PIP4P2

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

Basic information

Region (hg38): 8:90993802-91040872

Previous symbols: [ "TMEM55A" ]

Links

ENSG00000155099NCBI:55529OMIM:609864HGNC:25452Uniprot:Q8N4L2AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PIP4P2 gene.

  • not_specified (30 variants)

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. These statistics are base on transcript: NM_000018710.3. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
0
missense
30
clinvar
30
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 30 0 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PIP4P2protein_codingprotein_codingENST00000285419 747269
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0004220.9651257340141257480.0000557
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.211061470.7200.000007681638
Missense in Polyphen5178.6280.64862918
Synonymous1.034150.30.8160.00000234527
Loss of Function1.88816.10.4960.00000109162

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00009220.0000922
Ashkenazi Jewish0.000.00
East Asian0.00005450.0000544
Finnish0.000.00
European (Non-Finnish)0.00008940.0000879
Middle Eastern0.00005450.0000544
South Asian0.00003430.0000327
Other0.000.00

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

loftool
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_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
N
gene_indispensability_pred
gene_indispensability_score

Mouse Genome Informatics

Gene name
Pip4p2
Phenotype

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