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

• intellectual disability, X-linked 58 (Definitive), mode of inheritance: XLR
• 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.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	3	1	5
missense			11	1		12
nonsense			2			2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			2		1	3
non coding				1		1
Total	0	0	14	5	1

Variants in TSPAN7

This is a list of pathogenic ClinVar variants found in the TSPAN7 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-38561546-T-C			Likely benign (Dec 01, 2023)
X-38561624-C-T		not specified	Uncertain significance (Feb 23, 2017)
X-38666196-G-T			Uncertain significance (Jan 01, 2022)
X-38666229-G-A		not specified • Intellectual disability	Uncertain significance (Dec 18, 2015)
X-38666265-G-T			Uncertain significance (Dec 02, 2019)
X-38666276-T-C		not specified • Intellectual disability, X-linked 58	Benign/Likely benign (Nov 28, 2023)
X-38666284-G-A		not specified	Uncertain significance (May 31, 2023)
X-38666287-G-C		Intellectual disability, X-linked 58	Uncertain significance (Feb 01, 2022)
X-38666316-A-G		not specified	Uncertain significance (May 02, 2014)
X-38671377-A-G		TSPAN7-related disorder	Uncertain significance (Sep 19, 2024)
X-38671379-G-T		not specified	Likely benign (Jul 15, 2016)
X-38671391-TC-T		Intellectual disability, X-linked 58	Pathogenic (May 13, 2021)
X-38671415-G-A			Uncertain significance (Sep 01, 2018)
X-38674253-C-T		TSPAN7-related disorder	Likely benign (Jun 21, 2019)
X-38674283-G-C		TSPAN7-related disorder • not specified	Uncertain significance (Dec 02, 2021)
X-38674290-C-T		not specified	Uncertain significance (Jan 09, 2024)
X-38674291-G-A		not specified	Uncertain significance (Apr 05, 2017)
X-38674315-G-A			Uncertain significance (Jun 24, 2022)
X-38674316-C-T		not specified	Benign (Oct 12, 2015)
X-38675725-G-C			Uncertain significance (Jun 14, 2021)
X-38675736-A-G		not specified	Uncertain significance (Oct 13, 2023)
X-38675772-TC-T		Intellectual disability	Uncertain significance (Jan 01, 2019)
X-38675778-C-A		Intellectual disability, X-linked 58 • History of neurodevelopmental disorder	Conflicting classifications of pathogenicity (May 28, 2019)
X-38675779-C-A		not specified • TSPAN7-related disorder	Benign (Dec 31, 2019)
X-38675795-G-A		not specified	Uncertain significance (Sep 16, 2014)

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