PNPLA4

patatin like phospholipase domain containing 4, the group of Patatin like phospholipase domain containing

Basic information

Region (hg38): X:7898247-7927739

Links

ENSG00000006757 ∙ NCBI:8228 ∙ OMIM:300102 ∙ HGNC:24887 ∙ Uniprot:P41247 ∙ 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 PNPLA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PNPLA4 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				3	1	4
missense			21	2	2	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	5	3

Variants in PNPLA4

This is a list of pathogenic ClinVar variants found in the PNPLA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-7900694-A-C		not specified	Uncertain significance (Jan 29, 2025)
X-7900695-C-A		not specified	Uncertain significance (Dec 07, 2024)
X-7900772-G-C		not specified	Uncertain significance (Mar 14, 2023)
X-7900780-A-G		not specified	Uncertain significance (Dec 23, 2024)
X-7902054-C-T		not specified	Uncertain significance (Dec 21, 2023)
X-7902059-C-T		not specified	Uncertain significance (Jun 27, 2022)
X-7902060-G-A			Uncertain significance (Jul 28, 2020)
X-7902086-G-T		not specified	Uncertain significance (Feb 25, 2025)
X-7902089-C-T		not specified	Uncertain significance (Jan 04, 2024)
X-7902113-G-A		not specified	Uncertain significance (Jan 22, 2024)
X-7902114-C-T		not specified	Uncertain significance (Feb 03, 2023)
X-7902115-G-A			Likely benign (Dec 13, 2018)
X-7902124-G-A			Benign (Jul 11, 2018)
X-7902138-A-T		not specified	Uncertain significance (Aug 10, 2023)
X-7921766-T-C		not specified	Uncertain significance (Dec 06, 2022)
X-7921772-C-T		not specified	Likely benign (Dec 11, 2023)
X-7921775-T-C		not specified	Uncertain significance (Jan 02, 2024)
X-7921787-C-T			Benign (Dec 31, 2019)
X-7921795-C-T		not specified	Uncertain significance (Nov 10, 2024)
X-7922010-C-T		not specified	Likely benign (Dec 02, 2022)
X-7922028-C-T		not specified	Uncertain significance (Jan 04, 2025)
X-7922029-C-T		not specified	Uncertain significance (Jan 06, 2023)
X-7922036-T-C			Likely benign (Apr 01, 2023)
X-7922038-C-T			Uncertain significance (Aug 01, 2023)
X-7922048-A-C			Likely benign (May 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PNPLA4	protein_coding	protein_coding	ENST00000381042	6	29493

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00257	0.801	125699	9	11	125719	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.146	101	97.0	1.04	0.00000748	1632
Missense in Polyphen		42	40.263	1.0431		605
Synonymous	-0.0410	45	44.7	1.01	0.00000400	520
Loss of Function	1.05	5	8.25	0.606	7.51e-7	120

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000460	0.000396
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000728	0.0000544
Finnish	0.0000629	0.0000462
European (Non-Finnish)	0.0000611	0.0000440
Middle Eastern	0.0000728	0.0000544
South Asian	0.000214	0.000131
Other	0.000226	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Lipid hydrolase.
• Pathway: Retinol metabolism - Homo sapiens (human);Vitamin A Deficiency;Retinol Metabolism;Metabolism of lipids;Metabolism;Triglyceride catabolism;Triglyceride metabolism;triacylglycerol degradation (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.629
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.146
• hipred: N
• hipred_score: 0.256
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.317

Gene Damage Prediction

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

Gene ontology

• Biological process: biological_process;triglyceride catabolic process;retinol metabolic process
• Cellular component: mitochondrion;cytosol
• Molecular function: triglyceride lipase activity;retinyl-palmitate esterase activity