TSPAN8

tetraspanin 8, the group of Tetraspanins

Basic information

Region (hg38): 12:71125084-71441898

Previous symbols: [ "TM4SF3" ]

Links

ENSG00000127324 ∙ NCBI:7103 ∙ OMIM:600769 ∙ HGNC:11855 ∙ Uniprot:P19075 ∙ 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 TSPAN8 gene.

• Inborn genetic diseases (13 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPAN8 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					2	2
missense			11		2	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			2			2
Total	0	0	13	0	4

Variants in TSPAN8

This is a list of pathogenic ClinVar variants found in the TSPAN8 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-71125345-C-T		not specified	Uncertain significance (Dec 19, 2022)
12-71125393-G-A			Benign (May 21, 2018)
12-71129383-G-T		not specified	Uncertain significance (Jun 29, 2023)
12-71132733-C-G		not specified	Uncertain significance (Sep 14, 2022)
12-71132741-A-T		Breast ductal adenocarcinoma	Uncertain significance (Jul 20, 2015)
12-71132812-C-T		not specified	Uncertain significance (Jan 27, 2022)
12-71137977-T-G		not specified	Uncertain significance (Dec 13, 2023)
12-71138051-T-C		not specified	Uncertain significance (Jul 26, 2022)
12-71138223-A-G		not specified	Uncertain significance (Nov 18, 2022)
12-71139714-C-T			Benign (May 21, 2018)
12-71139727-C-T		not specified	Uncertain significance (Feb 28, 2023)
12-71139746-C-T		not specified	Uncertain significance (Sep 28, 2021)
12-71139801-G-A			Benign (May 21, 2018)
12-71139812-C-T			Benign (Jun 14, 2018)
12-71144171-C-T			Benign (May 25, 2018)
12-71144178-C-A		not specified	Uncertain significance (Aug 02, 2022)
12-71144183-T-C		not specified	Uncertain significance (May 11, 2022)
12-71157669-C-G		not specified	Uncertain significance (Aug 10, 2021)
12-71440117-C-A		not specified	Uncertain significance (Jul 19, 2023)
12-71440214-G-A		not specified	Uncertain significance (Jul 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPAN8	protein_coding	protein_coding	ENST00000393330	8	316814

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00551	0.973	125717	0	23	125740	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.352	113	124	0.911	0.00000598	1544
Missense in Polyphen		30	42.432	0.70701		560
Synonymous	0.0734	43	43.6	0.986	0.00000228	439
Loss of Function	2.01	6	14.2	0.423	6.96e-7	167

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000177	0.000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Extracellular vesicle-mediated signaling in recipient cells (Consensus)

Recessive Scores

• pRec: 0.0411

Intolerance Scores

• loftool: 0.603
• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.44

Haploinsufficiency Scores

• pHI: 0.0198
• hipred: N
• hipred_score: 0.243

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.285

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tspan8

Gene ontology

• Biological process: cell surface receptor signaling pathway;spermatogenesis;regulation of gene expression;negative regulation of blood coagulation
• Cellular component: integral component of plasma membrane;cell surface;extracellular exosome
• Molecular function: integrin binding