Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	6658
Gene name Gene Name - the full gene name approved by the HGNC.	SRY-box transcription factor 3
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	SOX3
Synonyms (NCBI Gene) Gene synonyms aliases	GHDX, MRGH, PHP, PHPX, SOXB
Chromosome Chromosome number	X
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	Xq27.1
Summary Summary of gene provided in NCBI Entrez Gene.	This 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 regulator after for

Show/Hide all(2)

SNP ID	Visualize variation	Clinical significance	Consequence
rs200361128	C>G	Benign, likely-pathogenic, likely-benign	Missense variant, coding sequence variant
rs1556518231	G>T	Likely-pathogenic	Missense variant, coding sequence variant

Show/Hide all(88)

miRTarBase ID	miRNA	Experiments	Reference
MIRT030124	hsa-miR-26b-5p	Microarray	19088304
MIRT449676	hsa-miR-548as-3p	PAR-CLIP	22100165
MIRT449674	hsa-miR-548e-5p	PAR-CLIP	22100165
MIRT449675	hsa-miR-100-3p	PAR-CLIP	22100165
MIRT449673	hsa-miR-570-3p	PAR-CLIP	22100165
MIRT733358	hsa-miR-483-3p	Luciferase reporter assay, qRT-PCR, Western blotting	32210581
MIRT449676	hsa-miR-548as-3p	PAR-CLIP	22100165
MIRT449674	hsa-miR-548e-5p	PAR-CLIP	22100165
MIRT449675	hsa-miR-100-3p	PAR-CLIP	22100165
MIRT449673	hsa-miR-570-3p	PAR-CLIP	22100165
MIRT1380444	hsa-miR-1275	CLIP-seq
MIRT1380445	hsa-miR-132	CLIP-seq
MIRT1380446	hsa-miR-1915	CLIP-seq
MIRT1380447	hsa-miR-212	CLIP-seq
MIRT1380448	hsa-miR-3163	CLIP-seq
MIRT1380449	hsa-miR-3180	CLIP-seq
MIRT1380450	hsa-miR-3180-3p	CLIP-seq
MIRT1380451	hsa-miR-3186-5p	CLIP-seq
MIRT1380452	hsa-miR-3196	CLIP-seq
MIRT1380453	hsa-miR-340	CLIP-seq
MIRT1380454	hsa-miR-342-5p	CLIP-seq
MIRT1380455	hsa-miR-4282	CLIP-seq
MIRT1380456	hsa-miR-4447	CLIP-seq
MIRT1380457	hsa-miR-4466	CLIP-seq
MIRT1380458	hsa-miR-4472	CLIP-seq
MIRT1380459	hsa-miR-4481	CLIP-seq
MIRT1380460	hsa-miR-4645-5p	CLIP-seq
MIRT1380461	hsa-miR-4664-5p	CLIP-seq
MIRT1380462	hsa-miR-4665-5p	CLIP-seq
MIRT1380463	hsa-miR-4673	CLIP-seq
MIRT1380464	hsa-miR-4695-3p	CLIP-seq
MIRT1380465	hsa-miR-4706	CLIP-seq
MIRT1380466	hsa-miR-4709-5p	CLIP-seq
MIRT1380467	hsa-miR-4726-3p	CLIP-seq
MIRT1380468	hsa-miR-4742-5p	CLIP-seq
MIRT1380469	hsa-miR-4745-5p	CLIP-seq
MIRT1380470	hsa-miR-4749-5p	CLIP-seq
MIRT1380471	hsa-miR-624	CLIP-seq
MIRT1380472	hsa-miR-675	CLIP-seq
MIRT1380473	hsa-miR-744	CLIP-seq
MIRT2113906	hsa-miR-1323	CLIP-seq
MIRT2113907	hsa-miR-3120-3p	CLIP-seq
MIRT1380449	hsa-miR-3180	CLIP-seq
MIRT1380450	hsa-miR-3180-3p	CLIP-seq
MIRT1380452	hsa-miR-3196	CLIP-seq
MIRT1380454	hsa-miR-342-5p	CLIP-seq
MIRT1380456	hsa-miR-4447	CLIP-seq
MIRT1380457	hsa-miR-4466	CLIP-seq
MIRT1380458	hsa-miR-4472	CLIP-seq
MIRT1380459	hsa-miR-4481	CLIP-seq
MIRT2113908	hsa-miR-4651	CLIP-seq
MIRT1380461	hsa-miR-4664-5p	CLIP-seq
MIRT1380465	hsa-miR-4706	CLIP-seq
MIRT1380469	hsa-miR-4745-5p	CLIP-seq
MIRT1380470	hsa-miR-4749-5p	CLIP-seq
MIRT2113909	hsa-miR-545	CLIP-seq
MIRT2113910	hsa-miR-548o	CLIP-seq
MIRT2113911	hsa-miR-548p	CLIP-seq
MIRT2113912	hsa-miR-548v	CLIP-seq
MIRT2113913	hsa-miR-608	CLIP-seq
MIRT1380472	hsa-miR-675	CLIP-seq
MIRT1380473	hsa-miR-744	CLIP-seq
MIRT2113906	hsa-miR-1323	CLIP-seq
MIRT2113907	hsa-miR-3120-3p	CLIP-seq
MIRT2113909	hsa-miR-545	CLIP-seq
MIRT2113910	hsa-miR-548o	CLIP-seq
MIRT2113911	hsa-miR-548p	CLIP-seq
MIRT2113912	hsa-miR-548v	CLIP-seq
MIRT2460286	hsa-miR-3664-3p	CLIP-seq
MIRT2460287	hsa-miR-4433	CLIP-seq
MIRT1380456	hsa-miR-4447	CLIP-seq
MIRT2460288	hsa-miR-4459	CLIP-seq
MIRT1380458	hsa-miR-4472	CLIP-seq
MIRT1380459	hsa-miR-4481	CLIP-seq
MIRT2460289	hsa-miR-4488	CLIP-seq
MIRT2460290	hsa-miR-4675	CLIP-seq
MIRT2460291	hsa-miR-4687-3p	CLIP-seq
MIRT2460292	hsa-miR-4697-5p	CLIP-seq
MIRT2460293	hsa-miR-4741	CLIP-seq
MIRT1380469	hsa-miR-4745-5p	CLIP-seq
MIRT2460294	hsa-miR-4768-3p	CLIP-seq
MIRT2460295	hsa-miR-510	CLIP-seq
MIRT2460296	hsa-miR-765	CLIP-seq
MIRT1380446	hsa-miR-1915	CLIP-seq
MIRT1380460	hsa-miR-4645-5p	CLIP-seq
MIRT1380463	hsa-miR-4673	CLIP-seq
MIRT1380467	hsa-miR-4726-3p	CLIP-seq
MIRT1380468	hsa-miR-4742-5p	CLIP-seq

