PIP4P2

phosphatidylinositol-4,5-bisphosphate 4-phosphatase 2, the group of Phosphoinositide phosphatases

Basic information

Region (hg38): 8:90993802-91040872

Previous symbols: [ "TMEM55A" ]

Links

ENSG00000155099 ∙ NCBI:55529 ∙ OMIM:609864 ∙ HGNC:25452 ∙ Uniprot:Q8N4L2 ∙ 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 PIP4P2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIP4P2 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in PIP4P2

This is a list of pathogenic ClinVar variants found in the PIP4P2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-90995712-T-C		not specified	Uncertain significance (Apr 13, 2022)
8-90995789-C-T		not specified	Uncertain significance (Dec 14, 2023)
8-90995795-C-T		not specified	Uncertain significance (Jun 29, 2023)
8-90996671-T-C		not specified	Uncertain significance (Dec 14, 2021)
8-90996674-A-T		not specified	Uncertain significance (Aug 16, 2021)
8-90996680-A-G		not specified	Uncertain significance (Apr 25, 2022)
8-90996715-C-G		not specified	Uncertain significance (Apr 21, 2022)
8-90996718-C-T		not specified	Uncertain significance (Aug 09, 2021)
8-91018506-T-C		not specified	Uncertain significance (Dec 12, 2022)
8-91020173-A-T		not specified	Uncertain significance (Dec 12, 2023)
8-91020184-C-T		not specified	Uncertain significance (Oct 06, 2021)
8-91020193-T-C		not specified	Uncertain significance (Jun 06, 2023)
8-91020221-G-C		not specified	Uncertain significance (Aug 08, 2022)
8-91020248-G-T		not specified	Uncertain significance (Apr 25, 2024)
8-91021368-G-A		not specified	Uncertain significance (Sep 16, 2021)
8-91040707-C-T		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIP4P2	protein_coding	protein_coding	ENST00000285419	7	47269

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000422	0.965	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	106	147	0.720	0.00000768	1638
Missense in Polyphen		51	78.628	0.64862		918
Synonymous	1.03	41	50.3	0.816	0.00000234	527
Loss of Function	1.88	8	16.1	0.496	0.00000109	162

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000922	0.0000922
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000894	0.0000879
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000343	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate. Does not hydrolyze phosphatidylinositol 3,4,5-trisphosphate, phosphatidylinositol 3,4-bisphosphate, inositol 3,5-bisphosphate, inositol 3,4- bisphosphate, phosphatidylinositol 5-monophosphate, phosphatidylinositol 4-monophosphate and phosphatidylinositol 3- monophosphate. {ECO:0000269|PubMed:16365287}.
• Pathway: Phosphatidylinositol signaling system - Homo sapiens (human);3-phosphoinositide degradation;D-<i>myo</i>-inositol-5-phosphate metabolism;superpathway of inositol phosphate compounds (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.424
• hipred: N
• hipred_score: 0.331
• ghis: 0.517

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Pip4p2

Gene ontology

• Biological process: phosphatidylinositol dephosphorylation
• Cellular component: lysosomal membrane;integral component of membrane;late endosome membrane
• Molecular function: phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity