LIPM

protein-coding

lipase family member M, the group of Lipases

Gene summary

Predicted to enable lipase activity. Predicted to be involved in lipid metabolic process. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

LIPL3

MANE transcript

NM_001128215.1

Inheritance

—

ClinVar variants

U:51B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr10:88,802,730-88,820,546

External References & Databases

Ensembl (ENSG00000173239)

Transcript & Mutation Effects

hg38 • Region Span ~17.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LIPM variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 53

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001128215.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			51 clinvar	2 clinvar		53
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	51	2	0	53

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001128215.1	RefSeq	NP_001121687.1	9	MANE Select
ENST00000404743.9	Ensembl	ENSP00000383901.3	9	MANE Select
ENST00000539337.2	Ensembl	ENSP00000440375.1	9	Standard
XM_011539748.4	RefSeq	XP_011538050.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Keratinization
Developmental Biology
Formation of the cornified envelope

Biological Process

lipid catabolic process
cellular lipid metabolic process
cornification

Molecular Function

lipoprotein lipase activity
lipase activity

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000404743
Coding exons: 9
Length: 17817
Individuals with no LoFs: 125168
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125179
p: 0.0000439

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.10	177	223	0.793	0.0000111	2805
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000071	0.000062	rare
Latino/Admixed American	0.00015	0.00015	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000048	0.000044	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.103

Intolerance Scores

RVIS EVS: 0.62
RVIS percentile EVS: 83.14

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.147

Gene Damage Prediction

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