Transcription factors

Show/Hide all(7)

Transcription factor	Regulation	Reference
MEIS1	Unknown	19799567
NFYA	Unknown	15656994;19799567
NFYB	Unknown	19799567
NFYC	Unknown	19799567
PBX1	Unknown	19799567
SP1	Unknown	15656994
TGIF1	Repression	22293114

Show/Hide all(25)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IBA
GO:0000785	Component	Chromatin	ISA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISS
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IBA
GO:0003677	Function	DNA binding	IEA
GO:0003677	Function	DNA binding	TAS	8625802
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0007417	Process	Central nervous system development	TAS	8625802
GO:0007420	Process	Brain development	IBA
GO:0007423	Process	Sensory organ development	ISS
GO:0007530	Process	Sex determination	IMP	21183788
GO:0021854	Process	Hypothalamus development	ISS
GO:0021983	Process	Pituitary gland development	ISS
GO:0030182	Process	Neuron differentiation	IBA
GO:0045665	Process	Negative regulation of neuron differentiation	ISS
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IBA
GO:0060324	Process	Face development	ISS
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536

MIM	HGNC	e!Ensembl
313430	11199	ENSG00000134595

Protein

UniProt ID

P41225

Protein name

Transcription factor SOX-3

Protein function

Transcription factor required during the formation of the hypothalamo-pituitary axis. May function as a switch in neuronal development. Keeps neural cells undifferentiated by counteracting the activity of proneural proteins and suppresses neuron

