PNPLA7

protein-coding

patatin like phospholipase domain containing 7, the group of Patatin like phospholipase domain containing

Gene summary

Human patatin-like phospholipases, such as PNPLA7, have been implicated in regulation of adipocyte differentiation and have been induced by metabolic stimuli (Wilson et al., 2006 [PubMed 16799181]).[supplied by OMIM, Jun 2008]

Previous symbols:

C9orf111

MANE transcript

NM_001098537.3

Inheritance

—

ClinVar variants

U:290B:32

Top phenotype

PNPLA7-related condition

gnomAD constraint

pLI —, LoF o/e 0.87

Max pathogenic AF

—

Genomic locus

chr9:137,459,952-137,550,402

External References & Databases

Ensembl (ENSG00000130653)

Transcript & Mutation Effects

hg38 • Region Span ~90.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PNPLA7 variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 292

not providedTotal: 10

PNPLA7-related conditionTotal: 2

Premature ovarian failureTotal: 1

Peripheral neuropathy, autosomal recessive, with or without impaired intellectual developmentTotal: 1

Mulibrey nanism syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001098537.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	6 clinvar	1 clinvar	9
missense			281 clinvar	23 clinvar	1 clinvar	305
nonsense			2 clinvar		1 clinvar	3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	290	29	3	322

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001098537.3	RefSeq	NP_001092007.2	35	MANE Select
ENST00000406427.6	Ensembl	ENSP00000384610.1	35	MANE Select
NM_152286.5	RefSeq	NP_689499.4	34	Standard
ENST00000277531.8	Ensembl	ENSP00000277531.4	34	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glycerophospholipid metabolism - Homo sapiens (human)
Metabolism of lipids
Metabolism
Glycerophospholipid catabolism
PI Metabolism

Biological Process

lipid catabolic process

Molecular Function

lysophospholipase activity

Cellular Component

lysosomal membrane
endoplasmic reticulum
integral component of membrane
nuclear membrane
mitochondrial membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000406427
Coding exons: 35
Length: 90583
Individuals with no LoFs: 121932
Homozygous LoFs: 16
Heterozygous LoFs: 3799
Defined: 125747
p: 0.0153

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.690	801	858	0.934	0.0000586	8580
Missense (PolyPhen)		309	347.3	0.88973		3639
Synonymous	-0.542	390	377	1.04	0.0000281	2747
Loss of Function	1.00	61	70.0	0.871	0.00000357	771

Population LoF Frequency

Population	CAF	p-value	Status
African	0.022	0.020	notable
Latino/Admixed American	0.0075	0.0073	notable
Ashkenazi Jewish	0.020	0.020	notable
East Asian	0.0018	0.0017	notable
Finnish	0.013	0.012	notable
European (Non-Finnish)	0.024	0.022	notable
South Asian	0.0046	0.0043	notable
Other	0.015	0.014	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Serine hydrolase, whose specific chemical modification by certain organophosphorus (OP) compounds leads to distal axonopathy. {ECO:0000250}.;

Recessive Scores

pRec: 0.0978

Intolerance Scores

LoFtool: 0.230
RVIS EVS: 0.16
RVIS percentile EVS: 64.97

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.359

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium