PIP4P1

phosphatidylinositol-4,5-bisphosphate 4-phosphatase 1, the group of Phosphoinositide phosphatases

Basic information

Region (hg38): 14:20457681-20461465

Previous symbols: [ "C14orf9", "TMEM55B" ]

Links

ENSG00000165782 ∙ NCBI:90809 ∙ OMIM:609865 ∙ HGNC:19299 ∙ Uniprot:Q86T03 ∙ 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 PIP4P1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIP4P1 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					1	1
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	19	0	1

Variants in PIP4P1

This is a list of pathogenic ClinVar variants found in the PIP4P1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-20458571-C-G		not specified	Uncertain significance (Jan 31, 2022)
14-20458608-A-G		not specified	Uncertain significance (Apr 23, 2024)
14-20458615-G-A		not specified	Uncertain significance (Aug 04, 2021)
14-20458632-G-A		not specified	Uncertain significance (Aug 05, 2024)
14-20458637-C-G			Benign (Dec 26, 2018)
14-20458677-C-T		not specified	Uncertain significance (Jan 08, 2024)
14-20458686-T-C		not specified	Uncertain significance (Jun 17, 2024)
14-20459262-A-G		not specified	Uncertain significance (Oct 12, 2023)
14-20459265-T-C		not specified	Uncertain significance (Feb 06, 2024)
14-20459270-C-T		not specified	Uncertain significance (Jan 05, 2022)
14-20459283-G-A		not specified	Uncertain significance (May 26, 2022)
14-20459422-G-A		not specified	Uncertain significance (Sep 01, 2021)
14-20460185-C-T			Likely benign (Aug 01, 2024)
14-20460767-G-C		not specified	Uncertain significance (Aug 11, 2024)
14-20460788-G-C		not specified	Uncertain significance (Aug 27, 2024)
14-20460843-A-G		not specified	Uncertain significance (Sep 16, 2021)
14-20461166-G-C		not specified	Uncertain significance (May 28, 2024)
14-20461187-C-T		not specified	Uncertain significance (Nov 09, 2024)
14-20461219-C-T		not specified	Uncertain significance (Apr 12, 2022)
14-20461232-C-T		not specified	Uncertain significance (Jul 30, 2023)
14-20461276-C-T		not specified	Uncertain significance (Mar 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIP4P1	protein_coding	protein_coding	ENST00000398020	7	3894

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.875	0.125	125744	0	4	125748	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.54	96	149	0.644	0.00000822	1798
Missense in Polyphen		28	57.39	0.48789		657
Synonymous	0.601	47	52.5	0.895	0.00000247	598
Loss of Function	3.19	2	15.6	0.128	0.00000103	166

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000267	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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);Gene expression (Transcription);Synthesis of PIPs in the nucleus;Generic Transcription Pathway;Metabolism of lipids;RNA Polymerase II Transcription;PI5P Regulates TP53 Acetylation;3-phosphoinositide degradation;Metabolism;D-<i>myo</i>-inositol-5-phosphate metabolism;superpathway of inositol phosphate compounds;Regulation of TP53 Activity through Acetylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;PI Metabolism;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• rvis_EVS: -0.27
• rvis_percentile_EVS: 33.97

Haploinsufficiency Scores

• pHI: 0.330
• hipred: Y
• hipred_score: 0.662
• ghis: 0.627

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Pip4p1

Gene ontology

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