LIPM

lipase family member M, the group of Lipases

Basic information

Region (hg38): 10:88802730-88820546

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.

• not_specified (44 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. These statistics are base on transcript: NM_001128215.1. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			44			44
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	44	0	0

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