LIPK

lipase family member K, the group of Lipases

Basic information

Region (hg38): 10:88706249-88752776

Previous symbols: [ "LIPL2" ]

Links

ENSG00000204021 ∙ NCBI:643414 ∙ OMIM:613922 ∙ HGNC:23444 ∙ Uniprot:Q5VXJ0 ∙ 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 LIPK gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIPK 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			21	3		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	3	0

Variants in LIPK

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

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

Position	Type	Phenotype	Significance	ClinVar
10-88724554-T-C		not specified	Uncertain significance (Sep 17, 2021)
10-88724599-G-A		not specified	Uncertain significance (Dec 19, 2022)
10-88724620-A-G		not specified	Uncertain significance (Oct 29, 2021)
10-88724634-G-A		not specified	Uncertain significance (Mar 03, 2022)
10-88726796-G-A		LIPK-related disorder	Likely benign (May 30, 2023)
10-88731079-C-T		not specified	Uncertain significance (May 12, 2024)
10-88731110-C-A		not specified	Uncertain significance (Feb 22, 2023)
10-88732200-G-A		not specified	Uncertain significance (Dec 13, 2022)
10-88732224-A-T		not specified	Uncertain significance (Nov 19, 2022)
10-88732227-A-G		not specified	Likely benign (Jan 04, 2022)
10-88732266-C-A		not specified	Uncertain significance (Dec 09, 2023)
10-88732513-A-G		not specified	Uncertain significance (May 09, 2023)
10-88732514-T-C		not specified	Uncertain significance (Sep 17, 2021)
10-88737723-G-A		not specified	Likely benign (Jan 05, 2022)
10-88737768-A-C		not specified	Uncertain significance (Apr 12, 2022)
10-88740006-A-T		not specified	Uncertain significance (Sep 16, 2021)
10-88740012-A-T		not specified	Uncertain significance (Sep 15, 2021)
10-88740016-G-T		not specified	Uncertain significance (Sep 15, 2021)
10-88740051-T-G		not specified	Uncertain significance (Jun 21, 2021)
10-88743253-G-T		not specified	Uncertain significance (Jul 06, 2021)
10-88743314-T-G		not specified	Uncertain significance (Oct 06, 2021)
10-88752521-C-G		not specified	Uncertain significance (Jun 28, 2023)
10-88752647-A-G		not specified	Uncertain significance (Dec 13, 2021)
10-88752668-A-G		not specified	Uncertain significance (Jun 22, 2021)
10-88752736-G-A		not specified	Uncertain significance (May 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LIPK	protein_coding	protein_coding	ENST00000404190	9	28243

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000176	0.879	124603	5	445	125053	0.00180

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.137	194	199	0.973	0.00000963	2599
Missense in Polyphen		56	64.991	0.86165		926
Synonymous	-0.276	69	66.1	1.04	0.00000317	707
Loss of Function	1.55	12	19.4	0.619	9.68e-7	242

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000818	0.000815
Ashkenazi Jewish	0.000100	0.0000993
East Asian	0.00135	0.00131
Finnish	0.0113	0.0110
European (Non-Finnish)	0.00120	0.00117
Middle Eastern	0.00135	0.00131
South Asian	0.000952	0.000915
Other	0.00152	0.00148

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a highly specific role in the last step of keratinocyte differentiation. May have an essential function in lipid metabolism of the most differentiated epidermal layers. {ECO:0000269|PubMed:17562024}.
• Pathway: Keratinization;Developmental Biology;Formation of the cornified envelope (Consensus)

Recessive Scores

• pRec: 0.0961

Intolerance Scores

• loftool: 0.799
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.49

Haploinsufficiency Scores

• pHI: 0.326
• hipred: N
• hipred_score: 0.131
• ghis: 0.418

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.165

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lipk

Gene ontology

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