PLIN1

perilipin 1, the group of Perilipins

Basic information

Region (hg38): 15:89664366-89679427

Previous symbols: [ "PLIN" ]

Links

ENSG00000166819 ∙ NCBI:5346 ∙ OMIM:170290 ∙ HGNC:9076 ∙ Uniprot:O60240 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• PLIN1-related familial partial lipodystrophy (Strong), mode of inheritance: AD
• PLIN1-related familial partial lipodystrophy (Disputed Evidence), mode of inheritance: AD
• PLIN1-related familial partial lipodystrophy (Supportive), mode of inheritance: AD
• PLIN1-related familial partial lipodystrophy (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Lipodystrophy, familial partial, type 4	AD	Cardiovascular; Endocrine; Gastrointestinal	Medical treatment of factors such as diabetes, hypertension, and lipid abnormalities may be beneficial to reduce morbidity/mortality; Recognition and treatment of hypertriglyceridemia can help avoid sequelae such as acute pancreatitis	Cardiovascular; Endocrine; Gastrointestinal	21345103; 21757733

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PLIN1 gene.

• not provided (40 variants)
• Inborn genetic diseases (31 variants)
• not specified (15 variants)
• Monogenic diabetes (12 variants)
• PLIN1-related familial partial lipodystrophy (11 variants)
• PLIN1-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLIN1 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	7	6	14
missense			38	6	5	49
nonsense		1				1
start loss						0
frameshift			1	1		2
inframe indel						0
splice donor/acceptor (+/-2bp)	1		1			2
splice region			1		1	2
non coding					16	16
Total	1	1	41	14	27

Highest pathogenic variant AF is 0.0000131

Variants in PLIN1

This is a list of pathogenic ClinVar variants found in the PLIN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-89665596-C-A		not specified	Uncertain significance (Feb 17, 2022)
15-89665596-C-G		not specified	Uncertain significance (Jul 07, 2017)
15-89665645-G-A		not specified	Uncertain significance (Feb 28, 2024)
15-89665704-C-G		not specified	Likely benign (Aug 08, 2022)
15-89665704-C-T		not specified	Uncertain significance (Jan 31, 2022)
15-89665712-CGGCGCTGCGGGCGT-C			Likely benign (Apr 10, 2018)
15-89665720-C-T		not specified	Uncertain significance (Feb 27, 2023)
15-89665757-G-T		PLIN1-related disorder	Likely benign (Jun 13, 2019)
15-89665760-C-A			Benign (Dec 28, 2018)
15-89665766-G-A		not specified	Likely benign (Mar 14, 2016)
15-89665766-G-C		PLIN1-related disorder	Likely benign (Apr 15, 2019)
15-89665767-G-A		not specified	Uncertain significance (Dec 21, 2022)
15-89665777-C-T		not specified	Uncertain significance (Oct 13, 2023)
15-89665828-C-T		not specified	Likely benign (Nov 21, 2022)
15-89665842-CCA-C		PLIN1-related familial partial lipodystrophy	Pathogenic (Feb 21, 2022)
15-89665846-A-G		not specified	Uncertain significance (Oct 05, 2023)
15-89665866-C-G		not specified	Uncertain significance (Mar 21, 2023)
15-89665872-T-C		PLIN1-related familial partial lipodystrophy	Uncertain significance (Oct 15, 2020)
15-89665904-G-A		not specified	Benign (Jun 09, 2021)
15-89665916-G-A			Likely benign (Apr 17, 2018)
15-89665921-C-T		not specified	Uncertain significance (Oct 12, 2022)
15-89665942-G-A		not specified	Uncertain significance (Sep 17, 2021)
15-89665942-GC-G		PLIN1-related familial partial lipodystrophy	Pathogenic (Dec 17, 2020)
15-89665943-C-A		PLIN1-related familial partial lipodystrophy	Pathogenic (Feb 24, 2011)
15-89666927-G-A			Benign (Oct 10, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLIN1	protein_coding	protein_coding	ENST00000300055	8	15063

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.15e-11	0.159	125663	0	85	125748	0.000338

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.930	317	274	1.16	0.0000157	3252
Missense in Polyphen		93	96.438	0.96435		1132
Synonymous	-1.17	134	118	1.14	0.00000729	1095
Loss of Function	0.640	18	21.2	0.850	0.00000131	221

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000597	0.000596
Ashkenazi Jewish	0.000398	0.000397
East Asian	0.000926	0.000925
Finnish	0.00	0.00
European (Non-Finnish)	0.000364	0.000360
Middle Eastern	0.000926	0.000925
South Asian	0.0000653	0.0000653
Other	0.000847	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Modulator of adipocyte lipid metabolism. Coats lipid storage droplets to protect them from breakdown by hormone- sensitive lipase (HSL). Its absence may result in leanness. Plays a role in unilocular lipid droplet formation by activating CIDEC. Their interaction promotes lipid droplet enlargement and directional net neutral lipid transfer. May modulate lipolysis and triglyceride levels. {ECO:0000269|PubMed:23399566}.
• Disease: DISEASE: Lipodystrophy, familial partial, 4 (FPLD4) [MIM:613877]: A form of lipodystrophy characterized by loss of subcutaneous adipose tissue primarily affecting the lower limbs, insulin- resistant diabetes mellitus, hypertriglyceridemia, and hypertension. {ECO:0000269|PubMed:21345103}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Regulation of lipolysis in adipocytes - Homo sapiens (human);Thermogenesis - Homo sapiens (human);Apelin signaling pathway - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);Transcriptional regulation of white adipocyte differentiation;Adipogenesis;PPAR signaling pathway;Lipid Metabolism Pathway;Metabolism of lipids;Metabolism;Triglyceride catabolism;Triglyceride metabolism (Consensus)

Recessive Scores

• pRec: 0.290

Intolerance Scores

• loftool: 0.856
• rvis_EVS: 0.76
• rvis_percentile_EVS: 86.8

Haploinsufficiency Scores

• pHI: 0.143
• hipred: N
• hipred_score: 0.170
• ghis: 0.402

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plin1
• Phenotype: muscle phenotype; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype

Gene ontology

• Biological process: lipid metabolic process;lipid catabolic process
• Cellular component: endoplasmic reticulum;lipid droplet;cytosol
• Molecular function: lipid binding