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00505	HMG_box	139 → 207	HMG (high mobility group) box	Domain
PF12336	SOXp	208 → 302	SOX transcription factor	Family

Sequence

MRPVRENSSGARSPRVPADLARSILISLPFPPDSLAHRPPSSAPTESQGLFTVAAPAPGA
PSPPATLAHLLPAPAMYSLLETELKNPVGTPTQAAGTGGPAAPGGAGKSSANAAGGANSG
GGSSGGASGGGGGTDQDRVKRPMNAFMVWSRGQRRKMALENPKMHNSEISKRLGADWKLL
TDAEKRPFIDEAKRLRAVHMKEYPDYKYRPRRKTKTLLKKDKYSLPSGLLPPGAAAAAAA
AAAAAAAASSPVGVGQRLDTYTHVNGWANGAYSLVQEQLGYAQPPSMSSPPPPPALPPMH
RYDMAGLQYSPMMPPGAQSYMNVAAAAAAASGYGGMAPSATAAAAAAYGQQPATAAAAAA
AAAAMSLGPMGSVVKSEPSSPPPAIASHSQRACLGDLRDMISMYLPPGGDAADAASPLPG
GRLHGVHQHYQGAGTAVNGTVPLTHI

Sequence length

446

Interactions

View interactions

	Reactome
			Deactivation of the beta-catenin transactivating complex

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Mental Retardation, X-Linked	Intellectual disability, X-linked, with panhypopituitarism	rs1556518231	N/A

Show/Hide Unknown Diseases (7)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
46, XX Gonadal Sex Reversal	46,XX sex reversal 1	N/A	N/A	GenCC
46, XX ovotesticular disorder of sex development	46,XX ovotesticular disorder of sex development	N/A	N/A	GenCC
46, XY Sex Reversal	46,XX sex reversal 3	N/A	N/A	GenCC
Congenital Hypertrichosis, X-Linked	X-linked congenital generalized hypertrichosis	N/A	N/A	GenCC
Intellectual Disability With Growth Hormone Deficiency, X-Linked	X-linked intellectual disability with isolated growth hormone deficiency	N/A	N/A	GenCC
Panhypopituitarism	panhypopituitarism, X-linked, panhypopituitarism	N/A	N/A	GenCC
panhypopituitarism, x-linked	Panhypopituitarism, X-linked	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (32)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
46 XX Testicular Disorders of Sex Development	Associate	29371155
Breast Neoplasms	Associate	20847343, 30915751
Carcinoma Ovarian Epithelial	Associate	27251670
Combined Pituitary Hormone Deficiency	Associate	25064402
Craniofacial Abnormalities	Associate	35295983
Disorders of Sex Development	Associate	25351776
Dwarfism Pituitary	Associate	12428212, 15800844, 34440302, 35295983
Dwarfism Pituitary	Stimulate	35114986
Endometrial Neoplasms	Associate	28618953
Glioblastoma	Associate	34953010
Growth Disorders	Associate	35114986
Hemophilia B	Associate	27477789, 30264515
Hyperphagia	Associate	15800844
Hypertrichosis congenital generalized X linked	Associate	21636067
Hypogonadism	Associate	25064402, 35295983
Hypopituitarism	Associate	15800844, 34440302, 35114986, 35295983
Intellectual Disability	Associate	25351776, 27477789, 35114986, 35295983
Learning Disabilities	Associate	15800844, 35295983
Lymphatic Metastasis	Associate	32363730
Mental Retardation X Linked	Associate	12428212
Neoplasms	Stimulate	27251670
Neoplasms	Associate	30915751, 32363730
Ovarian Neoplasms	Associate	27251670
Pituitary Diseases	Associate	15800844, 34440302
Pituitary Hormone Deficiency Combined 2	Associate	15800844
Pulmonary Subvalvular Stenosis	Associate	15800844
Rett Syndrome	Associate	10745042
Small Cell Lung Carcinoma	Associate	10760287, 15880380
Stomach Neoplasms	Associate	32363730
Thrombosis	Associate	32423094
Thyroiditis	Associate	35114986
X Linked Infantile Nystagmus	Associate	9973299

SOX3 (SRY-box transcription factor 3)