GSC (goosecoid homeobox)

Gene

• Entrez ID: 145258
• Gene name: Goosecoid homeobox
• Gene symbol: GSC
• Synonyms (NCBI Gene): GSC1, SAMS
• Chromosome: 14
• Chromosome location: 14q32.13
• Summary: This gene encodes a member of the bicoid subfamily of the paired (PRD) homeobox family of proteins. The encoded protein acts as a transcription factor and may be autoregulatory. A similar protein in mice plays a role in craniofacial and rib cage developme

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT019699	hsa-miR-375	Microarray	20215506
MIRT1035666	hsa-miR-19a	CLIP-seq
MIRT1035667	hsa-miR-19b	CLIP-seq
MIRT1035668	hsa-miR-3120-5p	CLIP-seq
MIRT1035669	hsa-miR-331-5p	CLIP-seq
MIRT1035670	hsa-miR-3620	CLIP-seq
MIRT1035671	hsa-miR-3714	CLIP-seq
MIRT1035672	hsa-miR-4444	CLIP-seq
MIRT1035673	hsa-miR-4640-3p	CLIP-seq
MIRT1035674	hsa-miR-4696	CLIP-seq
MIRT1035675	hsa-miR-4708-3p	CLIP-seq
MIRT1035676	hsa-miR-4775	CLIP-seq
MIRT1035677	hsa-miR-516a-5p	CLIP-seq
MIRT1035678	hsa-miR-551a	CLIP-seq
MIRT1035679	hsa-miR-551b	CLIP-seq
MIRT1035680	hsa-miR-562	CLIP-seq
MIRT1035681	hsa-miR-885-3p	CLIP-seq
MIRT2465418	hsa-miR-1587	CLIP-seq
MIRT2465419	hsa-miR-378g	CLIP-seq
MIRT2465420	hsa-miR-3944-3p	CLIP-seq
MIRT2465421	hsa-miR-4492	CLIP-seq
MIRT2465422	hsa-miR-4498	CLIP-seq
MIRT2465423	hsa-miR-4656	CLIP-seq
MIRT2465424	hsa-miR-4675	CLIP-seq
MIRT2465425	hsa-miR-4731-5p	CLIP-seq
MIRT2465426	hsa-miR-4741	CLIP-seq
MIRT2465427	hsa-miR-762	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
EVX1	Repression	22178155

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IEA
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	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0001227	Function	DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA
GO:0003677	Function	DNA binding	IEA
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005667	Component	Transcription regulator complex	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0007369	Process	Gastrulation	NAS	7916327
GO:0009653	Process	Anatomical structure morphogenesis	IEA
GO:0009888	Process	Tissue development	IEA
GO:0014036	Process	Neural crest cell fate specification	IMP	24290375
GO:0016055	Process	Wnt signaling pathway	IEA
GO:0021904	Process	Dorsal/ventral neural tube patterning	IEA
GO:0023019	Process	Signal transduction involved in regulation of gene expression	IEA
GO:0030178	Process	Negative regulation of Wnt signaling pathway	IEA
GO:0030900	Process	Forebrain development	IEA
GO:0042474	Process	Middle ear morphogenesis	IEA
GO:0042474	Process	Middle ear morphogenesis	ISS
GO:0043583	Process	Ear development	IEA
GO:0048513	Process	Animal organ development	IEA
GO:0048644	Process	Muscle organ morphogenesis	IEA
GO:0048704	Process	Embryonic skeletal system morphogenesis	IEA
GO:0061629	Function	RNA polymerase II-specific DNA-binding transcription factor binding	IEA
GO:0061629	Function	RNA polymerase II-specific DNA-binding transcription factor binding	ISS
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536

Other IDs

• MIM: 138890
• HGNC: 4612
• e!Ensembl: ENSG00000133937

Protein

• UniProt ID: P56915
• Protein name: Homeobox protein goosecoid
• Protein function: Regulates chordin (CHRD). May play a role in spatial programing within discrete embryonic fields or lineage compartments during organogenesis. In concert with NKX3-2, plays a role in defining the structural components of the middle ear; required
• PDB: 2DMU
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00046	Homeodomain	161 → 217	Homeodomain	Domain

• Sequence:

  MPASMFSIDNILAARPRCKDSVLPVAHSAAAPVVFPALHGDSLYGASGGASSDYGAFYPR
  PVAPGGAGLPAAVSGSRLGYNNYFYGQLHVQAAPVGPACCGAVPPLGAQQCSCVPTPPGY
  EGPGSVLVSPVPHQMLPYMNVGTLSRTELQLLNQLHCRRKRRHRTIFTDEQLEALENLFQ
  ETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRQKRSSSEESENAEKWNKTSSSKA
  SPEKREEEGKSDLDSDS

