TSPAN7 (tetraspanin 7)

Gene

• Entrez ID: 7102
• Gene name: Tetraspanin 7
• Gene symbol: TSPAN7
• Synonyms (NCBI Gene): A15, CCG-B7, CD231, DXS1692E, MRX58, MXS1, TALLA-1, TM4SF2, TM4SF2b, XLID58
• Chromosome: X
• Chromosome location: Xp11.4
• 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

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs104894950	G>T	Pathogenic	Coding sequence variant, stop gained
rs104894951	C>A,G	Likely-benign, conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT037691	hsa-miR-744-5p	CLASH	23622248
MIRT1459923	hsa-miR-3175	CLIP-seq
MIRT1459924	hsa-miR-3936	CLIP-seq
MIRT1459925	hsa-miR-4419a	CLIP-seq
MIRT1459926	hsa-miR-4510	CLIP-seq
MIRT1459927	hsa-miR-4716-3p	CLIP-seq
MIRT1459928	hsa-miR-4723-5p	CLIP-seq
MIRT1459929	hsa-miR-555	CLIP-seq
MIRT2138076	hsa-miR-1587	CLIP-seq
MIRT2138077	hsa-miR-4417	CLIP-seq
MIRT2138078	hsa-miR-4463	CLIP-seq
MIRT2138079	hsa-miR-4468	CLIP-seq
MIRT2138080	hsa-miR-4492	CLIP-seq
MIRT2138081	hsa-miR-4498	CLIP-seq
MIRT2138082	hsa-miR-4656	CLIP-seq
MIRT2138083	hsa-miR-4675	CLIP-seq
MIRT2138084	hsa-miR-4741	CLIP-seq
MIRT2138085	hsa-miR-4766-5p	CLIP-seq
MIRT2138086	hsa-miR-488	CLIP-seq
MIRT2138087	hsa-miR-762	CLIP-seq
MIRT2138076	hsa-miR-1587	CLIP-seq
MIRT2138077	hsa-miR-4417	CLIP-seq
MIRT2138079	hsa-miR-4468	CLIP-seq
MIRT2138080	hsa-miR-4492	CLIP-seq
MIRT2138081	hsa-miR-4498	CLIP-seq
MIRT2138082	hsa-miR-4656	CLIP-seq
MIRT2138083	hsa-miR-4675	CLIP-seq
MIRT2138084	hsa-miR-4741	CLIP-seq
MIRT2138085	hsa-miR-4766-5p	CLIP-seq
MIRT2138086	hsa-miR-488	CLIP-seq
MIRT2138087	hsa-miR-762	CLIP-seq
MIRT2396425	hsa-miR-4279	CLIP-seq
MIRT2396426	hsa-miR-490-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	TAS	8420826
GO:0016020	Component	Membrane	IEA

Other IDs

• MIM: 300096
• HGNC: 11854
• e!Ensembl: ENSG00000156298

Protein

• UniProt ID: P41732
• Protein name: Tetraspanin-7 (Tspan-7) (Cell surface glycoprotein A15) (Membrane component chromosome X surface marker 1) (T-cell acute lymphoblastic leukemia-associated antigen 1) (TALLA-1) (Transmembrane 4 superfamily member 2) (CD antigen CD231)
• Protein function: May be involved in cell proliferation and cell motility.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00335	Tetraspanin	15 → 239	Tetraspanin family	Family

• Tissue specificity: TISSUE SPECIFICITY: Not solely expressed in T-cells. Expressed in acute myelocytic leukemia cells of some patients.
• Sequence:

  MASRRMETKPVITCLKTLLIIYSFVFWITGVILLAVGVWGKLTLGTYISLIAENSTNAPY
  VLIGTGTTIVVFGLFGCFATCRGSPWMLKLYAMFLSLVFLAELVAGISGFVFRHEIKDTF
  LRTYTDAMQTYNGNDERSRAVDHVQRSLSCCGVQNYTNWSTSPYFLEHGIPPSCCMNETD
  CNPQDLHNLTVAATKVNQKGCYDLVTSFMETNMGIIAGVAFGIAFSQLIGMLLACCLSRF
  ITANQYEMV

• Sequence length: 249

Pathways

KEGG:

Transcriptional misregulation in cancer

Reactome:

