TSPAN31

tetraspanin 31, the group of Tetraspanins

Basic information

Region (hg38): 12:57738012-57750219

Previous symbols: [ "SAS" ]

Links

ENSG00000135452 ∙ NCBI:6302 ∙ OMIM:181035 ∙ HGNC:10539 ∙ Uniprot:Q12999 ∙ 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 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			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			192	132	13	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)
12-57741942-T-C		not specified	Uncertain significance (May 04, 2022)
12-57741966-C-T		not specified	Uncertain significance (Nov 17, 2022)
12-57741989-C-T		not specified	Uncertain significance (Jan 23, 2024)
12-57742040-G-A		AGAP2-related disorder	Likely benign (Sep 05, 2019)
12-57742050-C-T		not specified	Uncertain significance (Sep 06, 2022)
12-57742067-T-C		not specified	Uncertain significance (Jun 21, 2023)
12-57745182-A-G		not specified	Uncertain significance (Aug 21, 2023)
12-57745197-G-T		not specified	Uncertain significance (Feb 15, 2023)
12-57745888-C-A		not specified	Uncertain significance (Aug 02, 2023)
12-57745907-T-C		not specified	Uncertain significance (Dec 15, 2022)
12-57746249-G-C		not specified	Uncertain significance (Jul 20, 2021)
12-57746602-A-G		not specified	Uncertain significance (Jan 24, 2024)
12-57747085-C-G		not specified	Uncertain significance (Aug 03, 2022)
12-57747282-T-C		not specified	Uncertain significance (Nov 21, 2022)
12-57747747-C-CT		Cutaneous Malignant Melanoma, Dominant	Uncertain significance (Jun 14, 2016)
12-57747761-GAC-G		Cutaneous Malignant Melanoma, Dominant	Uncertain significance (Jun 14, 2016)
12-57747774-G-A		Melanoma, cutaneous malignant, susceptibility to, 3	Benign (Jan 13, 2018)
12-57747791-G-A		Melanoma, cutaneous malignant, susceptibility to, 3	Uncertain significance (Apr 27, 2017)
12-57747819-C-T		Melanoma, cutaneous malignant, susceptibility to, 3	Benign (Jan 12, 2018)
12-57747835-C-T		Melanoma, cutaneous malignant, susceptibility to, 3	Uncertain significance (Jan 13, 2018)
12-57747836-G-A		Melanoma, cutaneous malignant, susceptibility to, 3	Uncertain significance (Jan 13, 2018)
12-57748004-C-T		Melanoma, cutaneous malignant, susceptibility to, 3	Benign (Jan 13, 2018)
12-57748034-G-A		Melanoma, cutaneous malignant, susceptibility to, 3	Benign (Jan 12, 2018)
12-57748046-A-G		Melanoma, cutaneous malignant, susceptibility to, 3	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPAN31	protein_coding	protein_coding	ENST00000257910	6	12199

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.219	0.773	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.553	96	113	0.853	0.00000539	1369
Missense in Polyphen		44	55.647	0.79069		686
Synonymous	0.369	39	42.0	0.928	0.00000206	407
Loss of Function	2.31	3	11.4	0.263	5.69e-7	125

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000363	0.000363
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

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

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

Mouse Genome Informatics

• Gene name: Tspan31

Gene ontology

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