LPIN3

lipin 3, the group of Lipins

Basic information

Region (hg38): 20:41340821-41360582

Previous symbols: [ "LIPN3L" ]

Links

ENSG00000132793 ∙ NCBI:64900 ∙ OMIM:605520 ∙ HGNC:14451 ∙ Uniprot:Q9BQK8 ∙ 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 LPIN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LPIN3 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				4		4
missense			42	3	1	46
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				1		1
Total	0	0	43	8	1

Variants in LPIN3

This is a list of pathogenic ClinVar variants found in the LPIN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-41345827-G-A			Likely benign (Mar 01, 2023)
20-41345862-G-A			Benign (Mar 29, 2018)
20-41345887-C-G		not specified	Uncertain significance (Mar 20, 2024)
20-41345900-G-A		not specified	Uncertain significance (Jul 14, 2022)
20-41345944-C-G			Likely benign (Aug 01, 2022)
20-41345951-G-C		not specified	Uncertain significance (Nov 06, 2023)
20-41345955-G-A		not specified	Uncertain significance (Mar 18, 2024)
20-41345972-G-A		not specified	Uncertain significance (Aug 08, 2022)
20-41347616-C-A		not specified	Uncertain significance (Dec 15, 2022)
20-41348661-G-C		not specified	Uncertain significance (Feb 17, 2023)
20-41348724-G-A		not specified	Uncertain significance (Aug 14, 2023)
20-41348737-C-T		not specified	Likely benign (Oct 17, 2023)
20-41348749-GGCGGAGGAAGAGGC-G			Uncertain significance (Aug 01, 2022)
20-41348762-G-C		not specified	Uncertain significance (Mar 31, 2024)
20-41348764-G-A		not specified	Uncertain significance (Jun 29, 2023)
20-41348767-G-A		not specified	Uncertain significance (May 17, 2023)
20-41348767-G-T		not specified	Uncertain significance (Nov 14, 2023)
20-41349092-T-C			Likely benign (Aug 01, 2022)
20-41349799-C-T		not specified	Uncertain significance (Jan 19, 2022)
20-41349818-T-C		not specified	Uncertain significance (Oct 06, 2023)
20-41349827-G-A		not specified	Uncertain significance (Dec 13, 2023)
20-41349833-C-T		not specified	Uncertain significance (May 29, 2024)
20-41350080-C-T		not specified	Uncertain significance (May 20, 2024)
20-41350125-G-C		not specified	Uncertain significance (Feb 27, 2023)
20-41350139-A-C		not specified	Uncertain significance (Nov 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LPIN3	protein_coding	protein_coding	ENST00000373257	19	19663

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.25e-13	0.955	125313	1	434	125748	0.00173

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.652	466	507	0.919	0.0000302	5477
Missense in Polyphen		132	156.34	0.84429		1662
Synonymous	1.03	196	215	0.910	0.0000133	1755
Loss of Function	2.24	27	42.9	0.630	0.00000211	480

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00783	0.00780
Ashkenazi Jewish	0.00	0.00
East Asian	0.000435	0.000435
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00134	0.00132
Middle Eastern	0.000435	0.000435
South Asian	0.00131	0.00118
Other	0.00197	0.00196

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates fatty acid metabolism. Magnesium-dependent phosphatidate phosphatase enzyme which catalyzes the conversion of phosphatidic acid to diacylglycerol during triglyceride, phosphatidylcholine and phosphatidylethanolamine biosynthesis (By similarity). {ECO:0000250}.
• Pathway: Glycerolipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Adipogenesis;Metabolism of lipids;Metabolism;Synthesis of PC;Synthesis of PE;Triglyceride biosynthesis;Triglyceride metabolism;Depolymerisation of the Nuclear Lamina;Nuclear Envelope Breakdown;Mitotic Prophase;Glycerophospholipid biosynthesis;Phospholipid metabolism;M Phase;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.431
• rvis_EVS: 0.56
• rvis_percentile_EVS: 81.72

Haploinsufficiency Scores

• pHI: 0.147
• hipred: N
• hipred_score: 0.234
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.511

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lpin3
• Phenotype: immune system phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: phosphatidylethanolamine biosynthetic process;phosphatidylcholine biosynthetic process;fatty acid catabolic process;dephosphorylation;triglyceride biosynthetic process;cellular response to insulin stimulus;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;endoplasmic reticulum membrane
• Molecular function: transcription coactivator activity;phosphatidate phosphatase activity