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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	23554
Gene name	Tetraspanin 12
Gene symbol	TSPAN12
Synonyms (NCBI Gene)	EVR5NET-2NET2TM4SF12
Chromosome	7
Chromosome location	7q31.31
Summary	The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate

Show/Hide all (17)

SNP ID	Visualize variation	Clinical significance	Consequence
rs145449060	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs200519776	A>G	Pathogenic	Missense variant, coding sequence variant
rs267607151	C>G	Pathogenic	Missense variant, coding sequence variant
rs267607152	A>T	Pathogenic	Missense variant, coding sequence variant, intron variant
rs267607153	A>T	Pathogenic	Coding sequence variant, stop gained
rs267607154	C>G	Pathogenic	Missense variant, coding sequence variant
rs538591733	G>A,T	Pathogenic	Coding sequence variant, missense variant
rs587777283	T>C	Pathogenic	Coding sequence variant, missense variant
rs587777284	C>G	Pathogenic	Splice acceptor variant
rs587777285	C>T	Pathogenic	Splice donor variant
rs794726655	CTGGT>-	Pathogenic	Intron variant, splice acceptor variant
rs878853243	C>A	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs1057518477	T>C	Likely-pathogenic	Splice acceptor variant
rs1171910750	GAT>-	Likely-pathogenic	Coding sequence variant, inframe deletion
rs1335735639	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs1554403626	->ACAGCAA	Pathogenic	Coding sequence variant, frameshift variant
rs1554403767	A>-	Pathogenic	Coding sequence variant, frameshift variant

Show/Hide all (51)

miRTarBase ID	miRNA	Experiments	Reference
MIRT026095	hsa-miR-196a-5p	Sequencing	20371350
MIRT027371	hsa-miR-101-3p	Sequencing	20371350
MIRT029887	hsa-miR-26b-5p	Microarray	19088304
MIRT546162	hsa-miR-140-5p	PAR-CLIP	21572407
MIRT546161	hsa-miR-5692a	PAR-CLIP	21572407
MIRT546160	hsa-miR-132-3p	PAR-CLIP	21572407
MIRT546159	hsa-miR-212-3p	PAR-CLIP	21572407
MIRT546158	hsa-miR-203b-5p	PAR-CLIP	21572407
MIRT546157	hsa-miR-6718-5p	PAR-CLIP	21572407
MIRT546156	hsa-miR-8063	PAR-CLIP	21572407
MIRT546155	hsa-miR-4698	PAR-CLIP	21572407
MIRT546154	hsa-miR-4727-3p	PAR-CLIP	21572407
MIRT546153	hsa-miR-4460	PAR-CLIP	21572407
MIRT546152	hsa-miR-607	PAR-CLIP	21572407
MIRT319421	hsa-miR-1305	PAR-CLIP	21572407
MIRT735686	hsa-miR-196b-5p	Luciferase reporter assayWestern blottingImmunoprecipitaion (IP)Immunohistochemistry (IHC)qRT-PCRFlow cytometry	32041891
MIRT546162	hsa-miR-140-5p	PAR-CLIP	21572407
MIRT546161	hsa-miR-5692a	PAR-CLIP	21572407
MIRT546160	hsa-miR-132-3p	PAR-CLIP	21572407
MIRT546159	hsa-miR-212-3p	PAR-CLIP	21572407
MIRT546158	hsa-miR-203b-5p	PAR-CLIP	21572407
MIRT546157	hsa-miR-6718-5p	PAR-CLIP	21572407
MIRT546156	hsa-miR-8063	PAR-CLIP	21572407
MIRT546155	hsa-miR-4698	PAR-CLIP	21572407
MIRT546154	hsa-miR-4727-3p	PAR-CLIP	21572407
MIRT546153	hsa-miR-4460	PAR-CLIP	21572407
MIRT546152	hsa-miR-607	PAR-CLIP	21572407
MIRT319421	hsa-miR-1305	PAR-CLIP	21572407
MIRT1459324	hsa-miR-1270	CLIP-seq
MIRT1459325	hsa-miR-1323	CLIP-seq
MIRT1459326	hsa-miR-137	CLIP-seq
MIRT1459327	hsa-miR-300	CLIP-seq
MIRT1459328	hsa-miR-3613-3p	CLIP-seq
MIRT1459329	hsa-miR-371b-5p	CLIP-seq
MIRT1459330	hsa-miR-381	CLIP-seq
MIRT1459331	hsa-miR-3977	CLIP-seq
MIRT1459332	hsa-miR-4307	CLIP-seq
MIRT1459333	hsa-miR-432	CLIP-seq
MIRT1459334	hsa-miR-4531	CLIP-seq
MIRT1459335	hsa-miR-4666-3p	CLIP-seq
MIRT1459336	hsa-miR-4717-3p	CLIP-seq
MIRT1459337	hsa-miR-4799-5p	CLIP-seq
MIRT1459338	hsa-miR-4803	CLIP-seq
MIRT1459339	hsa-miR-499a-5p	CLIP-seq
MIRT1459340	hsa-miR-548c-3p	CLIP-seq
MIRT1459341	hsa-miR-548o	CLIP-seq
MIRT1459342	hsa-miR-578	CLIP-seq
MIRT1459343	hsa-miR-620	CLIP-seq
MIRT1459344	hsa-miR-890	CLIP-seq
MIRT1459345	hsa-miR-892a	CLIP-seq
MIRT2358744	hsa-miR-4775	CLIP-seq

