PLPPR4

phospholipid phosphatase related 4, the group of Phospholipid phosphatase related

Basic information

Region (hg38): 1:99264292-99309590

Links

ENSG00000117600 ∙ NCBI:9890 ∙ OMIM:607813 ∙ HGNC:23496 ∙ Uniprot:Q7Z2D5 ∙ 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 PLPPR4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLPPR4 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	2
missense			29			29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4			4
Total	0	0	33	1	1

Variants in PLPPR4

This is a list of pathogenic ClinVar variants found in the PLPPR4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-99264489-G-T		not specified	Uncertain significance (May 27, 2022)
1-99264523-A-G		not specified	Uncertain significance (Sep 22, 2023)
1-99264531-C-A		not specified	Uncertain significance (Oct 29, 2021)
1-99264555-T-C		not specified	Uncertain significance (Mar 16, 2024)
1-99264585-G-A		not specified	Uncertain significance (Mar 11, 2025)
1-99264598-C-T		not specified	Uncertain significance (Jan 08, 2025)
1-99288102-T-A			Benign (Mar 27, 2018)
1-99288122-G-C		not specified	Uncertain significance (Feb 07, 2025)
1-99288149-C-T		not specified	Uncertain significance (Oct 04, 2022)
1-99296792-G-T		not specified	Uncertain significance (Feb 08, 2025)
1-99299050-G-A		not specified	Uncertain significance (Aug 07, 2023)
1-99300955-G-A		not specified	Uncertain significance (Nov 01, 2022)
1-99301749-A-C		not specified	Uncertain significance (Feb 13, 2024)
1-99301777-G-C			Uncertain significance (May 01, 2019)
1-99305758-T-C		not specified	Uncertain significance (Oct 28, 2023)
1-99305770-A-G		not specified	Uncertain significance (Nov 21, 2023)
1-99305792-A-T		not specified	Uncertain significance (Dec 28, 2023)
1-99305838-G-A		not specified	Uncertain significance (Nov 25, 2024)
1-99305842-T-A		not specified	Uncertain significance (Dec 09, 2023)
1-99305950-T-C		not specified	Uncertain significance (Aug 26, 2024)
1-99305976-G-T		not specified	Uncertain significance (Sep 30, 2024)
1-99305977-C-T		not specified	Uncertain significance (Sep 30, 2024)
1-99306001-C-G		not specified	Uncertain significance (Feb 05, 2024)
1-99306016-C-T		not specified	Uncertain significance (Jun 10, 2022)
1-99306124-C-T		not specified	Uncertain significance (Dec 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLPPR4	protein_coding	protein_coding	ENST00000370185	7	45638

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.861	0.139	125613	0	7	125620	0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.88	266	435	0.612	0.0000232	4977
Missense in Polyphen		64	159.62	0.40095		1810
Synonymous	-0.0328	167	166	1.00	0.00000905	1541
Loss of Function	4.08	5	28.5	0.176	0.00000178	323

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000358	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes lysophosphatidic acid (LPA). Facilitates axonal outgrowth during development and regenerative sprouting. In the outgrowing axons acts as an ecto-enzyme and attenuates phospholipid-induced axon collapse in neurons and facilitates outgrowth in the hippocampus. {ECO:0000269|PubMed:12730698}.
• Pathway: Signaling by GPCR;Signal Transduction;Lysosphingolipid and LPA receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;triacylglycerol biosynthesis (Consensus)

Intolerance Scores

• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.69

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.800
• ghis: 0.528

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Plppr4
• Phenotype: growth/size/body region phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: phospholipid metabolic process;axonogenesis;phospholipid dephosphorylation;inner ear development
• Cellular component: plasma membrane;integral component of plasma membrane;glutamatergic synapse;integral component of postsynaptic density membrane
• Molecular function: phosphatidate phosphatase activity;phosphatase activity;lipid phosphatase activity