PNPLA5

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

Basic information

Region (hg38): 22:43879678-43892013

Links

ENSG00000100341 ∙ NCBI:150379 ∙ OMIM:611589 ∙ HGNC:24888 ∙ Uniprot:Q7Z6Z6 ∙ 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 PNPLA5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PNPLA5 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				1	6	7
missense			28	2	5	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding					1	1
Total	0	0	28	3	12

Variants in PNPLA5

This is a list of pathogenic ClinVar variants found in the PNPLA5 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-43880800-C-A		not specified	Uncertain significance (Sep 20, 2023)
22-43880880-G-A		not specified	Likely benign (Dec 05, 2022)
22-43881570-A-T		not specified	Uncertain significance (Aug 17, 2021)
22-43881580-C-T		not specified	Uncertain significance (May 11, 2022)
22-43881630-A-G		not specified	Uncertain significance (Nov 29, 2023)
22-43881655-C-T		not specified	Uncertain significance (Sep 12, 2023)
22-43881669-A-C		not specified	Uncertain significance (Jan 04, 2022)
22-43881679-A-T		PNPLA5-related disorder	Likely benign (Apr 25, 2019)
22-43884235-A-C		not specified	Uncertain significance (Aug 02, 2023)
22-43884331-A-G		not specified	Uncertain significance (Feb 28, 2023)
22-43886297-C-A		PNPLA5-related disorder	Benign (Aug 01, 2019)
22-43886390-C-G		not specified	Uncertain significance (Jun 12, 2023)
22-43886396-A-G		PNPLA5-related disorder	Benign (Oct 17, 2019)
22-43886400-T-C		PNPLA5-related disorder	Benign (Jun 21, 2019)
22-43886427-G-A		PNPLA5-related disorder	Benign (Oct 17, 2019)
22-43886434-G-A		not specified	Uncertain significance (Dec 19, 2023)
22-43886437-G-A		not specified	Uncertain significance (Dec 28, 2022)
22-43886441-G-A		not specified	Uncertain significance (Apr 12, 2022)
22-43886456-C-A		not specified	Uncertain significance (Aug 26, 2022)
22-43886461-G-A		not specified	Uncertain significance (Feb 17, 2024)
22-43886488-C-A		not specified	Uncertain significance (Apr 25, 2022)
22-43889331-C-T		not specified	Uncertain significance (Jul 19, 2022)
22-43889339-G-A		not specified	Uncertain significance (Feb 15, 2023)
22-43889346-T-C		not specified	Uncertain significance (Dec 22, 2023)
22-43889378-G-A		PNPLA5-related disorder	Benign (Mar 14, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PNPLA5	protein_coding	protein_coding	ENST00000216177	9	12336

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000119	0.822	125595	0	153	125748	0.000609

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.353	241	226	1.07	0.0000125	2725
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00153	0.00149
Ashkenazi Jewish	0.00	0.00
East Asian	0.000220	0.000217
Finnish	0.00117	0.00116
European (Non-Finnish)	0.000829	0.000791
Middle Eastern	0.000220	0.000217
South Asian	0.0000328	0.0000327
Other	0.000667	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Lipid hydrolase. {ECO:0000250}.
• Pathway: Metabolism of lipids;Metabolism;Triglyceride catabolism;Triglyceride metabolism (Consensus)

Recessive Scores

• pRec: 0.0945

Intolerance Scores

• loftool: 0.799
• rvis_EVS: 0.58
• rvis_percentile_EVS: 82.25

Haploinsufficiency Scores

• pHI: 0.180
• hipred: N
• hipred_score: 0.180
• ghis: 0.460

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0704

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pnpla5

Gene ontology

• Biological process: triglyceride catabolic process;lipid homeostasis
• Cellular component: cytoplasm;lipid droplet;cytosol;membrane
• Molecular function: triglyceride lipase activity