TSPAN18

tetraspanin 18, the group of Tetraspanins

Basic information

Region (hg38): 11:44726464-44932423

Links

ENSG00000157570 ∙ NCBI:90139 ∙ OMIM:619399 ∙ HGNC:20660 ∙ Uniprot:Q96SJ8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TSPAN18 gene.

• Inborn genetic diseases (15 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPAN18 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					1	1
missense			15		1	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	2

Variants in TSPAN18

This is a list of pathogenic ClinVar variants found in the TSPAN18 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-44906430-G-A		not specified	Uncertain significance (Jul 26, 2022)
11-44909729-A-T		not specified	Uncertain significance (Sep 27, 2022)
11-44909745-T-C		not specified	Uncertain significance (Feb 13, 2024)
11-44909757-C-T			Benign (Oct 09, 2017)
11-44909758-C-T		TSPAN18-related disorder	Likely benign (Dec 02, 2019)
11-44909759-G-A		not specified	Uncertain significance (Sep 06, 2022)
11-44909774-G-A		not specified	Uncertain significance (Dec 20, 2021)
11-44909828-G-T		not specified	Uncertain significance (Jan 26, 2022)
11-44909869-C-T		TSPAN18-related disorder	Likely benign (Jun 07, 2019)
11-44909873-C-T		not specified	Uncertain significance (Nov 09, 2022)
11-44917975-T-G		not specified	Uncertain significance (Jun 14, 2023)
11-44917989-G-T		TSPAN18-related disorder	Likely benign (Nov 08, 2019)
11-44918041-G-A		not specified	Uncertain significance (Dec 28, 2022)
11-44919277-G-A		TSPAN18-related disorder	Benign (Oct 17, 2019)
11-44919322-G-A		TSPAN18-related disorder	Benign (Nov 19, 2019)
11-44919844-G-A		not specified	Uncertain significance (Jul 16, 2021)
11-44919940-G-A		not specified	Uncertain significance (Nov 10, 2022)
11-44919955-C-T		not specified	Uncertain significance (Jun 26, 2023)
11-44919959-A-C		not specified	Uncertain significance (Jan 04, 2022)
11-44919967-C-T		not specified	Uncertain significance (Dec 16, 2021)
11-44919969-C-T		TSPAN18-related disorder	Benign (Aug 08, 2019)
11-44926684-C-T		not specified	Uncertain significance (Jun 26, 2023)
11-44926712-C-T			Benign (Oct 09, 2017)
11-44926750-C-T		not specified	Uncertain significance (Jul 20, 2021)
11-44929164-C-T		not specified	Uncertain significance (Jun 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPAN18	protein_coding	protein_coding	ENST00000340160	7	205958

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0820	0.909	125733	0	11	125744	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.804	128	156	0.819	0.00000984	1618
Missense in Polyphen		42	51.438	0.81652		543
Synonymous	-0.663	76	69.0	1.10	0.00000474	506
Loss of Function	2.27	4	12.8	0.314	6.94e-7	133

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.0000999	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.244
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.45

Haploinsufficiency Scores

• pHI: 0.0531
• hipred: N
• hipred_score: 0.420
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.131

Mouse Genome Informatics

• Gene name: Tspan18
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype

Gene ontology

• Biological process: cell surface receptor signaling pathway
• Cellular component: integral component of plasma membrane