TPTE

protein-coding

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

Gene summary

This gene encodes a PTEN-related tyrosine phosphatase which may play a role in the signal transduction pathways of the endocrine or spermatogenic function of the testis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]

MANE transcript

NM_199261.4

Inheritance

—

ClinVar variants

U:19B:1

Top phenotype

Autism spectrum disorder

Max pathogenic AF

—

Genomic locus

chr21:10,521,553-10,606,140

External References & Databases

Ensembl (ENSG00000274391)

Transcript & Mutation Effects

hg38 • Region Span ~84.6 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TPTE variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 3

not providedTotal: 2

Autism spectrum disorderTotal: 1

MacrocephalyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_199261.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			12 clinvar			12
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	19	1	0	20

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_199261.4	RefSeq	NP_954870.3	21	MANE Select
ENST00000618007.5	Ensembl	ENSP00000484403.1	21	MANE Select
NM_001290224.2	RefSeq	NP_001277153.2	15	Standard
NM_199259.4	RefSeq	NP_954868.2	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of lipids
Metabolism
Synthesis of PIPs at the Golgi membrane
PI Metabolism
Phospholipid metabolism

Biological Process

protein dephosphorylation
signal transduction
peptidyl-tyrosine dephosphorylation

Molecular Function

protein tyrosine phosphatase activity
protein tyrosine/serine/threonine phosphatase activity

Cellular Component

integral component of membrane

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Could be involved in signal transduction.;

Recessive Scores

pRec: 0.0587

Intolerance Scores

LoFtool: 0.0451
RVIS EVS: 2.94
RVIS percentile EVS: 99.15

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.160

Gene Damage Prediction

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