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TSPAN31

tetraspanin 31, the group of Tetraspanins

Basic information

Region (hg38): 12:57738012-57750219

Previous symbols: [ "SAS" ]

Links

ENSG00000135452NCBI:6302OMIM:181035HGNC:10539Uniprot:Q12999AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TSPAN31 gene.

  • Familial melanoma (261 variants)
  • Hereditary cancer-predisposing syndrome (172 variants)
  • not provided (59 variants)
  • not specified (38 variants)
  • Melanoma, cutaneous malignant, susceptibility to, 3 (31 variants)
  • Inborn genetic diseases (6 variants)
  • Cutaneous Malignant Melanoma, Dominant (4 variants)
  • CDK4-related condition (2 variants)
  • Ewing sarcoma (1 variants)
  • Diffuse pediatric-type high-grade glioma, H3-wildtype and IDH-wildtype (1 variants)
  • Ovarian cancer (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPAN31 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
6
clinvar
6
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
192
clinvar
132
clinvar
13
clinvar
337
Total 0 0 198 132 13

Variants in TSPAN31

This is a list of pathogenic ClinVar variants found in the TSPAN31 region.

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

Position Type Phenotype Significance ClinVar
12-57741915-G-T Likely benign (Jan 01, 2023)2643150
12-57741942-T-C not specified Uncertain significance (May 04, 2022)3093682
12-57741966-C-T not specified Uncertain significance (Nov 17, 2022)3093670
12-57741989-C-T not specified Uncertain significance (Jan 23, 2024)3093829
12-57742040-G-A AGAP2-related condition Likely benign (Sep 05, 2019)3052503
12-57742050-C-T not specified Uncertain significance (Sep 06, 2022)2212680
12-57742067-T-C not specified Uncertain significance (Jun 21, 2023)2590321
12-57745182-A-G not specified Uncertain significance (Aug 21, 2023)2619829
12-57745197-G-T not specified Uncertain significance (Feb 15, 2023)2484791
12-57745888-C-A not specified Uncertain significance (Aug 02, 2023)2589657
12-57745907-T-C not specified Uncertain significance (Dec 15, 2022)2354729
12-57746249-G-C not specified Uncertain significance (Jul 20, 2021)3183825
12-57746602-A-G not specified Uncertain significance (Jan 24, 2024)3183826
12-57747085-C-G not specified Uncertain significance (Aug 03, 2022)2357961
12-57747282-T-C not specified Uncertain significance (Nov 21, 2022)2402229
12-57747747-C-CT Cutaneous Malignant Melanoma, Dominant Uncertain significance (Jun 14, 2016)309963
12-57747761-GAC-G Cutaneous Malignant Melanoma, Dominant Uncertain significance (Jun 14, 2016)309964
12-57747774-G-A Melanoma, cutaneous malignant, susceptibility to, 3 Benign (Jan 13, 2018)882172
12-57747791-G-A Melanoma, cutaneous malignant, susceptibility to, 3 Uncertain significance (Apr 27, 2017)882173
12-57747819-C-T Melanoma, cutaneous malignant, susceptibility to, 3 Benign (Jan 12, 2018)309965
12-57747835-C-T Melanoma, cutaneous malignant, susceptibility to, 3 Uncertain significance (Jan 13, 2018)309966
12-57747836-G-A Melanoma, cutaneous malignant, susceptibility to, 3 Uncertain significance (Jan 13, 2018)309967
12-57748004-C-T Melanoma, cutaneous malignant, susceptibility to, 3 Benign (Jan 13, 2018)309968
12-57748034-G-A Melanoma, cutaneous malignant, susceptibility to, 3 Benign (Jan 12, 2018)309969
12-57748046-A-G Melanoma, cutaneous malignant, susceptibility to, 3 Uncertain significance (Jan 13, 2018)309970

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TSPAN31protein_codingprotein_codingENST00000257910 612199
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.2190.7731257230251257480.0000994
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.553961130.8530.000005391369
Missense in Polyphen4455.6470.79069686
Synonymous0.3693942.00.9280.00000206407
Loss of Function2.31311.40.2635.69e-7125

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003630.000363
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.0001320.000132
Middle Eastern0.00005440.0000544
South Asian0.00003270.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Recessive Scores

pRec
0.105

Intolerance Scores

loftool
0.600
rvis_EVS
0.17
rvis_percentile_EVS
65.33

Haploinsufficiency Scores

pHI
0.328
hipred
N
hipred_score
0.475
ghis
0.544

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.640

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Tspan31
Phenotype

Gene ontology

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