PLIN3

perilipin 3, the group of Perilipins

Basic information

Region (hg38): 19:4838340-4867694

Previous symbols: [ "M6PRBP1" ]

Links

ENSG00000105355 ∙ NCBI:10226 ∙ OMIM:602702 ∙ HGNC:16893 ∙ Uniprot:O60664 ∙ 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 PLIN3 gene.

• Inborn genetic diseases (26 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLIN3 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					2	2
missense			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	0	2

Variants in PLIN3

This is a list of pathogenic ClinVar variants found in the PLIN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-4839208-G-A		not specified	Uncertain significance (Aug 08, 2023)
19-4839293-C-T		not specified	Uncertain significance (Dec 05, 2022)
19-4839304-C-A		not specified	Uncertain significance (Feb 14, 2024)
19-4839305-G-A		not specified	Uncertain significance (Jul 30, 2023)
19-4839307-G-A		not specified	Uncertain significance (May 31, 2023)
19-4839320-G-A		not specified	Uncertain significance (Jan 26, 2023)
19-4839325-C-T		not specified	Uncertain significance (May 15, 2023)
19-4839326-G-C		not specified	Uncertain significance (Jan 26, 2022)
19-4839404-G-C		not specified	Uncertain significance (Feb 13, 2023)
19-4839410-G-C		not specified	Uncertain significance (Jan 02, 2024)
19-4839443-G-A		not specified	Uncertain significance (Mar 07, 2023)
19-4839487-A-C		not specified	Uncertain significance (Jun 22, 2021)
19-4839505-C-T		not specified	Uncertain significance (Nov 29, 2021)
19-4839536-G-C		not specified	Uncertain significance (Nov 21, 2022)
19-4847696-T-C		not specified	Uncertain significance (Jun 02, 2023)
19-4847734-C-G		not specified	Uncertain significance (Mar 07, 2024)
19-4847797-G-A		not specified	Uncertain significance (Aug 14, 2023)
19-4847813-G-A		not specified	Uncertain significance (Dec 05, 2022)
19-4847837-G-A		not specified	Uncertain significance (Oct 12, 2021)
19-4847875-G-C		not specified	Uncertain significance (Sep 09, 2021)
19-4847882-C-T		not specified	Uncertain significance (Jan 10, 2023)
19-4847890-G-A		not specified	Uncertain significance (Mar 06, 2023)
19-4852061-C-T		not specified	Uncertain significance (Apr 28, 2023)
19-4852062-C-T			Benign (Aug 16, 2018)
19-4852111-C-T		not specified	Uncertain significance (Sep 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLIN3	protein_coding	protein_coding	ENST00000221957	7	29428

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.18e-7	0.577	125690	0	55	125745	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0888	292	288	1.01	0.0000198	2798
Missense in Polyphen		80	68.667	1.165		691
Synonymous	-0.812	147	135	1.09	0.0000107	893
Loss of Function	1.03	13	17.7	0.735	8.22e-7	186

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000396	0.000392
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000356	0.000352
Middle Eastern	0.000163	0.000163
South Asian	0.00	0.00
Other	0.000332	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for the transport of mannose 6-phosphate receptors (MPR) from endosomes to the trans-Golgi network. {ECO:0000269|PubMed:9590177}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Metabolism of lipids;Metabolism;Triglyceride catabolism;Triglyceride metabolism;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.806
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.7

Haploinsufficiency Scores

• pHI: 0.0927
• hipred: N
• hipred_score: 0.314
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plin3
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: vesicle-mediated transport
• Cellular component: cytoplasm;endosome;Golgi apparatus;lipid droplet;cytosol;endosome membrane;membrane;transport vesicle
• Molecular function: protein binding;cadherin binding