TSPAN3

tetraspanin 3, the group of Tetraspanins

Basic information

Region (hg38): 15:77041403-77083984

Previous symbols: [ "TM4SF8" ]

Links

ENSG00000140391 ∙ NCBI:10099 ∙ OMIM:613134 ∙ HGNC:17752 ∙ Uniprot:O60637 ∙ 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 TSPAN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPAN3 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			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in TSPAN3

This is a list of pathogenic ClinVar variants found in the TSPAN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-77046903-T-C		not specified	Uncertain significance (Feb 14, 2023)
15-77052835-C-G		not specified	Uncertain significance (Feb 17, 2024)
15-77052866-T-C		not specified	Uncertain significance (Apr 13, 2022)
15-77052890-T-C		not specified	Uncertain significance (May 14, 2024)
15-77054230-T-G		not specified	Uncertain significance (Jun 05, 2024)
15-77054233-T-C		not specified	Uncertain significance (Sep 22, 2021)
15-77056197-T-C		not specified	Uncertain significance (Dec 20, 2023)
15-77056233-T-C		not specified	Uncertain significance (Mar 07, 2024)
15-77070905-T-C		not specified	Uncertain significance (Jun 21, 2023)
15-77070935-G-A		not specified	Uncertain significance (Jul 26, 2022)
15-77070951-C-T		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPAN3	protein_coding	protein_coding	ENST00000267970	7	39968

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0598	0.925	125738	0	7	125745	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.81	73	131	0.556	0.00000658	1634
Missense in Polyphen		15	32.738	0.45818		441
Synonymous	-0.420	53	49.2	1.08	0.00000262	490
Loss of Function	2.12	4	11.9	0.337	5.02e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000617	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000559	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000354	0.0000352
Middle Eastern	0.0000559	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates the proliferation and migration of oligodendrocytes, a process essential for normal myelination and repair. {ECO:0000250}.

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.170
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.376
• hipred: N
• hipred_score: 0.451
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.702

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tspan3
• Phenotype: hematopoietic system phenotype; neoplasm

Gene ontology

• Biological process: cell surface receptor signaling pathway;biological_process
• Cellular component: integral component of plasma membrane;extracellular exosome
• Molecular function: molecular_function