Trafficking of GluR2-containing AMPA receptors

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
Intellectual disability, X-linked 58	Pathogenic	rs2147452502, rs104894950, rs2518967233	RCV001788537 RCV000012395 RCV000012397	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
History of neurodevelopmental disorder	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED 58	—	Disgenet, HPO Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual disability	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
MENTAL RETARDATION, X-LINKED 58	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MENTAL RETARDATION, X-LINKED NONSYNDROMIC	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-SYNDROMIC X-LINKED INTELLECTUAL DISABILITY	—	ClinGen, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TSPAN7-related disorder	Uncertain significance; Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
X-LINKED NON-SYNDROMIC INTELLECTUAL DISABILITY	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
2-3 toe syndactyly	Syndactyly Of The Toes	HPO_DG			★☆☆☆☆ Found in Text Mining only
Age related macular degeneration	Age-related macular degeneration	BEFREE	29961824		★☆☆☆☆ Found in Text Mining only
Attention deficit hyperactivity disorder	Attention Deficit Hyperactivity Disorder	HPO_DG			★☆☆☆☆ Found in Text Mining only
Autistic behavior	Autism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune Diseases	BEFREE	27221092		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	35201289	Associate	★☆☆☆☆ Found in Text Mining only
Chronic Lymphocytic Leukemia	Lymphocytic Leukemia	BEFREE	24445867		★☆☆☆☆ Found in Text Mining only
Cone Dystrophy	Cone Dystrophy	BEFREE	30819798		★☆☆☆☆ Found in Text Mining only
Conventional (Clear Cell) Renal Cell Carcinoma	Renal Carcinoma	BEFREE	22213152		★☆☆☆☆ Found in Text Mining only
Desmoplastic Small Round Cell Tumor	Desmoplastic Tumor	BEFREE	14633590		★☆☆☆☆ Found in Text Mining only
Desmoplastic Small Round Cell Tumor	Desmoplastic small round cell tumor	Pubtator	14633590	Associate	★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	24372385	Associate	★☆☆☆☆ Found in Text Mining only
Diabetes	Diabetes	BEFREE	27221092, 31256036		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes mellitus	Pubtator	20587347	Associate	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes Mellitus	BEFREE	27221092, 31256036		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Insulin-Dependent	Diabetes Mellitus	BEFREE	27221092, 30789994		★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	Pubtator	24372385	Associate	★☆☆☆☆ Found in Text Mining only
Esophageal carcinoma	Esophageal Carcinoma	BEFREE	28599425		★☆☆☆☆ Found in Text Mining only
Esophageal Neoplasms	Esophagus Neoplasm	BEFREE	28599425		★☆☆☆☆ Found in Text Mining only
Ewings sarcoma	Ewing sarcoma	BEFREE	14633590		★☆☆☆☆ Found in Text Mining only
Facial paralysis	Facial paralysis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	16320026		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	36845098	Inhibit	★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hematologic Neoplasms	Hematologic Neoplasms	BEFREE	25637218		★☆☆☆☆ Found in Text Mining only
Impaired cognition	Impaired Cognition	BEFREE	28968657		★☆☆☆☆ Found in Text Mining only
insulinoma	Insulinoma	BEFREE	27221092		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	12376945, 27328461, 28207852, 28223337, 28968657		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Intellectual Disability	Mental retardation	LHGDN	14735593		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Kidney Neoplasms	Kidney neoplasm	Pubtator	39175035	Stimulate	★☆☆☆☆ Found in Text Mining only
Latent Autoimmune Diabetes in Adults	Autoimmune Diabetes	BEFREE	30594957		★☆☆☆☆ Found in Text Mining only
Lymphoma, Non-Hodgkin	Non-Hodgkin lymphoma	BEFREE	24445867		★☆☆☆☆ Found in Text Mining only
Lymphoma, Non-Hodgkin, Familial	Lymphoma	BEFREE	24445867		★☆☆☆☆ Found in Text Mining only
Macrocephaly	Macrocephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Macular dystrophy	Macular dystrophy	BEFREE	29961824		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of esophagus	Esophagus Neoplasm	BEFREE	28599425		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	17406028, 26036626		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	17406028, 19549254, 21428937, 25351816, 28408487		★☆☆☆☆ Found in Text Mining only
Meckel Diverticulum	Meckel Diverticulum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Mental Retardation	Mental retardation	BEFREE	12376945		★☆☆☆☆ Found in Text Mining only
Mental Retardation, X-Linked	Mental retardation	BEFREE	10449641		★☆☆☆☆ Found in Text Mining only
Mental Retardation, X-Linked 1	Mental Retardation, X-Linked	BEFREE	10449641		★☆☆☆☆ Found in Text Mining only
Mental Retardation, X-Linked 1	Mental Retardation, X-Linked	ORPHANET_DG	10655063, 12070254		★☆☆☆☆ Found in Text Mining only
Mental Retardation, X-Linked 58	Mental retardation	GENOMICS_ENGLAND_DG	10655063		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mental Retardation, X-Linked 58	Mental retardation	CLINGEN_DG	10655063, 12070254, 22445342		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mental Retardation, X-Linked 58	Mental retardation	UNIPROT_DG	10655063		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mental Retardation, X-Linked 58	Mental retardation	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mental Retardation, X-Linked 58	Mental retardation	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mild Mental Retardation	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Mild neurosensory hearing impairment	Neurosensory Hearing impairment	HPO_DG			★☆☆☆☆ Found in Text Mining only
Moderate intellectual disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Multiple Myeloma	Multiple myeloma	BEFREE	25637218		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	16320026, 22213152, 23955570, 25637218, 30588007		★☆☆☆☆ Found in Text Mining only
Nephroblastoma	Nephroblastoma	BEFREE	14633590		★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	29283339, 30588007		★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ornithine carbamoyltransferase deficiency	Ornithine Carbamoyltransferase Deficiency	BEFREE	17570074		★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	17406028, 26036626		★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis Pigmentosa	BEFREE	29961824		★☆☆☆☆ Found in Text Mining only
Sarcoma	Sarcoma	Pubtator	32084007	Inhibit	★☆☆☆☆ Found in Text Mining only
Severe intellectual disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	37591783	Associate	★☆☆☆☆ Found in Text Mining only
Tonic - clonic seizures	Seizure	HPO_DG			★☆☆☆☆ Found in Text Mining only
X-linked non-syndromic intellectual disability	Non-Syndromic Intellectual Disability, X-Linked	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations