TSPAN13

tetraspanin 13, the group of Tetraspanins

Basic information

Region (hg38): 7:16753755-16784536

Previous symbols: [ "TM4SF13" ]

Links

ENSG00000106537 ∙ NCBI:27075 ∙ OMIM:613139 ∙ HGNC:21643 ∙ Uniprot:O95857 ∙ 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 TSPAN13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPAN13 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		1
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	0

Variants in TSPAN13

This is a list of pathogenic ClinVar variants found in the TSPAN13 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-16754009-C-T			Likely benign (Sep 01, 2022)
7-16776259-G-C		not specified	Uncertain significance (May 29, 2024)
7-16776278-G-C		not specified	Uncertain significance (Oct 20, 2021)
7-16777084-G-A		not specified	Uncertain significance (May 27, 2022)
7-16777802-A-G		not specified	Uncertain significance (Jan 27, 2022)
7-16777888-A-C		not specified	Uncertain significance (Feb 10, 2023)
7-16779015-A-G		not specified	Uncertain significance (Oct 20, 2021)
7-16779045-A-C		not specified	Uncertain significance (Jun 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPAN13	protein_coding	protein_coding	ENST00000262067	6	31002

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000116	0.841	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	82	115	0.713	0.00000604	1318
Missense in Polyphen		22	48.037	0.45798		563
Synonymous	-0.699	54	47.9	1.13	0.00000281	419
Loss of Function	1.29	8	13.0	0.613	8.01e-7	125

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000545	0.0000544
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000444	0.0000439
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.305
• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• pHI: 0.331
• hipred: Y
• hipred_score: 0.699
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.177

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tspan13

Gene ontology

• Biological process: cell surface receptor signaling pathway;regulation of calcium ion transmembrane transport
• Cellular component: integral component of plasma membrane;membrane
• Molecular function: calcium channel regulator activity