TSPAN9

tetraspanin 9, the group of Tetraspanins

Basic information

Region (hg38): 12:3077355-3286564

Links

ENSG00000011105NCBI:10867OMIM:613137HGNC:21640Uniprot:O75954AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TSPAN9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPAN9 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
15
clinvar
1
clinvar
16
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 15 1 0

Variants in TSPAN9

This is a list of pathogenic ClinVar variants found in the TSPAN9 region.

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

Position Type Phenotype Significance ClinVar
12-3201215-T-C not specified Uncertain significance (Feb 26, 2024)3183854
12-3201253-C-G not specified Uncertain significance (Mar 22, 2023)2528201
12-3278451-A-G not specified Uncertain significance (Mar 03, 2022)2226409
12-3278521-A-C not specified Uncertain significance (Apr 05, 2023)2532998
12-3278522-C-A not specified Uncertain significance (May 15, 2023)2546291
12-3278523-C-A not specified Uncertain significance (Jul 27, 2022)2379261
12-3278532-G-A not specified Uncertain significance (Dec 20, 2023)3183852
12-3278536-T-C not specified Uncertain significance (Sep 25, 2023)3183853
12-3278602-T-G not specified Uncertain significance (May 24, 2023)2551020
12-3278996-T-G not specified Uncertain significance (Jan 23, 2024)3183855
12-3279010-G-A not specified Likely benign (Mar 15, 2024)3329662
12-3280394-G-A not specified Uncertain significance (Mar 18, 2024)3329661
12-3281202-G-A not specified Uncertain significance (Feb 22, 2023)2462232
12-3281238-C-T not specified Uncertain significance (Jun 04, 2024)3329665
12-3281268-G-A not specified Uncertain significance (May 06, 2024)3329664
12-3281306-G-A not specified Likely benign (Dec 11, 2023)3183856
12-3281786-G-T not specified Uncertain significance (Oct 21, 2024)2263256
12-3281789-C-T not specified Uncertain significance (Dec 04, 2024)3462969
12-3281799-G-A not specified Uncertain significance (Oct 17, 2023)3183857
12-3281810-T-C not specified Uncertain significance (Jul 26, 2021)2379939
12-3283057-G-A not specified Uncertain significance (Feb 01, 2023)2455720

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TSPAN9protein_codingprotein_codingENST00000011898 7209210
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.6590.3401257340101257440.0000398
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.38961420.6740.000008061577
Missense in Polyphen2748.2220.55991564
Synonymous-0.4606560.41.080.00000411451
Loss of Function2.70212.10.1655.14e-7143

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00008670.0000867
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00002640.0000264
Middle Eastern0.000.00
South Asian0.00009810.0000980
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Recessive Scores

pRec
0.124

Intolerance Scores

loftool
0.270
rvis_EVS
-0.65
rvis_percentile_EVS
16.36

Haploinsufficiency Scores

pHI
0.166
hipred
Y
hipred_score
0.696
ghis
0.611

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.135

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Tspan9
Phenotype

Gene ontology

Biological process
cell surface receptor signaling pathway;biological_process
Cellular component
plasma membrane;integral component of plasma membrane;focal adhesion;tetraspanin-enriched microdomain
Molecular function
molecular_function