TSPAN16

tetraspanin 16, the group of Tetraspanins

Basic information

Region (hg38): 19:11296138-11326996

Previous symbols: [ "TM4SF16" ]

Links

ENSG00000130167 ∙ NCBI:26526 ∙ OMIM:617580 ∙ HGNC:30725 ∙ Uniprot:Q9UKR8 ∙ 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 TSPAN16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPAN16 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			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	12	1	0

Variants in TSPAN16

This is a list of pathogenic ClinVar variants found in the TSPAN16 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-11296317-C-T		not specified	Uncertain significance (Jun 26, 2023)
19-11296323-C-T		not specified	Uncertain significance (Nov 07, 2023)
19-11296361-G-A		not specified	Uncertain significance (Feb 15, 2023)
19-11298146-C-T		not specified	Uncertain significance (Feb 01, 2023)
19-11298151-A-G		not specified	Likely benign (Aug 08, 2022)
19-11298172-A-G		not specified	Uncertain significance (Jan 23, 2023)
19-11298329-C-A		not specified	Uncertain significance (Oct 04, 2022)
19-11301231-G-A		not specified	Uncertain significance (Dec 12, 2022)
19-11301235-C-T		not specified	Uncertain significance (Dec 27, 2023)
19-11301264-G-A		not specified	Uncertain significance (Dec 01, 2022)
19-11312206-G-A		not specified	Uncertain significance (Aug 13, 2021)
19-11325497-C-T		not specified	Uncertain significance (Mar 06, 2023)
19-11325526-G-A		not specified	Uncertain significance (Apr 07, 2023)
19-11325529-C-T		not specified	Uncertain significance (Mar 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPAN16	protein_coding	protein_coding	ENST00000316737	7	30849

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000409	0.393	125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.417	155	141	1.10	0.00000791	1566
Missense in Polyphen		45	41.52	1.0838		521
Synonymous	-0.186	65	63.1	1.03	0.00000428	509
Loss of Function	0.445	9	10.6	0.852	4.42e-7	141

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000337	0.000337
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.00	0.00
South Asian	0.000523	0.000523
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0857

Intolerance Scores

• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.29

Haploinsufficiency Scores

• pHI: 0.0491
• hipred: N
• hipred_score: 0.146
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0626

Gene Damage Prediction

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

Gene ontology

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