TSPAN32

tetraspanin 32, the group of Tetraspanins

Basic information

Region (hg38): 11:2301996-2318204

Previous symbols: [ "TSSC6", "PHEMX" ]

Links

ENSG00000064201 ∙ NCBI:10077 ∙ OMIM:603853 ∙ HGNC:13410 ∙ Uniprot:Q96QS1 ∙ 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 TSPAN32 gene.

• Inborn genetic diseases (25 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPAN32 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			24	1	1	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	1

Variants in TSPAN32

This is a list of pathogenic ClinVar variants found in the TSPAN32 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-2302174-G-T		not specified	Uncertain significance (Mar 29, 2023)
11-2302889-G-T		not specified	Uncertain significance (Jun 23, 2023)
11-2302893-C-T		not specified	Uncertain significance (Feb 05, 2024)
11-2302910-C-T		not specified	Uncertain significance (Aug 15, 2023)
11-2302914-G-T		not specified	Uncertain significance (May 10, 2023)
11-2302943-G-C		not specified	Uncertain significance (Nov 12, 2021)
11-2304154-G-A			Benign (Apr 20, 2018)
11-2304163-G-A		not specified	Uncertain significance (Nov 13, 2023)
11-2304175-G-A		not specified	Uncertain significance (Dec 01, 2022)
11-2304184-G-T		not specified	Uncertain significance (Mar 28, 2023)
11-2313679-A-G		not specified	Uncertain significance (Nov 09, 2021)
11-2313681-G-A		not specified	Uncertain significance (May 16, 2022)
11-2313712-C-T		not specified	Uncertain significance (Dec 06, 2022)
11-2313720-G-T		not specified	Uncertain significance (Jun 29, 2023)
11-2313723-C-T		not specified	Likely benign (Oct 12, 2021)
11-2316248-G-A		not specified	Uncertain significance (Dec 01, 2022)
11-2316289-A-G		not specified	Uncertain significance (Mar 02, 2023)
11-2316298-G-A		not specified	Uncertain significance (Dec 22, 2023)
11-2316582-G-A		not specified	Uncertain significance (Jul 08, 2022)
11-2316616-T-C		not specified	Uncertain significance (Sep 25, 2023)
11-2316618-C-A		not specified	Uncertain significance (Dec 13, 2022)
11-2316619-G-A		not specified	Uncertain significance (Oct 20, 2023)
11-2316663-C-T		not specified	Uncertain significance (May 22, 2023)
11-2317375-C-T		not specified	Likely benign (Oct 17, 2023)
11-2317388-C-G		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPAN32	protein_coding	protein_coding	ENST00000182290	10	16204

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000217	0.913	125456	0	102	125558	0.000406

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.329	197	184	1.07	0.0000113	1988
Missense in Polyphen		47	47.492	0.98963		646
Synonymous	-0.203	82	79.7	1.03	0.00000531	648
Loss of Function	1.60	10	17.2	0.582	9.45e-7	184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000147	0.000147
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000474	0.0000441
Middle Eastern	0.000165	0.000163
South Asian	0.00285	0.00285
Other	0.000327	0.000327

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.692
• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.51

Haploinsufficiency Scores

• pHI: 0.0736
• hipred: N
• hipred_score: 0.180
• ghis: 0.463

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tspan32
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: cytoskeleton organization;cell surface receptor signaling pathway;integrin-mediated signaling pathway;cell-cell signaling;negative regulation of cell population proliferation;negative regulation of myeloid dendritic cell activation;defense response to protozoan;regulation of defense response to virus;platelet aggregation
• Cellular component: integral component of plasma membrane;cell surface;integrin alphaIIb-beta3 complex
• Molecular function: molecular_function