PLPPR1

phospholipid phosphatase related 1, the group of Phospholipid phosphatase related

Basic information

Region (hg38): 9:101028726-101325135

Links

ENSG00000148123 ∙ NCBI:54886 ∙ OMIM:619590 ∙ HGNC:25993 ∙ Uniprot:Q8TBJ4 ∙ 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 PLPPR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLPPR1 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			13
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	0	0

Variants in PLPPR1

This is a list of pathogenic ClinVar variants found in the PLPPR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-101269925-T-G		not specified	Uncertain significance (Jun 07, 2024)
9-101269926-G-A		not specified	Uncertain significance (Apr 08, 2024)
9-101270000-A-G		not specified	Uncertain significance (Aug 21, 2023)
9-101286134-A-G		not specified	Uncertain significance (Mar 29, 2022)
9-101286224-A-G		not specified	Uncertain significance (Dec 13, 2023)
9-101309337-C-T		not specified	Uncertain significance (May 04, 2022)
9-101309384-G-A		not specified	Uncertain significance (Apr 05, 2023)
9-101309460-C-T		not specified	Uncertain significance (May 24, 2023)
9-101312823-C-T		not specified	Uncertain significance (Oct 26, 2021)
9-101312912-C-T		not specified	Uncertain significance (Jul 08, 2022)
9-101317416-C-T		not specified	Uncertain significance (Dec 14, 2023)
9-101317430-T-A		not specified	Uncertain significance (Aug 16, 2022)
9-101324035-C-T		not specified	Uncertain significance (Oct 06, 2021)
9-101324040-A-G		not specified	Uncertain significance (Sep 22, 2022)
9-101324043-A-G		not specified	Uncertain significance (Mar 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLPPR1	protein_coding	protein_coding	ENST00000374874	7	296427

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.566	0.433	125719	0	4	125723	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.44	135	191	0.707	0.0000106	2109
Missense in Polyphen		38	72.198	0.52633		756
Synonymous	-0.537	80	74.1	1.08	0.00000454	659
Loss of Function	2.94	3	15.5	0.194	8.83e-7	177

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.809
• ghis: 0.591

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Plppr1

Gene ontology

• Biological process: phospholipid metabolic process;nervous system development;phospholipid dephosphorylation
• Cellular component: nucleoplasm;integral component of plasma membrane
• Molecular function: phosphatidate phosphatase activity;phosphatase activity;lipid phosphatase activity