PNPLA5

protein-coding

patatin like phospholipase domain containing 5, the group of Patatin like phospholipase domain containing

Gene summary

This gene is a member of the patatin-like phospholipase family; its encoded protein has been shown to inhibit transacylation. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Apr 2010]

MANE transcript

NM_138814.4

Inheritance

—

ClinVar variants

U:71B:10

Top phenotype

PNPLA5-related disorder

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr22:43,879,678-43,892,013

External References & Databases

Ensembl (ENSG00000100341)

Transcript & Mutation Effects

hg38 • Region Span ~12.3 kb

Loading mutation effect viewer...

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 PNPLA5 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 73

PNPLA5-related disorderTotal: 9

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138814.4. 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				1 clinvar	3 clinvar	4
missense			70 clinvar	3 clinvar	3 clinvar	76
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	71	4	6	81

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138814.4	RefSeq	NP_620169.1	9	MANE Select
ENST00000216177.9	Ensembl	ENSP00000216177.3	9	MANE Select
NM_001177675.2	RefSeq	NP_001171146.1	7	Standard
NM_001371410.1	RefSeq	NP_001358339.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of lipids
Metabolism
Triglyceride catabolism
Triglyceride metabolism

Biological Process

triglyceride catabolic process
lipid homeostasis

Molecular Function

triglyceride lipase activity

Cellular Component

cytoplasm
lipid droplet
cytosol
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000216177
Coding exons: 9
Length: 12336
Individuals with no LoFs: 125595
Homozygous LoFs: 0
Heterozygous LoFs: 153
Defined: 125748
p: 0.000609

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.353	241	226	1.07	0.0000125	2725
Missense (PolyPhen)		78	73.735	1.0578		892
Synonymous	-0.00928	102	102	1.00	0.00000617	878
Loss of Function	1.40	12	18.5	0.648	7.95e-7	215

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0013	0.0012	notable
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.0012	0.0012	notable
European (Non-Finnish)	0.00083	0.00079	rare
South Asian	0.000033	0.000033	rare
Other	0.00067	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Lipid hydrolase. {ECO:0000250}.;

Recessive Scores

pRec: 0.0945

Intolerance Scores

LoFtool: 0.799
RVIS EVS: 0.58
RVIS percentile EVS: 82.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.0704

Gene Damage Prediction

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