Show/Hide all (16)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001525	Process	Angiogenesis	IEA
GO:0005515	Function	Protein binding	IPI	19587294, 25416956, 32296183
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	ISS
GO:0007166	Process	Cell surface receptor signaling pathway	IEA
GO:0007166	Process	Cell surface receptor signaling pathway	ISS
GO:0010842	Process	Retina layer formation	IEA
GO:0010842	Process	Retina layer formation	ISS
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	TAS	10719184
GO:0035633	Process	Maintenance of blood-brain barrier	IEA
GO:0042813	Function	Wnt receptor activity	ISS
GO:0045765	Process	Regulation of angiogenesis	IEA
GO:0045765	Process	Regulation of angiogenesis	ISS
GO:0110135	Process	Norrin signaling pathway	IEA

MIM	HGNC	e!Ensembl
613138	21641	ENSG00000106025

O95859

Protein name

Tetraspanin-12 (Tspan-12) (Tetraspan NET-2) (Transmembrane 4 superfamily member 12)

Protein function

Regulator of cell surface receptor signal transduction. Plays a central role in retinal vascularization by regulating norrin (NDP) signal transduction. Acts in concert with norrin (NDP) to promote FZD4 multimerization and subsequent activation o

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00335	Tetraspanin	10 → 247	Tetraspanin family	Family

Sequence

MAREDSVKCLRCLLYALNLLFWLMSISVLAVSAWMRDYLNNVLTLTAETRVEEAVILTYF
PVVHPVMIAVCCFLIIVGMLGYCGTVKRNLLLLAWYFGSLLVIFCVELACGVWTYEQELM
VPVQWSDMVTLKARMTNYGLPRYRWLTHAWNFFQREFKCCGVVYFTDWLEMTEMDWPPDS
CCVREFPGCSKQAHQEDLSDLYQEGCGKKMYSFLRGTKQLQVLRFLGISIGVTQILAMIL
TITLLWALYYDRREPGTDQMMSLKNDNSQHLSCPSVELLKPSLSRIFEHTSMANSFNTHF
EMEEL

Sequence length

305

Interactions

View interactions

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)

