TSPAN11

tetraspanin 11, the group of Tetraspanins

Basic information

Region (hg38): 12:30926427-30996602

Links

ENSG00000110900 ∙ NCBI:441631 ∙ ∙ HGNC:30795 ∙ Uniprot:A1L157 ∙ 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 TSPAN11 gene.

• Inborn genetic diseases (10 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPAN11 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	3		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	7	3	0

Variants in TSPAN11

This is a list of pathogenic ClinVar variants found in the TSPAN11 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-30954071-T-C		not specified	Uncertain significance (Jan 24, 2023)
12-30963928-A-T		not specified	Uncertain significance (Dec 16, 2023)
12-30963941-C-T		not specified	Uncertain significance (Dec 12, 2023)
12-30963997-C-T		not specified	Uncertain significance (Mar 14, 2023)
12-30963998-G-A		not specified	Likely benign (May 09, 2023)
12-30978596-G-C		not specified	Uncertain significance (Feb 09, 2023)
12-30979626-G-A		not specified	Likely benign (Dec 06, 2022)
12-30982525-C-A			Likely benign (Dec 01, 2022)
12-30982544-G-A		not specified	Uncertain significance (Apr 22, 2022)
12-30982593-G-A		not specified	Likely benign (Mar 14, 2023)
12-30982598-G-A		not specified	Uncertain significance (Nov 03, 2022)
12-30982631-A-G		not specified	Uncertain significance (Aug 02, 2021)
12-30983100-G-A		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPAN11	protein_coding	protein_coding	ENST00000261177	7	70173

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.94e-7	0.481	125627	0	121	125748	0.000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0637	156	158	0.986	0.00000992	1616
Missense in Polyphen		54	55.118	0.97972		645
Synonymous	0.679	65	72.3	0.899	0.00000501	504
Loss of Function	0.764	11	14.1	0.780	6.85e-7	155

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000177	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000469	0.0000462
European (Non-Finnish)	0.000344	0.000334
Middle Eastern	0.000109	0.000109
South Asian	0.00238	0.00239
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.528
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.77

Haploinsufficiency Scores

• pHI: 0.0633
• hipred: N
• hipred_score: 0.284
• ghis: 0.510

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.190

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tspan11

Gene ontology

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