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.

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.

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 clinvar		1
missense			3 clinvar			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding					1 clinvar	1
Total	0	0	3	1	1

Variants in TPTE

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

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

Position	Phenotype	Significance	ClinVar
21-10541121-G-T		Likely benign (Mar 28, 2018)	713837
21-10541137-G-C	not specified	Uncertain significance (Aug 02, 2021)	2333487
21-10552695-C-G	not specified	Uncertain significance (Aug 13, 2021)	2361661
21-10561044-T-C	not specified	Uncertain significance (Oct 26, 2021)	2214242
21-10561201-A-G		Benign (Sep 01, 2017)	791664
21-10602053-CAT-C	Autism spectrum disorder;Macrocephaly	Uncertain significance (Dec 22, 2014)	189392

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

pHI
hipred: N
hipred_score: 0.112
ghis

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2
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