TPTE2

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

Basic information

Region (hg38): 13:19422876-19561625

Links

ENSG00000132958 ∙ NCBI:93492 ∙ OMIM:606791 ∙ HGNC:17299 ∙ Uniprot:Q6XPS3 ∙ 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 TPTE2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPTE2 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						0
missense			31	3		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	31	3	1

Variants in TPTE2

This is a list of pathogenic ClinVar variants found in the TPTE2 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-19423164-C-G		not specified	Uncertain significance (Apr 08, 2022)
13-19425001-T-C		not specified	Uncertain significance (Oct 06, 2021)
13-19426462-G-A		not specified	Uncertain significance (Feb 14, 2023)
13-19430472-C-T		not specified	Uncertain significance (Feb 16, 2023)
13-19430509-T-C		not specified	Uncertain significance (Dec 01, 2022)
13-19432475-C-G		not specified	Uncertain significance (Feb 07, 2023)
13-19432533-A-G		not specified	Uncertain significance (Sep 01, 2021)
13-19436268-T-G		not specified	Uncertain significance (Jan 17, 2024)
13-19436272-T-C		not specified	Uncertain significance (Oct 25, 2022)
13-19438145-C-T		not specified	Uncertain significance (Feb 28, 2024)
13-19450099-G-A		not specified	Likely benign (Apr 19, 2024)
13-19450160-T-C		not specified	Uncertain significance (Feb 07, 2023)
13-19450306-C-T		not specified	Uncertain significance (Jul 14, 2023)
13-19450326-G-T		not specified	Uncertain significance (Dec 19, 2022)
13-19451213-A-C		not specified	Uncertain significance (May 26, 2022)
13-19451215-C-T		not specified	Uncertain significance (Oct 10, 2023)
13-19451216-G-A		not specified	Uncertain significance (Aug 30, 2021)
13-19464461-T-C		not specified	Uncertain significance (Mar 02, 2023)
13-19464497-G-A		not specified	Uncertain significance (Mar 02, 2023)
13-19464518-G-A		not specified	Uncertain significance (Feb 16, 2023)
13-19465293-G-T		not specified	Likely benign (Jan 17, 2023)
13-19465305-T-C		not specified	Uncertain significance (Jan 23, 2024)
13-19465544-A-G		not specified	Likely benign (Jan 18, 2022)
13-19467258-A-C		not specified	Uncertain significance (Jul 19, 2023)
13-19467286-G-A		not specified	Uncertain significance (May 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TPTE2	protein_coding	protein_coding	ENST00000400230	20	113887

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.88e-12	0.820	125103	0	640	125743	0.00255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0509	267	269	0.991	0.0000139	3414
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00374	0.00372
Ashkenazi Jewish	0.000300	0.000298
East Asian	0.000937	0.000925
Finnish	0.000603	0.000601
European (Non-Finnish)	0.00382	0.00380
Middle Eastern	0.000937	0.000925
South Asian	0.00171	0.00170
Other	0.00278	0.00277

dbNSFP

Source: dbNSFP

• Pathway: Metabolism of lipids;3-phosphoinositide degradation;Metabolism;Phosphatidylinositol phosphate metabolism;Synthesis of PIPs at the Golgi membrane;PI Metabolism;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.188

Intolerance Scores

• loftool: 0.118
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.45

Haploinsufficiency Scores

• pHI: 0.0779
• hipred: N
• hipred_score: 0.251

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0365

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tpte

Gene ontology

• Biological process: phosphatidylinositol biosynthetic process;peptidyl-tyrosine dephosphorylation
• Cellular component: Golgi membrane;endoplasmic reticulum membrane;integral component of membrane
• 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