PLPP5

phospholipid phosphatase 5, the group of Phospholipid phosphatases

Basic information

Region (hg38): 8:38263130-38269243

Previous symbols: [ "PPAPDC1B" ]

Links

ENSG00000147535 ∙ NCBI:84513 ∙ OMIM:610626 ∙ HGNC:25026 ∙ Uniprot:Q8NEB5 ∙ 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 PLPP5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLPP5 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			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	0

Variants in PLPP5

This is a list of pathogenic ClinVar variants found in the PLPP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-38264466-T-G		not specified	Uncertain significance (Jan 06, 2023)
8-38264512-G-A		not specified	Uncertain significance (Dec 18, 2023)
8-38266162-C-G		not specified	Uncertain significance (Aug 12, 2021)
8-38267329-C-T		not specified	Uncertain significance (Feb 28, 2024)
8-38267345-G-A		not specified	Uncertain significance (Dec 09, 2023)
8-38267368-C-A		not specified	Uncertain significance (Nov 22, 2022)
8-38267383-G-C		not specified	Uncertain significance (Mar 28, 2023)
8-38267937-T-G		not specified	Uncertain significance (May 04, 2023)
8-38267943-C-T		not specified	Uncertain significance (Oct 12, 2021)
8-38267949-C-G		not specified	Uncertain significance (Dec 03, 2021)
8-38268394-C-G		not specified	Likely benign (Apr 04, 2024)
8-38269141-A-T		not specified	Uncertain significance (Mar 23, 2022)
8-38269178-C-A		not specified	Uncertain significance (Apr 06, 2022)
8-38269186-G-A		not specified	Uncertain significance (Aug 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLPP5	protein_coding	protein_coding	ENST00000424479	7	6114

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.86e-12	0.00449	124592	0	160	124752	0.000641

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.691	113	136	0.833	0.00000698	1693
Missense in Polyphen		41	46.016	0.89099		494
Synonymous	0.503	49	53.7	0.913	0.00000266	531
Loss of Function	-1.50	15	9.92	1.51	5.06e-7	122

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00940	0.00735
Ashkenazi Jewish	0.00	0.00
East Asian	0.000279	0.000278
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000155	0.000150
Middle Eastern	0.000279	0.000278
South Asian	0.000628	0.000621
Other	0.000217	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Displays magnesium-independent phosphatidate phosphatase activity in vitro. Catalyzes the conversion of phosphatidic acid to diacylglycerol. May be a metastatic suppressor for hepatocellular carcinoma. {ECO:0000269|PubMed:16261160, ECO:0000269|PubMed:17590538}.
• Pathway: Glycerolipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Role of phospholipids in phagocytosis;Fcgamma receptor (FCGR) dependent phagocytosis;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• rvis_EVS: 0.22
• rvis_percentile_EVS: 67.92

Haploinsufficiency Scores

• pHI: 0.100
• hipred: N
• hipred_score: 0.187
• ghis: 0.468

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Plpp5

Gene ontology

• Biological process: phospholipid metabolic process;phospholipid dephosphorylation
• Cellular component: cytoplasm;plasma membrane;integral component of plasma membrane
• Molecular function: phosphatidate phosphatase activity;phosphatase activity