TSPAN15

tetraspanin 15, the group of Tetraspanins

Basic information

Region (hg38): 10:69451465-69507666

Previous symbols: [ "TM4SF15" ]

Links

ENSG00000099282 ∙ NCBI:23555 ∙ OMIM:613140 ∙ HGNC:23298 ∙ Uniprot:O95858 ∙ 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 TSPAN15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPAN15 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in TSPAN15

This is a list of pathogenic ClinVar variants found in the TSPAN15 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-69483715-G-C		not specified	Uncertain significance (Jul 13, 2021)
10-69483733-G-A		not specified	Uncertain significance (Feb 21, 2024)
10-69483740-G-A		not specified	Uncertain significance (Aug 21, 2023)
10-69483817-A-G		not specified	Uncertain significance (Oct 04, 2024)
10-69483830-T-C		not specified	Uncertain significance (May 05, 2023)
10-69483874-G-C		not specified	Uncertain significance (Feb 06, 2024)
10-69485172-T-C		not specified	Uncertain significance (Feb 22, 2023)
10-69485186-G-A		not specified	Uncertain significance (Jun 11, 2021)
10-69485189-G-A		not specified	Uncertain significance (Sep 01, 2021)
10-69495603-T-C		not specified	Uncertain significance (Sep 22, 2022)
10-69495643-A-G		not specified	Uncertain significance (Sep 24, 2024)
10-69498295-G-A		not specified	Uncertain significance (Oct 06, 2022)
10-69498317-G-A		not specified	Uncertain significance (Oct 24, 2024)
10-69498334-G-A		not specified	Uncertain significance (Feb 03, 2022)
10-69498395-C-T		not specified	Uncertain significance (Jun 26, 2024)
10-69506152-T-A		not specified	Uncertain significance (Feb 23, 2023)
10-69506154-C-T		not specified	Uncertain significance (Dec 07, 2024)
10-69506221-T-C		not specified	Uncertain significance (Oct 27, 2022)
10-69506941-C-T		not specified	Uncertain significance (Feb 05, 2024)
10-69506947-G-T		not specified	Uncertain significance (Dec 04, 2024)
10-69506950-C-T		not specified	Uncertain significance (Mar 17, 2023)
10-69506963-G-T		not specified	Uncertain significance (Jun 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPAN15	protein_coding	protein_coding	ENST00000373290	8	56197

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00796	0.979	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.877	141	174	0.813	0.00000994	1913
Missense in Polyphen		58	66.75	0.86892		687
Synonymous	0.396	69	73.3	0.941	0.00000466	579
Loss of Function	2.18	6	15.1	0.396	7.95e-7	167

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000880	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates maturation and trafficking of the transmembrane metalloprotease ADAM10. Promotes ADAM10-mediated cleavage of CDH2. Negatively regulates ligand-induced Notch activity probably by regulating ADAM10 activity. {ECO:0000269|PubMed:26686862}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.495
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.37

Haploinsufficiency Scores

• pHI: 0.292
• hipred: N
• hipred_score: 0.335
• ghis: 0.456

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tspan15

Gene ontology

• Biological process: cell surface receptor signaling pathway;regulation of Notch signaling pathway;cellular protein metabolic process;protein maturation;protein localization to plasma membrane
• Cellular component: endoplasmic reticulum lumen;plasma membrane;integral component of plasma membrane;cell surface;late endosome membrane;tetraspanin-enriched microdomain
• Molecular function: protein binding;enzyme binding