TSPAN17

protein-coding

tetraspanin 17, the group of Tetraspanins

Gene summary

This gene encodes a member of the transmembrane 4 superfamily. It is characterized by four tetraspanin transmembrane segments. The function of this gene has not yet been determined. [provided by RefSeq, Mar 2014]

Previous symbols:

FBXO23
TM4SF17

MANE transcript

NM_130465.5

Inheritance

—

ClinVar variants

U:37B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.63

Max pathogenic AF

—

Genomic locus

chr5:176,647,387-176,659,054

External References & Databases

Ensembl (ENSG00000048140)

Transcript & Mutation Effects

hg38 • Region Span ~11.7 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 TSPAN17 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 32

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_130465.5. 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 clinvar		4
missense			30 clinvar			30
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	37	2	0	39

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 63 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_130465.5	RefSeq	NP_569732.2	9	MANE Select
ENST00000508164.6	Ensembl	ENSP00000422053.1	9	MANE Select
NM_001006616.3	RefSeq	NP_001006617.2	9	Standard
NM_001366491.2	RefSeq	NP_001353420.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell surface receptor signaling pathway
protein ubiquitination
establishment of protein localization to organelle

Molecular Function

ubiquitin-protein transferase activity
enzyme binding

Cellular Component

ubiquitin ligase complex
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000310032
Coding exons: 9
Length: 11671
Individuals with no LoFs: 125702
Homozygous LoFs: 1
Heterozygous LoFs: 42
Defined: 125745
p: 0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.924	158	194	0.813	0.0000115	2170
Missense (PolyPhen)		53	65.068	0.81454		775
Synonymous	0.251	80	82.9	0.965	0.00000539	649
Loss of Function	1.49	12	19.0	0.630	0.00000107	174

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.00072	0.00062	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Regulates ADAM10 maturation. {ECO:0000250|UniProtKB:Q9D7W4}.;

Intolerance Scores

LoFtool: 0.589
RVIS EVS: -0.25
RVIS percentile EVS: 35.99

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.508

Gene Damage Prediction

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