PLPP7

phospholipid phosphatase 7 (inactive), the group of Phospholipid phosphatases

Basic information

Region (hg38): 9:131289459-131359022

Previous symbols: [ "C9orf67", "PPAPDC3" ]

Links

ENSG00000160539 ∙ NCBI:84814 ∙ OMIM:618743 ∙ HGNC:28174 ∙ Uniprot:Q8NBV4 ∙ 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 PLPP7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLPP7 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			35	1		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	1	0

Variants in PLPP7

This is a list of pathogenic ClinVar variants found in the PLPP7 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-131290029-G-A		not specified	Uncertain significance (Oct 05, 2023)
9-131290044-T-A		not specified	Uncertain significance (Jan 24, 2025)
9-131290052-C-T		not specified	Uncertain significance (Apr 01, 2024)
9-131290065-T-C		not specified	Uncertain significance (Feb 08, 2025)
9-131290082-C-A		not specified	Uncertain significance (Feb 24, 2025)
9-131290095-C-T		not specified	Uncertain significance (Jul 20, 2021)
9-131290136-G-T		not specified	Uncertain significance (Dec 02, 2022)
9-131290142-C-T		not specified	Uncertain significance (Mar 21, 2023)
9-131290173-G-A		not specified	Uncertain significance (May 12, 2024)
9-131290175-C-T		not specified	Uncertain significance (Aug 09, 2021)
9-131290176-G-A		not specified	Uncertain significance (Nov 16, 2021)
9-131290214-C-G		not specified	Uncertain significance (Aug 02, 2021)
9-131290233-G-A		not specified	Uncertain significance (Mar 29, 2022)
9-131290267-C-G		not specified	Uncertain significance (Jul 08, 2022)
9-131290295-G-C		not specified	Uncertain significance (Jul 26, 2024)
9-131290301-C-T		not specified	Uncertain significance (Mar 16, 2024)
9-131290326-G-T		not specified	Uncertain significance (Aug 26, 2024)
9-131290331-A-G		not specified	Uncertain significance (Jun 22, 2021)
9-131290346-G-A		not specified	Uncertain significance (Aug 19, 2023)
9-131290353-C-T		not specified	Uncertain significance (Feb 16, 2023)
9-131290361-G-A		not specified	Uncertain significance (Mar 14, 2025)
9-131290376-G-A		not specified	Uncertain significance (Apr 06, 2023)
9-131290433-A-G		not specified	Uncertain significance (Jul 30, 2024)
9-131307928-C-T		not specified	Uncertain significance (Mar 25, 2024)
9-131307952-G-A		not specified	Uncertain significance (Sep 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLPP7	protein_coding	protein_coding	ENST00000372264	2	19569

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00800	0.801	125653	0	35	125688	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.730	152	180	0.847	0.0000124	1706
Missense in Polyphen		61	71.946	0.84786		626
Synonymous	0.538	76	82.2	0.925	0.00000611	595
Loss of Function	1.01	4	6.87	0.582	3.70e-7	67

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000121
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000257	0.000246
Middle Eastern	0.0000547	0.0000544
South Asian	0.0000655	0.0000653
Other	0.000172	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role as negative regulator of myoblast differentiation, in part through effects on MTOR signaling. Has no detectable enzymatic activity (By similarity). {ECO:0000250}.

Intolerance Scores

• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.2

Haploinsufficiency Scores

• pHI: 0.132
• hipred: Y
• hipred_score: 0.566
• ghis: 0.539

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Plpp7

Gene ontology

• Biological process: negative regulation of myotube differentiation
• Cellular component: nuclear envelope;endoplasmic reticulum membrane;integral component of membrane