• Sequence length: 257

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Short stature-auditory canal atresia-mandibular hypoplasia-skeletal anomalies syndrome	Pathogenic	rs587777288, rs587777289, rs587777290	RCV000114411 RCV000114412 RCV000114413	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ANDROGENETIC ALOPECIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CRANIOFACIAL ABNORMALITIES	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GSC-related disorder	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERTROPHIC CARDIOMYOPATHY	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Anaplasia	Anaplasia	BEFREE	30250190		★☆☆☆☆ Found in Text Mining only
Byzanthine arch palate	High palate	HPO_DG			★☆☆☆☆ Found in Text Mining only
Carcinoma	Carcinoma	BEFREE	24858567		★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	25343336	Associate	★☆☆☆☆ Found in Text Mining only
Conductive hearing loss	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital clubfoot	Congenital Clubfoot	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital dislocation of radial head	Dislocated radial head	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital Dysplasia Of The Hip	Developmental dysplasia of the hip	BEFREE	30320955		★☆☆☆☆ Found in Text Mining only
Congenital malformation syndrome	Congenital Malformation Syndrome	BEFREE	9475592		★☆☆☆☆ Found in Text Mining only
Congenital small ears	Microtia	BEFREE	19935299		★☆☆☆☆ Found in Text Mining only
Congenital small ears	Microtia	GENOMICS_ENGLAND_DG	9144415		★☆☆☆☆ Found in Text Mining only
Cornelia De Lange Syndrome	Cornelia De Lange Syndrome	BEFREE	10480362		★☆☆☆☆ Found in Text Mining only
Cryptorchidism	Cryptorchidism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	BEFREE	21294870		★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	23258844, 23524267, 27903708, 29463580, 29734672		★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	Pubtator	34066996	Associate	★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	23258844, 23284888, 23524267, 24115218, 24657832, 25128061, 26354413, 27903708, 28419967, 29463580, 29734672		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	21769436, 23524267, 24601786, 26354413, 26755664, 28666797, 29348889, 29575236, 30195875, 30208924, 30801931, 31847378		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	28410224	Associate	★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	8903381		★☆☆☆☆ Found in Text Mining only
Malignant Glioma	Glioma	BEFREE	26755664		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of liver	Liver Cancer	BEFREE	8903381		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	30208924, 30379370		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	23258844, 27903708, 28419967		★☆☆☆☆ Found in Text Mining only
Micrognathism	Micrognathism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Microstomia	Microstomia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	26354413, 27605047, 27723576, 29390972, 30195875		★☆☆☆☆ Found in Text Mining only
Orofacial Cleft 1	Orofacial cleft	Pubtator	28232668	Associate	★☆☆☆☆ Found in Text Mining only
Rhizomelia	Rhizomelia	HPO_DG			★☆☆☆☆ Found in Text Mining only
SHORT STATURE, AUDITORY CANAL ATRESIA, MANDIBULAR HYPOPLASIA, SKELETAL ABNORMALITIES	Short stature, auditory canal atresia, mandibular hypoplasia, and skeletal abnormalities(SAMS)	BEFREE	12116210, 24290375, 9475592		★☆☆☆☆ Found in Text Mining only
SHORT STATURE, AUDITORY CANAL ATRESIA, MANDIBULAR HYPOPLASIA, SKELETAL ABNORMALITIES	Short stature, auditory canal atresia, mandibular hypoplasia, and skeletal abnormalities(SAMS)	ORPHANET_DG	24290375		★☆☆☆☆ Found in Text Mining only
SHORT STATURE, AUDITORY CANAL ATRESIA, MANDIBULAR HYPOPLASIA, SKELETAL ABNORMALITIES	Short stature, auditory canal atresia, mandibular hypoplasia, and skeletal abnormalities(SAMS)	GENOMICS_ENGLAND_DG	9144415		★☆☆☆☆ Found in Text Mining only
SHORT STATURE, AUDITORY CANAL ATRESIA, MANDIBULAR HYPOPLASIA, SKELETAL ABNORMALITIES	Short stature, auditory canal atresia, mandibular hypoplasia, and skeletal abnormalities(SAMS)	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Short stature-auditory canal atresia-mandibular hypoplasia-skeletal anomalies syndrome	Short Stature, Auditory Canal Atresia, Mandibular Hypoplasia, And Skeletal Abnormalities	Orphanet			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Stomach Carcinoma	Stomach Carcinoma	BEFREE	26676563, 30208924, 30379370		★☆☆☆☆ Found in Text Mining only
Thyroid Nodule	Thyroid Nodule	BEFREE	30383497		★☆☆☆☆ Found in Text Mining only