LIPJ

lipase family member J, the group of Lipases

Basic information

Region (hg38): 10:88586753-88606976

Previous symbols: [ "LIPL1" ]

Links

ENSG00000204022 ∙ NCBI:142910 ∙ OMIM:613921 ∙ HGNC:21773 ∙ Uniprot:Q5W064 ∙ 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 LIPJ gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIPJ 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						0
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in LIPJ

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

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

Position	Type	Phenotype	Significance	ClinVar
10-88591411-G-A		not specified	Uncertain significance (Feb 13, 2024)
10-88591439-G-A		not specified	Uncertain significance (Jun 16, 2023)
10-88591484-A-G		not specified	Uncertain significance (Jan 31, 2024)
10-88593967-T-G		not specified	Uncertain significance (Apr 25, 2023)
10-88594018-A-G		not specified	Uncertain significance (Nov 15, 2021)
10-88594024-G-A		not specified	Uncertain significance (Nov 18, 2023)
10-88594080-G-A		not specified	Uncertain significance (Oct 05, 2023)
10-88594117-C-T		not specified	Uncertain significance (Jun 05, 2023)
10-88594764-G-T		not specified	Uncertain significance (Jan 03, 2022)
10-88596827-C-T		not specified	Uncertain significance (May 01, 2022)
10-88596845-G-A		not specified	Uncertain significance (Jun 28, 2022)
10-88596880-A-G		not specified	Uncertain significance (Jun 29, 2023)
10-88602632-G-T		not specified	Uncertain significance (Nov 15, 2021)
10-88606764-G-A		not specified	Uncertain significance (Mar 25, 2024)
10-88606774-T-C		not specified	Uncertain significance (Nov 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LIPJ	protein_coding	protein_coding	ENST00000371939	9	20224

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.82e-8	0.489	125693	0	35	125728	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.198	169	176	0.958	0.00000795	2429
Missense in Polyphen		61	67.601	0.90235		937
Synonymous	0.147	59	60.5	0.976	0.00000295	617
Loss of Function	0.905	13	17.0	0.763	7.19e-7	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000257	0.000253
Ashkenazi Jewish	0.00	0.00
East Asian	0.000294	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000172	0.000167
Middle Eastern	0.000294	0.000272
South Asian	0.000171	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Keratinization;Developmental Biology;Formation of the cornified envelope (Consensus)

Recessive Scores

• pRec: 0.0913

Intolerance Scores

• loftool: 0.734
• rvis_EVS: 1.4
• rvis_percentile_EVS: 94.7

Haploinsufficiency Scores

• pHI: 0.0943
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.135

Gene Damage Prediction

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

Gene ontology

• Biological process: lipid catabolic process;cellular lipid metabolic process
• Cellular component: intracellular membrane-bounded organelle
• Molecular function: lipase activity