LIPM

lipase family member M, the group of Lipases

Basic information

Region (hg38): 10:88802729-88820546

Previous symbols: [ "LIPL3" ]

Links

ENSG00000173239 ∙ NCBI:340654 ∙ OMIM:613923 ∙ HGNC:23455 ∙ Uniprot:Q5VYY2 ∙ 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 LIPM gene.

• Inborn genetic diseases (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIPM 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in LIPM

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

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

Position	Type	Phenotype	Significance	ClinVar
10-88802950-G-C		not specified	Uncertain significance (Dec 19, 2023)
10-88808308-T-C		not specified	Uncertain significance (Sep 20, 2023)
10-88808367-C-T		not specified	Uncertain significance (Aug 14, 2023)
10-88814573-T-C		not specified	Uncertain significance (Jan 10, 2023)
10-88814591-G-A		not specified	Uncertain significance (May 27, 2022)
10-88814607-A-G		not specified	Uncertain significance (Oct 14, 2021)
10-88815172-A-G		not specified	Uncertain significance (Mar 22, 2023)
10-88815184-C-T		not specified	Uncertain significance (May 24, 2023)
10-88815202-T-C		not specified	Uncertain significance (Dec 08, 2023)
10-88815214-T-C		not specified	Uncertain significance (May 18, 2023)
10-88816820-G-C		not specified	Uncertain significance (Jan 18, 2023)
10-88816838-C-G		not specified	Uncertain significance (Jan 17, 2024)
10-88817838-G-T		not specified	Uncertain significance (Nov 02, 2023)
10-88817846-C-T		not specified	Uncertain significance (Jan 24, 2024)
10-88817861-G-C		not specified	Uncertain significance (Feb 12, 2024)
10-88817894-C-G		not specified	Uncertain significance (Nov 14, 2023)
10-88820330-G-A		not specified	Uncertain significance (Aug 22, 2023)
10-88820479-G-C		not specified	Uncertain significance (Mar 01, 2023)
10-88820482-G-A		not specified	Uncertain significance (Aug 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LIPM	protein_coding	protein_coding	ENST00000404743	9	17817

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.02e-10	0.292	125168	0	11	125179	0.0000439

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	177	223	0.793	0.0000111	2805
Missense in Polyphen		60	74.728	0.80291		996
Synonymous	1.13	65	77.7	0.836	0.00000404	775
Loss of Function	0.844	17	21.2	0.802	0.00000111	244

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000218	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000476	0.0000442
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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: 0.103

Intolerance Scores

• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.14

Haploinsufficiency Scores

• pHI: 0.191
• hipred: N
• hipred_score: 0.170
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.147

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lipm

Gene ontology

• Biological process: lipid catabolic process;cellular lipid metabolic process;cornification
• Cellular component: extracellular region
• Molecular function: lipoprotein lipase activity;lipase activity