TSPAN5

tetraspanin 5, the group of Tetraspanins

Basic information

Region (hg38): 4:98470367-98658611

Previous symbols: [ "TM4SF9" ]

Links

ENSG00000168785 ∙ NCBI:10098 ∙ OMIM:613136 ∙ HGNC:17753 ∙ Uniprot:P62079 ∙ 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 TSPAN5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPAN5 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	5	0	2

Variants in TSPAN5

This is a list of pathogenic ClinVar variants found in the TSPAN5 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-98472597-G-A			Benign (Jul 26, 2018)
4-98476427-C-T		not specified	Uncertain significance (Jan 09, 2024)
4-98478706-G-A			Benign (Jul 26, 2018)
4-98482130-C-T		not specified	Uncertain significance (Nov 22, 2022)
4-98482135-G-A		not specified	Uncertain significance (Sep 28, 2022)
4-98482169-C-T		not specified	Uncertain significance (May 27, 2022)
4-98486749-G-T		Malignant tumor of prostate	Uncertain significance (-)
4-98507685-T-C		not specified	Uncertain significance (Jan 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPAN5	protein_coding	protein_coding	ENST00000305798	8	188263

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.910	0.0905	125742	0	5	125747	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.08	78	150	0.521	0.00000774	1784
Missense in Polyphen		22	46.827	0.46981		586
Synonymous	-0.268	61	58.4	1.04	0.00000345	492
Loss of Function	3.31	2	16.5	0.121	8.52e-7	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates ADAM10 maturation and trafficking to the cell surface. Promotes ADAM10-mediated cleavage of CD44. {ECO:0000269|PubMed:26686862}.

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.234
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.330
• hipred: Y
• hipred_score: 0.731
• ghis: 0.648

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.450

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tspan5

Zebrafish Information Network

• Gene name: tspan5b
• Affected structure: central artery
• Phenotype tag: abnormal
• Phenotype quality: decreased branchiness

Gene ontology

• Biological process: cell surface receptor signaling pathway;cellular protein metabolic process;positive regulation of Notch signaling pathway;protein maturation;protein localization to plasma membrane
• Cellular component: endoplasmic reticulum lumen;plasma membrane;integral component of plasma membrane
• Molecular function: enzyme binding