Show/Hide Causal Diseases (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Atrophia bulborum hereditaria	Pathogenic	rs878853243	RCV000225020	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Exudative vitreoretinopathy 5	Pathogenic; Likely pathogenic	rs1407226293, rs587777283, rs587777284, rs587777285, rs1278815943, rs267607154, rs1554403626, rs267607153, rs794726655, rs1437503069, rs2116347776, rs878853243, rs2485460699, rs1057518477, rs1335735639, rs1793956510 View all (1 more)	RCV001526704 RCV000114398 RCV000114399 RCV000114401 RCV001814865 RCV000000347 RCV000000349 RCV000000350 RCV000000351 RCV002251264 RCV002251293 RCV000225062 RCV003598858 RCV001253220 RCV000991312 RCV001197349	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Familial exudative vitreoretinopathy	Pathogenic	rs878853243	RCV001003234	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Persistent hyperplastic primary vitreous, autosomal recessive	Pathogenic	rs878853243	RCV000225079	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinal dystrophy	Likely pathogenic; Pathogenic	rs1793956441	RCV001073344	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Vitreoretinopathy	Pathogenic	rs1554403767	RCV000626911	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (12)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
EXUDATIVE VITREORETINOPATHY	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GESTATIONAL DIABETES	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
IGA GLOMERULONEPHRITIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of urinary bladder	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MIGRAINE DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OPTIC ATROPHY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TSPAN12-related disorder	Likely benign; Benign; Uncertain significance; Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
UTERINE FIBROID	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
VITREORETINAL DEGENERATION	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (22)

Disease Name	Relationship Type	References	Evidence Score
Associations from Text MiningDisease associations identified through Pubtator
Alzheimer Disease	Associate	19587294	★★★★★ ★☆☆☆☆ Found in Text Mining only
Astigmatism	Associate	30747064	★★★★★ ★☆☆☆☆ Found in Text Mining only
Atrophy	Associate	28211206	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Associate	32222644	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Non Small Cell Lung	Associate	32963220	★★★★★ ★☆☆☆☆ Found in Text Mining only
Ectopia Lentis with Ectopia of Pupil	Associate	21552475	★★★★★ ★☆☆☆☆ Found in Text Mining only
Eosinophilic Esophagitis	Associate	34687736	★★★★★ ★☆☆☆☆ Found in Text Mining only
Exudative vitreoretinopathy 1	Associate	21552475	★★★★★ ★☆☆☆☆ Found in Text Mining only
Familial Exudative Vitreoretinopathies	Associate	20159111, 20159112, 21552475, 23441120, 25352738, 25711638, 27316669, 28211206, 28420620, 28575650, 28867931, 31452356, 34738848, 34860240, 34924743 View all (6 more)	★★★★★ ★☆☆☆☆ Found in Text Mining only
Fibrosis	Associate	34687736	★★★★★ ★☆☆☆☆ Found in Text Mining only
Genetic Diseases Inborn	Associate	34738848	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypertensive Retinopathy	Associate	25352738	★★★★★ ★☆☆☆☆ Found in Text Mining only
Intervertebral Disc Degeneration	Associate	21552475	★★★★★ ★☆☆☆☆ Found in Text Mining only
Microvascular Angina	Associate	32222644	★★★★★ ★☆☆☆☆ Found in Text Mining only
Myopia	Associate	38243264	★★★★★ ★☆☆☆☆ Found in Text Mining only
Myopia Degenerative	Associate	30747064	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Associate	19211836	★★★★★ ★☆☆☆☆ Found in Text Mining only
Norrie disease	Associate	35328049	★★★★★ ★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Associate	20132413	★★★★★ ★☆☆☆☆ Found in Text Mining only
Retinal Detachment	Associate	28211206, 28867931	★★★★★ ★☆☆☆☆ Found in Text Mining only
Retinitis	Associate	28211206, 31452356	★★★★★ ★☆☆☆☆ Found in Text Mining only
Vision Disorders	Associate	28211206	★★★★★ ★☆☆☆☆ Found in Text Mining only

TSPAN12 (tetraspanin 12)