TSPAN4

tetraspanin 4, the group of Tetraspanins

Basic information

Region (hg38): 11:842812-867116

Previous symbols: [ "TM4SF7" ]

Links

ENSG00000214063 ∙ ∙ OMIM:602644 ∙ HGNC:11859 ∙ Uniprot:O14817 ∙ 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 TSPAN4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPAN4 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in TSPAN4

This is a list of pathogenic ClinVar variants found in the TSPAN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-850311-C-G		not specified	Uncertain significance (Apr 18, 2024)
11-862565-G-A		not specified	Uncertain significance (Sep 29, 2023)
11-862592-G-A		not specified	Uncertain significance (Mar 29, 2024)
11-862610-G-A		not specified	Uncertain significance (Sep 27, 2021)
11-862688-G-A		not specified	Uncertain significance (Apr 07, 2023)
11-862694-G-A		not specified	Uncertain significance (Feb 06, 2023)
11-862701-G-A		not specified	Uncertain significance (Jul 19, 2023)
11-862727-T-C		not specified	Uncertain significance (May 31, 2023)
11-864477-C-T		not specified	Uncertain significance (Apr 25, 2023)
11-864497-G-A		not specified	Uncertain significance (Jun 18, 2021)
11-865709-G-A		not specified	Uncertain significance (Jul 09, 2021)
11-865731-T-C		not specified	Uncertain significance (Nov 30, 2022)
11-865966-G-A		not specified	Uncertain significance (Feb 05, 2024)
11-865991-C-T		not specified	Uncertain significance (Nov 19, 2022)
11-865997-T-C		not specified	Uncertain significance (Sep 14, 2023)
11-866580-G-A		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPAN4	protein_coding	protein_coding	ENST00000397404	7	24309

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.42e-8	0.263	125534	0	50	125584	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.397	167	153	1.09	0.00000991	1525
Missense in Polyphen		54	53.395	1.0113		576
Synonymous	-3.12	112	77.1	1.45	0.00000603	487
Loss of Function	0.438	12	13.8	0.872	6.87e-7	139

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000300	0.000298
Ashkenazi Jewish	0.00	0.00
East Asian	0.000492	0.000489
Finnish	0.00	0.00
European (Non-Finnish)	0.000198	0.000194
Middle Eastern	0.000492	0.000489
South Asian	0.000360	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.343
• rvis_EVS: -0.96
• rvis_percentile_EVS: 9.17

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.463
• ghis: 0.615

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.967

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tspan4

Gene ontology

• Biological process: cell surface receptor signaling pathway;protein-containing complex assembly
• Cellular component: plasma membrane;integral component of plasma membrane;focal adhesion;vesicle
• Molecular function: antigen binding;integrin binding;protein binding