PIP5KL1

phosphatidylinositol-4-phosphate 5-kinase like 1

Basic information

Region (hg38): 9:127920881-127930785

Links

ENSG00000167103 ∙ NCBI:138429 ∙ OMIM:612865 ∙ HGNC:28711 ∙ Uniprot:Q5T9C9 ∙ 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 PIP5KL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIP5KL1 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			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	1	0

Variants in PIP5KL1

This is a list of pathogenic ClinVar variants found in the PIP5KL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-127921860-G-A		not specified	Uncertain significance (Aug 31, 2022)
9-127922011-G-A		not specified	Uncertain significance (May 15, 2023)
9-127922043-T-C		not specified	Uncertain significance (Nov 15, 2021)
9-127922086-C-T		not specified	Uncertain significance (Aug 20, 2024)
9-127922095-T-A		not specified	Uncertain significance (Dec 15, 2023)
9-127922101-C-T		not specified	Uncertain significance (Aug 29, 2024)
9-127925117-G-A		not specified	Uncertain significance (Jan 16, 2024)
9-127925153-C-T		not specified	Uncertain significance (Feb 20, 2025)
9-127925183-T-C		not specified	Uncertain significance (Nov 03, 2023)
9-127925207-G-A		not specified	Uncertain significance (May 04, 2022)
9-127925210-G-A		not specified	Uncertain significance (Jun 04, 2024)
9-127925884-C-A		not specified	Uncertain significance (Dec 19, 2022)
9-127925920-G-A		not specified	Uncertain significance (Mar 20, 2024)
9-127925936-C-T		not specified	Uncertain significance (Nov 21, 2022)
9-127927757-G-C		not specified	Uncertain significance (Aug 22, 2022)
9-127928120-C-T		not specified	Uncertain significance (Jul 28, 2021)
9-127928144-A-G		not specified	Uncertain significance (Oct 29, 2021)
9-127928148-C-G		not specified	Likely benign (Apr 06, 2023)
9-127928151-C-A		not specified	Uncertain significance (Dec 18, 2023)
9-127928171-G-A		not specified	Uncertain significance (Mar 06, 2023)
9-127928177-G-T		not specified	Uncertain significance (Jan 22, 2024)
9-127928182-G-A		not specified	Uncertain significance (Jul 09, 2021)
9-127928200-A-G		not specified	Uncertain significance (Mar 20, 2024)
9-127928213-C-T		not specified	Uncertain significance (Dec 23, 2024)
9-127929773-G-A		not specified	Uncertain significance (Jun 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIP5KL1	protein_coding	protein_coding	ENST00000388747	10	9919

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000293	0.939	125723	0	17	125740	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.787	194	227	0.853	0.0000135	2454
Missense in Polyphen		70	72.085	0.97107		860
Synonymous	1.25	83	98.7	0.841	0.00000577	818
Loss of Function	1.73	10	17.9	0.559	8.54e-7	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000205	0.000205
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.000144	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a scaffold to localize and regulate type I PI(4)P 5-kinases to specific compartments within the cell, where they generate PI(4,5)P2 for actin nucleation, signaling and scaffold protein recruitment and conversion to PI(3,4,5)P3. {ECO:0000250}.
• Pathway: Inositol phosphate metabolism - Homo sapiens (human);Endocytosis - Homo sapiens (human);Regulation of Actin Cytoskeleton;D-<i>myo</i>-inositol (1,4,5)-trisphosphate biosynthesis;3-phosphoinositide biosynthesis;superpathway of inositol phosphate compounds (Consensus)

Intolerance Scores

• loftool: 0.733
• rvis_EVS: 0.19
• rvis_percentile_EVS: 67.03

Haploinsufficiency Scores

• pHI: 0.0810
• hipred: N
• hipred_score: 0.441
• ghis: 0.473

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.820

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pip5kl1

Gene ontology

• Biological process: negative regulation of protein phosphorylation;negative regulation of cell migration;phosphatidylinositol phosphorylation
• Cellular component: cytosol;membrane;cell projection
• Molecular function: ATP binding;1-phosphatidylinositol-4-phosphate 5-kinase activity