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.

• not_specified (32 variants)
• not_provided (9 variants)
• PNPLA4-related_disorder (1 variants)
• Abnormality_of_neuronal_migration (1 variants)

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. These statistics are base on transcript: NM_000004650.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3	1	4
missense			33	2	2	37
nonsense			1			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	34	5	3

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