TSPAN19

tetraspanin 19, the group of Tetraspanins

Basic information

Region (hg38): 12:85014311-85036277

Links

ENSG00000231738 ∙ NCBI:144448 ∙ ∙ HGNC:31886 ∙ Uniprot:P0C672 ∙ 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 TSPAN19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPAN19 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	2		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	2	0

Variants in TSPAN19

This is a list of pathogenic ClinVar variants found in the TSPAN19 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-85014491-A-G		not specified	Likely benign (May 25, 2022)
12-85015890-C-G		not specified	Uncertain significance (Jan 04, 2022)
12-85017511-T-C		not specified	Uncertain significance (Dec 08, 2021)
12-85017527-G-A		not specified	Uncertain significance (Feb 28, 2024)
12-85017532-T-C		not specified	Uncertain significance (Jul 09, 2021)
12-85017538-G-A		not specified	Uncertain significance (Aug 17, 2022)
12-85017599-A-C		not specified	Uncertain significance (May 12, 2024)
12-85019676-T-C		not specified	Uncertain significance (Feb 08, 2023)
12-85019682-T-C		not specified	Uncertain significance (Oct 12, 2021)
12-85023388-T-A		not specified	Likely benign (Feb 11, 2022)
12-85027936-A-G		not specified	Uncertain significance (Feb 15, 2023)
12-85027951-C-A		not specified	Uncertain significance (Sep 25, 2023)
12-85027961-C-G		not specified	Uncertain significance (Dec 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPAN19	protein_coding	protein_coding	ENST00000532498	8	21962

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.98e-12	0.00898	124118	1	50	124169	0.000205

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.114	95	98.2	0.968	0.00000424	1590
Missense in Polyphen		19	22.271	0.85312		372
Synonymous	0.910	27	33.7	0.801	0.00000158	415
Loss of Function	-0.873	16	12.7	1.26	5.36e-7	188

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000832	0.000819
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.000133
Middle Eastern	0.00	0.00
South Asian	0.000456	0.000393
Other	0.000170	0.000167

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.22
• rvis_percentile_EVS: 67.92

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

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