TSPAN7

tetraspanin 7, the group of Tetraspanins|CD molecules

Basic information

Region (hg38): X:38561542-38688920

Previous symbols: [ "MXS1", "TM4SF2", "MRX58" ]

Links

ENSG00000156298 ∙ NCBI:7102 ∙ OMIM:300096 ∙ HGNC:11854 ∙ Uniprot:P41732 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• non-syndromic X-linked intellectual disability (Supportive), mode of inheritance: XL
• intellectual disability, X-linked 58 (Definitive), mode of inheritance: XL
• intellectual disability, X-linked 58 (Strong), mode of inheritance: XL
• non-syndromic X-linked intellectual disability (Moderate), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, X-linked 58	XL	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	10449641; 10655063; 14735593

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TSPAN7 gene.

• not_specified (22 variants)
• not_provided (13 variants)
• Intellectual_disability,_X-linked_58 (8 variants)
• TSPAN7-related_disorder (4 variants)
• Intellectual_disability (2 variants)
• History_of_neurodevelopmental_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPAN7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004615.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	3	2	6
missense			21	3		24
nonsense	1		2			3
start loss						0
frameshift	2		1			3
splice donor/acceptor (+/-2bp)		1				1
Total	3	1	25	6	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPAN7	protein_coding	protein_coding	ENST00000378482	7	127547

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.746	0.252	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.91	48	102	0.470	0.00000796	1622
Missense in Polyphen		2	23.027	0.086853		411
Synonymous	-0.180	43	41.5	1.04	0.00000343	496
Loss of Function	2.45	1	8.86	0.113	6.45e-7	145

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in cell proliferation and cell motility.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human);Neuronal System;Cell surface interactions at the vascular wall;Hemostasis;Trafficking of GluR2-containing AMPA receptors;Trafficking of AMPA receptors;Glutamate binding, activation of AMPA receptors and synaptic plasticity;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses (Consensus)

Recessive Scores

• pRec: 0.171

Intolerance Scores

• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.272
• hipred: N
• hipred_score: 0.431
• ghis: 0.635

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.233

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Tspan7
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: cell surface receptor signaling pathway;viral process
• Cellular component: integral component of plasma membrane