TSPAN6

tetraspanin 6, the group of Tetraspanins

Basic information

Region (hg38): X:100627108-100639991

Previous symbols: [ "TM4SF6" ]

Links

ENSG00000000003 ∙ NCBI:7105 ∙ OMIM:300191 ∙ HGNC:11858 ∙ Uniprot:O43657 ∙ 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 TSPAN6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPAN6 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				2	1	3
missense			4	2		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	4	1

Variants in TSPAN6

This is a list of pathogenic ClinVar variants found in the TSPAN6 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-100630848-C-T		not specified	Uncertain significance (Dec 30, 2023)
X-100633480-T-C			Likely benign (Sep 01, 2022)
X-100633518-C-T		not specified	Likely benign (Jan 16, 2024)
X-100633968-T-A		not specified	Uncertain significance (Aug 08, 2022)
X-100633985-C-T			Benign (May 02, 2018)
X-100635229-A-G			Likely benign (Apr 01, 2022)
X-100635575-C-T			Likely benign (Dec 01, 2022)
X-100635647-C-G		not specified	Uncertain significance (Jul 14, 2021)
X-100636666-G-A		not specified	Uncertain significance (Jul 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPAN6	protein_coding	protein_coding	ENST00000373020	7	11322

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0661	0.877	125723	1	3	125727	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.592	66	81.0	0.815	0.00000591	1599
Missense in Polyphen		13	18.408	0.7062		384
Synonymous	-0.475	34	30.7	1.11	0.00000248	457
Loss of Function	1.61	3	7.87	0.381	5.56e-7	166

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000771	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0692

Intolerance Scores

• loftool: 0.568
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.89

Haploinsufficiency Scores

• pHI: 0.0712
• hipred: N
• hipred_score: 0.231
• ghis: 0.490

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tspan6

Gene ontology

• Biological process: cell surface receptor signaling pathway;negative regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway;positive regulation of I-kappaB kinase/NF-kappaB signaling;negative regulation of NIK/NF-kappaB signaling
• Cellular component: integral component of plasma membrane;extracellular exosome
• Molecular function: protein binding