PLPPR5

phospholipid phosphatase related 5, the group of Phospholipid phosphatase related

Basic information

Region (hg38): 1:98890245-99227929

Links

ENSG00000117598 ∙ NCBI:163404 ∙ OMIM:617287 ∙ HGNC:31703 ∙ Uniprot:Q32ZL2 ∙ 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 PLPPR5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLPPR5 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in PLPPR5

This is a list of pathogenic ClinVar variants found in the PLPPR5 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-98914823-C-T		not specified	Uncertain significance (Apr 19, 2024)
1-98914920-C-T		not specified	Uncertain significance (Jan 30, 2024)
1-98921896-T-C		not specified	Uncertain significance (Jul 30, 2023)
1-98922045-T-C		not specified	Uncertain significance (Jan 31, 2024)
1-98922056-C-T		not specified	Uncertain significance (Aug 17, 2022)
1-98956617-C-T		not specified	Uncertain significance (Mar 15, 2023)
1-98956630-G-A		not specified	Uncertain significance (Oct 20, 2023)
1-98956638-G-A		not specified	Uncertain significance (Jan 30, 2024)
1-98956645-T-C		not specified	Uncertain significance (Jul 12, 2023)
1-98956690-A-G		not specified	Uncertain significance (May 13, 2024)
1-99004455-C-A		not specified	Uncertain significance (Aug 02, 2021)
1-99004470-G-A		not specified	Uncertain significance (Mar 31, 2023)
1-99004658-G-A		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLPPR5	protein_coding	protein_coding	ENST00000263177	6	114783

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0593	0.938	125709	0	7	125716	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	126	182	0.693	0.00000857	2084
Missense in Polyphen		30	71.813	0.41775		827
Synonymous	-2.27	92	68.2	1.35	0.00000326	646
Loss of Function	2.58	5	16.2	0.308	0.00000115	158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.000110	0.0000993
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000355	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Induces filopodia formation and promotes neurite growth in a CDC42-independent manner; impedes neurite growth inhibitory- mediated axonal retraction. {ECO:0000250|UniProtKB:Q8BJ52}.
• Pathway: Signaling by GPCR;Signal Transduction;Lysosphingolipid and LPA receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding (Consensus)

Intolerance Scores

• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.42

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.800
• ghis: 0.635

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Plppr5

Gene ontology

• Biological process: phospholipid metabolic process;positive regulation of neuron projection development;phospholipid dephosphorylation;positive regulation of filopodium assembly
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: phosphatidate phosphatase activity;phosphatase activity;lipid phosphatase activity