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.

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.

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			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	0

Variants in PLPP6

This is a list of pathogenic ClinVar variants found in the PLPP6 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-4662369-A-C		PLPP6-related disorder	Benign (Oct 17, 2019)
9-4662394-A-G		PLPP6-related disorder	Benign (Nov 05, 2019)
9-4662398-T-C		PLPP6-related disorder	Benign (Mar 06, 2019)
9-4662433-A-G		not specified	Uncertain significance (Mar 14, 2025)
9-4662464-G-A		not specified	Uncertain significance (Oct 12, 2022)
9-4662490-G-A		not specified	Uncertain significance (Feb 14, 2025)
9-4662498-G-T		not specified	Uncertain significance (Jan 17, 2025)
9-4662508-A-G		not specified	Uncertain significance (Dec 10, 2024)
9-4662518-C-G		not specified	Uncertain significance (Mar 17, 2023)
9-4662544-C-T		not specified	Uncertain significance (Apr 12, 2024)
9-4662564-C-G		not specified	Uncertain significance (Dec 30, 2023)
9-4662580-G-A		PLPP6-related disorder	Benign (Mar 22, 2019)
9-4662581-G-C		not specified	Uncertain significance (Mar 05, 2025)
9-4662602-C-T		not specified	Uncertain significance (Mar 18, 2024)
9-4662626-C-T		not specified	Uncertain significance (Mar 07, 2025)
9-4662637-G-C		not specified	Uncertain significance (Sep 01, 2024)
9-4662647-G-A		not specified	Uncertain significance (Jan 16, 2024)
9-4662661-C-G		not specified	Uncertain significance (Nov 30, 2022)
9-4662692-T-G		not specified	Uncertain significance (Sep 16, 2021)
9-4662719-A-G		not specified	Uncertain significance (May 24, 2023)
9-4662730-G-T		not specified	Uncertain significance (May 04, 2022)
9-4662744-G-C		not specified	Uncertain significance (Oct 19, 2024)
9-4662748-T-C		not specified	Uncertain significance (Sep 25, 2023)
9-4662882-G-A		PLPP6-related disorder	Likely benign (Jul 11, 2022)
9-4662905-T-C		not specified	Uncertain significance (Feb 15, 2023)

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