TSPAN10

tetraspanin 10, the group of Tetraspanins

Basic information

Region (hg38): 17:81637171-81648754

Links

ENSG00000182612 ∙ NCBI:83882 ∙ ∙ HGNC:29942 ∙ Uniprot:Q9H1Z9 ∙ 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 TSPAN10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPAN10 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			26	1	2	29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	2

Variants in TSPAN10

This is a list of pathogenic ClinVar variants found in the TSPAN10 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-81644996-C-T		not specified	Uncertain significance (Mar 08, 2024)
17-81645001-G-A		not specified	Uncertain significance (Feb 13, 2024)
17-81645002-G-A		not specified	Uncertain significance (May 24, 2024)
17-81645017-C-G		not specified	Uncertain significance (Jun 07, 2024)
17-81645104-C-G		not specified	Uncertain significance (Dec 21, 2024)
17-81645169-G-C		not specified	Uncertain significance (Jan 23, 2024)
17-81645173-G-T		not specified	Uncertain significance (Oct 06, 2023)
17-81645238-C-G		not specified	Uncertain significance (Sep 17, 2021)
17-81645256-G-A		not specified	Uncertain significance (Aug 08, 2023)
17-81645265-G-A		not specified	Uncertain significance (Sep 27, 2022)
17-81645352-G-A		not specified	Likely benign (Dec 31, 2024)
17-81645371-A-G			Benign (Apr 19, 2019)
17-81645431-C-G		not specified	Uncertain significance (Jun 30, 2022)
17-81645439-G-C		not specified	Uncertain significance (Jan 26, 2025)
17-81645500-T-C		not specified	Uncertain significance (Mar 27, 2023)
17-81645541-G-A		not specified	Uncertain significance (May 29, 2024)
17-81645553-C-T		not specified	Likely benign (Nov 16, 2021)
17-81645554-G-A		not specified	Uncertain significance (Apr 26, 2023)
17-81645565-G-A		not specified	Uncertain significance (Dec 21, 2022)
17-81645580-G-A		not specified	Uncertain significance (Jan 20, 2025)
17-81645580-G-C		not specified	Uncertain significance (Jan 26, 2022)
17-81645592-T-C		not specified	Uncertain significance (Mar 06, 2023)
17-81645604-T-G		not specified	Uncertain significance (Mar 18, 2024)
17-81647992-G-C			Benign (Apr 01, 2024)
17-81647995-C-A		not specified	Uncertain significance (Oct 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPAN10	polymorphic_pseudogene	protein_coding	ENST00000328585	4	11583

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000971	0.197	124576	0	10	124586	0.0000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0233	168	169	0.995	0.00000891	2143
Missense in Polyphen		27	21.334	1.2656		187
Synonymous	-1.03	95	83.1	1.14	0.00000481	795
Loss of Function	-0.423	7	5.89	1.19	2.50e-7	73

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000136	0.000129
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.0000371	0.0000354
Middle Eastern	0.000112	0.000111
South Asian	0.0000754	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates maturation of the transmembrane metalloprotease ADAM10. {ECO:0000250|UniProtKB:Q8VCF5}.

Recessive Scores

• pRec: 0.0993

Haploinsufficiency Scores

• pHI: 0.0817
• hipred: N
• hipred_score: 0.153

Essentials

• essential_gene_CRISPR2: S

Mouse Genome Informatics

• Gene name: Tspan10

Gene ontology

• Biological process: cell surface receptor signaling pathway;establishment of protein localization to organelle
• Cellular component: integral component of plasma membrane
• Molecular function: enzyme binding