PLPP4

phospholipid phosphatase 4, the group of Phospholipid phosphatases

Basic information

Region (hg38): 10:120457227-120592065

Previous symbols: [ "PPAPDC1", "PPAPDC1A" ]

Links

ENSG00000203805 ∙ NCBI:196051 ∙ ∙ HGNC:23531 ∙ Uniprot:Q5VZY2 ∙ 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 PLPP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLPP4 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in PLPP4

This is a list of pathogenic ClinVar variants found in the PLPP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-120503895-A-G		not specified	Uncertain significance (Oct 21, 2024)
10-120513975-A-C		not specified	Uncertain significance (Jul 26, 2021)
10-120520981-G-A		not specified	Uncertain significance (May 17, 2023)
10-120520994-G-A		not specified	Uncertain significance (Dec 09, 2023)
10-120521047-G-A		not specified	Uncertain significance (Nov 13, 2023)
10-120521066-G-A		not specified	Uncertain significance (Nov 29, 2023)
10-120575181-C-T		not specified	Uncertain significance (Oct 04, 2022)
10-120575186-C-G		not specified	Uncertain significance (Dec 19, 2022)
10-120575193-G-A		not specified	Uncertain significance (Aug 07, 2024)
10-120575193-G-C		not specified	Uncertain significance (Sep 06, 2022)
10-120575220-C-T		not specified	Uncertain significance (Jan 03, 2024)
10-120575256-A-T		not specified	Uncertain significance (Mar 15, 2024)
10-120589390-A-G		not specified	Uncertain significance (Feb 13, 2024)
10-120589401-G-A		not specified	Uncertain significance (Nov 13, 2024)
10-120589452-G-A		not specified	Uncertain significance (Jul 14, 2024)
10-120589457-C-T		not specified	Likely benign (May 22, 2023)
10-120589458-G-A		not specified	Uncertain significance (Nov 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLPP4	protein_coding	protein_coding	ENST00000398250	7	132902

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000183	0.903	124785	0	22	124807	0.0000881

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.15	124	166	0.748	0.00000992	1753
Missense in Polyphen		40	59.242	0.6752		607
Synonymous	0.991	55	65.2	0.844	0.00000421	542
Loss of Function	1.50	8	14.1	0.568	7.66e-7	158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000398	0.000397
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000223
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000353
Middle Eastern	0.000223	0.000223
South Asian	0.0000658	0.0000654
Other	0.000332	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Displays magnesium-independent phosphatidate phosphatase activity in vitro. Catalyzes the conversion of phosphatidic acid to diacylglycerol. {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;triacylglycerol biosynthesis (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.186
• hipred: Y
• hipred_score: 0.661
• ghis: 0.563

Mouse Genome Informatics

• Gene name: Plpp4

Gene ontology

• Biological process: blastocyst hatching;phospholipid metabolic process;Fc-gamma receptor signaling pathway involved in phagocytosis;phospholipid dephosphorylation
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: phosphatidate phosphatase activity;phosphatase activity;identical protein binding