TSPAN2

tetraspanin 2, the group of Tetraspanins

Basic information

Region (hg38): 1:115048011-115089503

Links

ENSG00000134198 ∙ NCBI:10100 ∙ OMIM:613133 ∙ HGNC:20659 ∙ Uniprot:O60636 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TSPAN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPAN2 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						0
missense			9		1	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	9	0	2

Variants in TSPAN2

This is a list of pathogenic ClinVar variants found in the TSPAN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-115050512-C-T		not specified	Uncertain significance (Oct 12, 2024)
1-115050518-G-A		not specified	Uncertain significance (Jun 29, 2023)
1-115050537-T-A		not specified	Uncertain significance (Dec 09, 2024)
1-115053380-G-A		not specified	Uncertain significance (Dec 14, 2023)
1-115053386-C-A		not specified	Uncertain significance (Feb 01, 2023)
1-115058893-A-G		not specified	Uncertain significance (Jun 02, 2024)
1-115058900-T-C		not specified	Uncertain significance (Dec 23, 2022)
1-115058924-T-C		not specified	Uncertain significance (Aug 14, 2024)
1-115058953-T-G		not specified	Uncertain significance (Sep 30, 2024)
1-115058974-C-A			Benign (Dec 31, 2019)
1-115060547-G-A			Benign (Feb 25, 2018)
1-115062151-T-G		not specified	Uncertain significance (Oct 20, 2021)
1-115062170-C-G		not specified	Uncertain significance (Oct 11, 2024)
1-115062183-G-T		not specified	Uncertain significance (Dec 17, 2021)
1-115072968-G-A		not specified	Uncertain significance (Jul 14, 2023)
1-115072974-A-G		not specified	Uncertain significance (Nov 18, 2022)
1-115089398-T-G		not specified	Uncertain significance (Sep 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPAN2	protein_coding	protein_coding	ENST00000369516	8	41490

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000235	0.756	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.325	115	125	0.918	0.00000681	1404
Missense in Polyphen		52	51.774	1.0044		580
Synonymous	-0.141	49	47.8	1.03	0.00000282	430
Loss of Function	1.13	9	13.5	0.668	6.56e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000214
Ashkenazi Jewish	0.00	0.00
East Asian	0.000328	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.0000378	0.0000352
Middle Eastern	0.000328	0.000326
South Asian	0.000197	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in signalling in oligodendrocytes in the early stages of their terminal differentiation into myelin-forming glia and may also function in stabilizing the mature sheath. {ECO:0000250}.

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.533
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• pHI: 0.166
• hipred: N
• hipred_score: 0.350
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.766

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tspan2
• Phenotype: 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); immune system phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: inflammatory response;cell surface receptor signaling pathway;brain development;astrocyte development;microglia development;myelination;oligodendrocyte differentiation;axon development
• Cellular component: integral component of plasma membrane;integral component of membrane;myelin sheath
• Molecular function: protein binding