TSPAN1

protein-coding

tetraspanin 1, the group of Tetraspanins

Gene summary

The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. [provided by RefSeq, Jul 2008]

MANE transcript

NM_005727.4

Inheritance

—

ClinVar variants

U:36B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.79

Max pathogenic AF

—

Genomic locus

chr1:46,175,073-46,185,962

External References & Databases

Ensembl (ENSG00000117472)

Transcript & Mutation Effects

hg38 • Region Span ~10.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TSPAN1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 35

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005727.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			33 clinvar	3 clinvar		36
nonsense						0
start loss					1 clinvar	1
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	36	3	1	40

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005727.4	RefSeq	NP_005718.2	7	MANE Select
ENST00000372003.6	Ensembl	ENSP00000361072.1	7	MANE Select
ENST00000893420.1	Ensembl	ENSP00000563479.1	7	Standard
ENST00000893421.1	Ensembl	ENSP00000563480.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell surface receptor signaling pathway
cell population proliferation
cell migration
positive regulation of endocytosis
protein stabilization

Molecular Function

protein binding

Cellular Component

nucleoplasm
cytoplasm
lysosomal membrane
plasma membrane
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372003
Coding exons: 7
Length: 10886
Individuals with no LoFs: 125726
Homozygous LoFs: 0
Heterozygous LoFs: 22
Defined: 125748
p: 0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.544	113	130	0.866	0.00000736	1591
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000097	0.000097	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0825

Intolerance Scores

LoFtool: 0.591
RVIS EVS: 0.08
RVIS percentile EVS: 60.09

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.120

Gene Damage Prediction

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