PLPP6

phospholipid phosphatase 6, the group of Phospholipid phosphatases

Basic information

Region (hg38): 9:4662294-4665258

Previous symbols: [ "PPAPDC2" ]

Links

ENSG00000205808 ∙ NCBI:403313 ∙ OMIM:611666 ∙ HGNC:23682 ∙ Uniprot:Q8IY26 ∙ 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 PLPP6 gene.

• not_specified (52 variants)
• PLPP6-related_disorder (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLPP6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000203453.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			52	3	2	57
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	52	5	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLPP6	protein_coding	protein_coding	ENST00000381883	1	2959

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000561	0.484	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.616	190	168	1.13	0.00000837	1838
Missense in Polyphen		69	68.414	1.0086		724
Synonymous	-1.86	104	82.5	1.26	0.00000425	669
Loss of Function	0.205	5	5.52	0.906	2.38e-7	55

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Phosphatase that dephosphorylates presqualene diphosphate (PSDP) into presqualene monophosphate (PSMP), suggesting that it may be indirectly involved in innate immunity. PSDP is a bioactive lipid that rapidly remodels to presqualene monophosphate PSMP upon cell activation. Displays diphosphate phosphatase activity with a substrate preference for PSDP > FDP > phosphatidic acid. {ECO:0000269|PubMed:16464866}.
• Pathway: Metabolism of lipids;Metabolism;Metabolism of steroids;Cholesterol biosynthesis (Consensus)

Intolerance Scores

• rvis_EVS: 0.19
• rvis_percentile_EVS: 67.03

Haploinsufficiency Scores

• pHI: 0.166
• hipred: Y
• hipred_score: 0.505
• ghis: 0.406

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Plpp6
• Phenotype: hematopoietic system phenotype

Gene ontology

• Biological process: cholesterol biosynthetic process;phospholipid dephosphorylation
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: hydrolase activity;lipid phosphatase activity