TPTE

transmembrane phosphatase with tensin homology, the group of C2 tensin-type domain containing|PTEN protein phosphatases

Basic information

Region (hg38): 21:10521553-10606140

Links

ENSG00000274391 ∙ NCBI:7179 ∙ OMIM:604336 ∙ HGNC:12023 ∙ Uniprot:P56180 ∙ 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 TPTE gene.

• not_specified (3 variants)
• not_provided (2 variants)
• Autism_spectrum_disorder (1 variants)
• Macrocephaly (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPTE gene is commonly pathogenic or not. These statistics are base on transcript: NM_000199261.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			3			3
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	4	1	0

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Could be involved in signal transduction.
• Pathway: Metabolism of lipids;Metabolism;Synthesis of PIPs at the Golgi membrane;PI Metabolism;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.0587

Intolerance Scores

• loftool: 0.0451
• rvis_EVS: 2.94
• rvis_percentile_EVS: 99.15

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.160

Gene Damage Prediction

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

Gene ontology

• Biological process: protein dephosphorylation;signal transduction;peptidyl-tyrosine dephosphorylation
• Cellular component: integral component of membrane
• Molecular function: protein tyrosine phosphatase activity;protein tyrosine/serine/threonine phosphatase activity