TSPAN16

tetraspanin 16, the group of Tetraspanins

Basic information

Region (hg38): 19:11296139-11326996

Previous symbols: [ "TM4SF16" ]

Links

ENSG00000130167NCBI:26526OMIM:617580HGNC:30725Uniprot:Q9UKR8AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TSPAN16 gene.

  • not_specified (29 variants)

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. These statistics are base on transcript: NM_001282509.2. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
0
missense
27
clinvar
2
clinvar
29
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 27 2 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TSPAN16protein_codingprotein_codingENST00000316737 730849
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.000004090.3931257110371257480.000147
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.4171551411.100.000007911566
Missense in Polyphen4541.521.0838521
Synonymous-0.1866563.11.030.00000428509
Loss of Function0.445910.60.8524.42e-7141

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003370.000337
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.0001320.000132
Middle Eastern0.000.00
South Asian0.0005230.000523
Other0.000.00

dbNSFP

Source: dbNSFP

Recessive Scores

pRec
0.0857

Intolerance Scores

loftool
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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Gene ontology

Biological process
cell surface receptor signaling pathway
Cellular component
integral component of plasma membrane;integral component of membrane
Molecular function