TSPAN1

tetraspanin 1, the group of Tetraspanins

Basic information

Region (hg38): 1:46175072-46185962

Links

ENSG00000117472 ∙ NCBI:10103 ∙ OMIM:613170 ∙ HGNC:20657 ∙ Uniprot:O60635 ∙ 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 TSPAN1 gene.

• Inborn genetic diseases (8 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPAN1 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			7	1		8
nonsense						0
start loss					1	1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	1	2
Total	0	0	7	2	2

Variants in TSPAN1

This is a list of pathogenic ClinVar variants found in the TSPAN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-46176412-G-A			Likely benign (Jul 01, 2022)
1-46177421-A-G			Benign (Jan 11, 2019)
1-46181108-A-G			Benign (Dec 31, 2019)
1-46184236-G-A		not specified	Uncertain significance (Aug 02, 2022)
1-46184286-G-A		not specified	Uncertain significance (Apr 25, 2022)
1-46184299-G-A		not specified	Uncertain significance (Jan 24, 2024)
1-46184323-G-A		not specified	Uncertain significance (Jun 21, 2022)
1-46184330-T-C		not specified	Uncertain significance (Jan 02, 2024)
1-46184396-C-T		not specified	Likely benign (Dec 03, 2021)
1-46184653-G-C		not specified	Uncertain significance (Feb 14, 2023)
1-46184870-C-A		not specified	Uncertain significance (Dec 07, 2021)
1-46185086-A-G		not specified	Likely benign (Oct 10, 2023)
1-46185108-A-C		not specified	Uncertain significance (Jun 18, 2021)
1-46185273-G-A		not specified	Uncertain significance (Aug 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPAN1	protein_coding	protein_coding	ENST00000372003	7	10886

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000735	0.509	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.544	113	130	0.866	0.00000736	1591
Missense in Polyphen		36	50.138	0.71801		641
Synonymous	-0.918	62	53.5	1.16	0.00000375	461
Loss of Function	0.668	9	11.4	0.787	5.87e-7	140

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000173	0.000173
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000967	0.0000967
Middle Eastern	0.0000545	0.0000544
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0825

Intolerance Scores

• loftool: 0.591
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.0343
• hipred: N
• hipred_score: 0.187
• ghis: 0.385

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.120

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tspan1

Gene ontology

• Biological process: cell surface receptor signaling pathway;cell population proliferation;cell migration;positive regulation of endocytosis;protein stabilization
• Cellular component: nucleoplasm;cytoplasm;lysosomal membrane;plasma membrane;integral component of plasma membrane;membrane;cell junction;vesicle;intracellular membrane-bounded organelle;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: protein binding