TSPAN17

tetraspanin 17, the group of Tetraspanins

Basic information

Region (hg38): 5:176647386-176659054

Previous symbols: [ "FBXO23", "TM4SF17" ]

Links

ENSG00000048140 ∙ NCBI:26262 ∙ ∙ HGNC:13594 ∙ Uniprot:Q96FV3 ∙ 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 TSPAN17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPAN17 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in TSPAN17

This is a list of pathogenic ClinVar variants found in the TSPAN17 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-176651785-A-G		not specified	Uncertain significance (Jun 07, 2024)
5-176651805-G-A		not specified	Uncertain significance (Nov 27, 2023)
5-176651837-G-A		not specified	Uncertain significance (Jun 13, 2024)
5-176651874-C-G		not specified	Uncertain significance (Feb 11, 2022)
5-176651874-C-T		not specified	Uncertain significance (Jun 29, 2022)
5-176656111-G-A		not specified	Uncertain significance (Aug 14, 2023)
5-176656776-T-C		not specified	Uncertain significance (Jul 25, 2023)
5-176656788-G-C		not specified	Uncertain significance (Jan 16, 2024)
5-176656806-C-T		not specified	Uncertain significance (Nov 18, 2022)
5-176656898-T-G		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPAN17	protein_coding	protein_coding	ENST00000310032	9	11671

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000151	0.859	125702	1	42	125745	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.924	158	194	0.813	0.0000115	2170
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000307	0.000306
Ashkenazi Jewish	0.000205	0.000198
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000117	0.000105
Middle Eastern	0.000109	0.000109
South Asian	0.000719	0.000621
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0713
• hipred: N
• hipred_score: 0.197
• ghis: 0.480

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tspan17

Gene ontology

• Biological process: cell surface receptor signaling pathway;protein ubiquitination;establishment of protein localization to organelle
• Cellular component: ubiquitin ligase complex;integral component of plasma membrane
• Molecular function: ubiquitin-protein transferase activity;enzyme binding