PLPPR2

protein-coding

phospholipid phosphatase related 2, the group of Phospholipid phosphatase related

Gene summary

Predicted to enable phosphatidate phosphatase activity. Predicted to be involved in phospholipid dephosphorylation; phospholipid metabolic process; and signal transduction. Predicted to be located in membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001393892.1

Inheritance

—

ClinVar variants

U:54B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.05

Max pathogenic AF

—

Genomic locus

chr19:11,355,386-11,365,698

External References & Databases

Ensembl (ENSG00000105520)

Transcript & Mutation Effects

hg38 • Region Span ~10.3 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PLPPR2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 55

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001393892.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				5 clinvar		5
missense			51 clinvar	1 clinvar		52
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	54	6	0	60

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001393892.1	RefSeq	NP_001380821.1	8	MANE Select
ENST00000688289.1	Ensembl	ENSP00000510269.1	8	MANE Select
NM_001170635.2	RefSeq	NP_001164106.1	8	Standard
NM_001393893.1	RefSeq	NP_001380822.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signaling by GPCR
Signal Transduction
Lysosphingolipid and LPA receptors
Class A/1 (Rhodopsin-like receptors)
GPCR ligand binding

Biological Process

phospholipid metabolic process
phospholipid dephosphorylation

Molecular Function

phosphatidate phosphatase activity
phosphatase activity
lipid phosphatase activity

Cellular Component

integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000591608
Coding exons: 8
Length: 10313
Individuals with no LoFs: 125137
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 125138
p: 0.00000400

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.69	203	283	0.717	0.0000192	2645
Missense (PolyPhen)		58	110.11	0.52677		1077
Synonymous	0.401	128	134	0.956	0.00000969	995
Loss of Function	3.75	1	18.3	0.0546	0.00000108	179

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: -0.36
RVIS percentile EVS: 29.16

Essentials

Essential (gene trap): N