TPTE2

protein-coding

transmembrane phosphoinositide 3-phosphatase and tensin homolog 2, the group of C2 tensin-type domain containing|PTEN protein phosphatases

Gene summary

TPIP is a member of a large class of membrane-associated phosphatases with substrate specificity for the 3-position phosphate of inositol phospholipids.[supplied by OMIM, Jul 2002]

MANE transcript

NM_001395978.1

Inheritance

—

ClinVar variants

U:82B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chr13:19,422,876-19,561,625

External References & Databases

Ensembl (ENSG00000132958)

Transcript & Mutation Effects

hg38 • Region Span ~138.7 kb

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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 TPTE2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 81

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001395978.1. 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						0
missense			78 clinvar	7 clinvar		85
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	82	7	0	89

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001395978.1	RefSeq	NP_001382907.1	20	MANE Select
ENST00000697147.1	Ensembl	ENSP00000513136.1	20	MANE Select
NM_001141968.2	RefSeq	NP_001135440.1	17	Standard
NM_001271850.2	RefSeq	NP_001258779.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of lipids
3-phosphoinositide degradation
Metabolism
Phosphatidylinositol phosphate metabolism
Synthesis of PIPs at the Golgi membrane

Biological Process

phosphatidylinositol biosynthetic process
peptidyl-tyrosine dephosphorylation

Molecular Function

protein tyrosine phosphatase activity
protein tyrosine/serine/threonine phosphatase activity
phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity
phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity

Cellular Component

Golgi membrane
endoplasmic reticulum membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000400230
Coding exons: 20
Length: 113887
Individuals with no LoFs: 125103
Homozygous LoFs: 0
Heterozygous LoFs: 640
Defined: 125743
p: 0.00255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0509	267	269	0.991	0.0000139	3414
Missense (PolyPhen)		62	68.51	0.90498		971
Synonymous	-0.0128	92	91.8	1.00	0.00000480	935
Loss of Function	1.82	24	35.7	0.672	0.00000205	417

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0010	0.00098	notable
Latino/Admixed American	0.0027	0.0026	notable
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00094	0.00092	rare
Finnish	0.00060	0.00060	rare
European (Non-Finnish)	0.0038	0.0038	notable
South Asian	0.0017	0.0017	notable
Other	0.0028	0.0028	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.188

Intolerance Scores

LoFtool: 0.118
RVIS EVS: -0.18
RVIS percentile EVS: 40.45

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0365

Gene Damage Prediction

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