TSPAN14

tetraspanin 14, the group of Tetraspanins

Basic information

Region (hg38): 10:80454265-80533124

Previous symbols: [ "TM4SF14" ]

Links

ENSG00000108219 ∙ NCBI:81619 ∙ ∙ HGNC:23303 ∙ Uniprot:Q8NG11 ∙ 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 TSPAN14 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSPAN14 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					1	1
missense			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	1

Variants in TSPAN14

This is a list of pathogenic ClinVar variants found in the TSPAN14 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-80489284-C-T			Benign (Feb 09, 2018)
10-80507261-A-T		not specified	Likely benign (Jun 16, 2023)
10-80509403-G-A		not specified	Uncertain significance (Mar 29, 2022)
10-80509451-A-C		not specified	Uncertain significance (Nov 03, 2022)
10-80509470-C-T		not specified	Uncertain significance (Feb 16, 2023)
10-80512159-G-T		not specified	Uncertain significance (Jan 26, 2022)
10-80512244-T-A		not specified	Uncertain significance (Jul 15, 2021)
10-80512255-G-A		not specified	Uncertain significance (Nov 08, 2021)
10-80514035-C-T		not specified	Uncertain significance (Oct 02, 2023)
10-80516235-C-T		not specified	Uncertain significance (Feb 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSPAN14	protein_coding	protein_coding	ENST00000429989	8	78958

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.979	0.0209	125745	0	3	125748	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.21	90	171	0.525	0.0000109	1772
Missense in Polyphen		23	69.885	0.32911		759
Synonymous	-0.0666	75	74.3	1.01	0.00000523	509
Loss of Function	3.50	1	16.2	0.0616	7.78e-7	173

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates maturation and trafficking of the transmembrane metalloprotease ADAM10 (PubMed:26668317, PubMed:23035126, PubMed:26686862). Negatively regulates ADAM10- mediated cleavage of GP6 (By similarity). Promotes ADAM10-mediated cleavage of CDH5 (By similarity). {ECO:0000250|UniProtKB:Q8QZY6, ECO:0000269|PubMed:23035126, ECO:0000269|PubMed:26668317, ECO:0000269|PubMed:26686862}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.162
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.07

Haploinsufficiency Scores

• pHI: 0.161
• hipred: Y
• hipred_score: 0.728
• ghis: 0.614

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.415

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tspan14

Gene ontology

• Biological process: cell surface receptor signaling pathway;neutrophil degranulation;cellular protein metabolic process;positive regulation of Notch signaling pathway;protein maturation;protein localization to plasma membrane
• Cellular component: endoplasmic reticulum lumen;plasma membrane;integral component of plasma membrane;cell surface;specific granule membrane;tertiary granule membrane;tetraspanin-enriched microdomain
• Molecular function: enzyme binding