Conversion In Patients With Epilepsy
NCT00132223	PHASE4	UNKNOWN	Effects on the Diagnostic Accuracy of Magnetic Imaging Angiographies of the Supra-Aortic Vessels by Three Different Magnetic Resonance Contrast Agents in Patients
NCT00133081	PHASE4	UNKNOWN	Study to Improve the Treatment of Epilepsy (SITE)
NCT00137709	PHASE4	UNKNOWN	Hormone Profiles in Adults With Newly Diagnosed Epilepsy
NCT00154076	PHASE4	COMPLETED	A Multicenter Comparative Trial of Zonisamide and Topiramate as Initial Monotherapy in Untreated Epilepsies
NCT00165828	PHASE4	TERMINATED	Efficacy and Safety of an add-on Treatment With Zonisamide in Adults With Focal Epileptic Seizures With or Without Secondary Generalization
NCT00181116	PHASE4	COMPLETED	Levetiracetam for Benign Rolandic Epilepsy
NCT00207935	PHASE4	COMPLETED	Use of Sustained Release Antiepileptic Medication (Depakote® ER) for Pediatric Epilepsy in a Mental Retardation/Developmental Disorder Population
NCT00215592	PHASE4	COMPLETED	Open Label, Zonegran (Zonisamide) In Partial Onset Seizures
NCT00266604	PHASE4	COMPLETED	A Study to Evaluate the Dosing, Effectiveness and Safety of Topiramate for the Treatment of Epilepsy
NCT00288639	PHASE4	COMPLETED	Lyrica (Pregabalin) Administered as an Add-on Therapy for Partial Seizures (LEADER).
NCT00312676	PHASE4	UNKNOWN	Compare Tolerability of an Overnight Switch to Gradual Switch Between Two Different Forms of Depakote
NCT00323947	PHASE4	COMPLETED	Methylphenidate for Treating Attention Deficit Hyperactivity Disorder in Children With Both ADHD and Epilepsy
NCT00385411	PHASE4	COMPLETED	Study of Valproate in Young Patients Suffering From Epilepsy
NCT00522418	PHASE4	TERMINATED	Study Comparing Best Medical Practice With or Without VNS Therapy in Pharmacoresistant Partial Epilepsy Patients
NCT00537940	PHASE4	COMPLETED	Comparative Study Of Pregabalin And Gabapentin As Adjunctive Therapy In Subjects With Partial Seizures
NCT00552526	PHASE4	UNKNOWN	Ketogenic Diet vs.Antiepileptic Drug Treatment in Drug Resistant Epilepsy
NCT00564915	PHASE4	COMPLETED	RCT of the Efficacy of the Ketogenic Diet in the Treatment of Epilepsy
NCT00571155	PHASE4	COMPLETED	Trial of Levetiracetam in Patients With Primary Brain Tumors and Symptomatic Seizures Who Undergo Surgery
NCT00572195	PHASE4	COMPLETED	RNS® System LTT Study
NCT00610532	PHASE4	TERMINATED	Evaluating the Transporter Protein Inhibitor Probenecid In Patients With Epilepsy
NCT00630357	PHASE4	COMPLETED	Trial to Evaluate the Safety and Efficacy of Keppra After Conversion to Mono-therapy in Subjects With Partial Epilepsy
NCT00630630	PHASE4	COMPLETED	Study on Safety and Efficacy of Levetiracetam in the Adjunctive Treatment of Female Subjects With C1 Catamenial Epilepsy
NCT00630968	PHASE4	COMPLETED	S.K.A.T.E.: Safety of Keppra as Adjunctive Therapy in Epilepsy
NCT00631150	PHASE4	COMPLETED	A Phase IV-Pharmacovigilance Study of Keppra Greece - S.K.A.T.E.: Safety of Keppra as Adjunctive Therapy in Epilepsy
NCT00659958	PHASE4	COMPLETED	ZAGAL Study: Evaluating Effectiveness and Tolerability of Zonisamide as Adjunctive Therapy in Patients With Partial Onset Seizures Treated With Two Antiepileptic Drugs
NCT00713622	PHASE4	COMPLETED	Comparing The Effect On Cognition Of Adjunctive Therapy With Zonisamide Versus Sodium Valproate
NCT00807989	PHASE4	COMPLETED	The Efficacy and Safety of Low Dose Combination of LTG and VPA Compared to CBZ Monotherapy
NCT00832884	PHASE4	COMPLETED	The Safety of Intravenous Lacosamide
NCT00869622	PHASE4	COMPLETED	Antiepileptic Drugs and Osteoporotic Prevention Trial
NCT00896987	PHASE4	COMPLETED	Lamotrigine Cognitive Function Study in Adult Untreated Epilepsies
NCT00952081	PHASE4	COMPLETED	A Pilot Study to Evaluate Efficacy and Safety of Clevidipine in Neurosurgical Patients
NCT01118455	PHASE4	TERMINATED	Trial to Assess Vagus Nerve Stimulation Therapy vs. Anti-Epileptic Drug (AED) Treatment in Children With Refractory Seizures
NCT01127165	PHASE4	COMPLETED	Low and High Dose Zonisamide in Children as Monotherapy
NCT01127256	PHASE4	COMPLETED	Comparative Study of Zonisamide and Carbamazepine as an Initial Monotherapy: Efficacy and Safety Evaluation
NCT01140867	PHASE4	COMPLETED	Open-label, Multi-center Trial of Zonisamide as Adjunctive Therapy in Patients With Uncontrolled Partial Epilepsy
NCT01175954	PHASE4	COMPLETED	Cognitive and Behavioral Effects of Lacosamide
NCT01229735	PHASE4	COMPLETED	Levetiracetam Versus Topiramate as Adjunctive Therapy to Evaluate Efficacy and Safety in Subjects With Refractory Partial Onset Seizures
NCT01244724	PHASE4	TERMINATED	Lexapro for Major Depression in Patients With Epilepsy