LIPM

Summary

LIPM (lipase family member M, HGNC:23455) is a protein-coding gene on chromosome 10q23.31, encoding Lipase member M (Q5VYY2). Plays a highly specific role in the last step of keratinocyte differentiation.

Predicted to enable lipoprotein lipase activity. Predicted to be involved in cornification. Predicted to be located in extracellular region.

Source: NCBI Gene 340654 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 45 total
• MANE Select transcript: NM_001128215

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23455
Approved symbol	LIPM
Name	lipase family member M
Location	10q23.31
Locus type	gene with protein product
Status	Approved
Aliases	bA304I5.1
Ensembl gene	ENSG00000173239
Ensembl biotype	protein_coding
OMIM	613923
Entrez	340654

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000404743, ENST00000539337

RefSeq mRNA: 1 — MANE Select: NM_001128215 NM_001128215

CCDS: CCDS44457

Canonical transcript exons

ENST00000404743 — 9 exons

Exon	Start	End
ENSE00001006983	88808298	88808415
ENSE00001097597	88816816	88816887
ENSE00001097600	88817825	88817896
ENSE00001097602	88815357	88815503
ENSE00001097605	88814530	88814639
ENSE00001097611	88815088	88815224
ENSE00001551500	88802730	88803043
ENSE00002522684	88813097	88813295
ENSE00003903572	88820232	88820546

Expression profiles

Bgee: expression breadth broad, 39 present calls, max score 85.94.

Top tissues by expression

107 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
skin of leg	UBERON:0001511	85.94	gold quality
zone of skin	UBERON:0000014	85.68	gold quality
skin of abdomen	UBERON:0001416	85.23	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	50.41	silver quality
body of stomach	UBERON:0001161	46.66	gold quality
granulocyte	CL:0000094	45.60	silver quality
stomach	UBERON:0000945	44.10	gold quality
lower esophagus mucosa	UBERON:0035834	43.70	silver quality
blood	UBERON:0000178	42.66	gold quality
vermiform appendix	UBERON:0001154	42.60	gold quality
colonic epithelium	UBERON:0000397	42.55	gold quality
fundus of stomach	UBERON:0001160	40.46	gold quality
rectum	UBERON:0001052	39.43	silver quality
mucosa of transverse colon	UBERON:0004991	38.47	silver quality
bone marrow cell	CL:0002092	38.37	gold quality
bone marrow	UBERON:0002371	38.05	gold quality
skeletal muscle tissue	UBERON:0001134	37.38	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
muscle tissue	UBERON:0002385	35.22	gold quality
monocyte	CL:0000576	34.29	gold quality
body of pancreas	UBERON:0001150	33.51	gold quality
vagina	UBERON:0000996	33.49	gold quality
lymph node	UBERON:0000029	33.02	gold quality
omental fat pad	UBERON:0010414	32.21	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
multicellular organism	UBERON:0000468	31.69	gold quality
pancreas	UBERON:0001264	31.63	silver quality
gall bladder	UBERON:0002110	31.55	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.43

Regulation

Is transcription factor: no

Cross-species orthologs

30 orthologs

Organism	Symbol	Gene ID
mus_musculus	Lipm	ENSMUSG00000056078
rattus_norvegicus	Lipm	ENSRNOG00000019301
drosophila_melanogaster	Lip3	FBGN0023495
drosophila_melanogaster	Lip1	FBGN0023496
drosophila_melanogaster	Lip2	FBGN0024740
drosophila_melanogaster	CG2772	FBGN0031533
drosophila_melanogaster	Lip4	FBGN0032264
drosophila_melanogaster	CG18301	FBGN0032265
drosophila_melanogaster	CG18302	FBGN0032266
drosophila_melanogaster	CG7329	FBGN0032271
drosophila_melanogaster	CG3635	FBGN0032981
drosophila_melanogaster	CG8093	FBGN0033999
drosophila_melanogaster	CG11406	FBGN0034990
drosophila_melanogaster	mag	FBGN0036996
drosophila_melanogaster	CG11598	FBGN0038067
drosophila_melanogaster	CG11600	FBGN0038068
drosophila_melanogaster	CG11608	FBGN0038069
drosophila_melanogaster	CG6753	FBGN0038070
drosophila_melanogaster	CG18530	FBGN0042207
drosophila_melanogaster	CG18284	FBGN0043825
drosophila_melanogaster	CG31089	FBGN0051089
drosophila_melanogaster	CG31091	FBGN0051091
drosophila_melanogaster	CG31871	FBGN0051871
drosophila_melanogaster	CG31872	FBGN0051872
drosophila_melanogaster	CG17097	FBGN0265264
caenorhabditis_elegans		WBGENE00009773
caenorhabditis_elegans		WBGENE00010062
caenorhabditis_elegans		WBGENE00020016
caenorhabditis_elegans		WBGENE00021963
caenorhabditis_elegans		WBGENE00022642

Paralogs (5): LIPA (ENSG00000107798), LIPF (ENSG00000182333), LIPN (ENSG00000204020), LIPK (ENSG00000204021), LIPJ (ENSG00000204022)

Protein

Protein identifiers

Lipase member M — Q5VYY2 (reviewed: Q5VYY2)

Alternative names: Lipase-like abhydrolase domain-containing protein 3

All UniProt accessions (1): Q5VYY2

UniProt curated annotations — full annotation on UniProt →

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.

Subcellular location. Secreted.

Tissue specificity. Exclusively expressed in the epidermis within the granular keratinocytes.

Similarity. Belongs to the AB hydrolase superfamily. Lipase family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q5VYY2-1	1	yes
Q5VYY2-2	2

RefSeq proteins (1): NP_001121687* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000073	AB_hydrolase_1	Domain
IPR025483	Lipase_euk	Family
IPR029058	AB_hydrolase_fold	Homologous_superfamily

Pfam: PF00561

UniProt features (11 total): active site 3, sequence variant 2, signal peptide 1, chain 1, domain 1, glycosylation site 1, disulfide bond 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5VYY2-F1	88.92	0.71

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (3): 186 (nucleophile); 357 (charge relay system); 386 (charge relay system)

Disulfide bonds (1): 260–269

Glycosylation sites (1): 48

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-6809371	Formation of the cornified envelope
R-HSA-1266738	Developmental Biology
R-HSA-6805567	Keratinization

MSigDB gene sets: 27 (showing top): GOBP_EPITHELIUM_DEVELOPMENT, GOBP_EPIDERMAL_CELL_DIFFERENTIATION, GOBP_EPIDERMIS_DEVELOPMENT, GOBP_LIPID_METABOLIC_PROCESS, GOBP_KERATINIZATION, GOBP_LIPID_CATABOLIC_PROCESS, GOBP_SKIN_DEVELOPMENT, GOMF_TRIACYLGLYCEROL_LIPASE_ACTIVITY, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ESTER_BONDS, GOMF_CARBOXYLIC_ESTER_HYDROLASE_ACTIVITY, GOMF_LIPASE_ACTIVITY, chr10q23, GOBP_CORNIFICATION, REACTOME_KERATINIZATION, REACTOME_FORMATION_OF_THE_CORNIFIED_ENVELOPE

GO Biological Process (3): lipid metabolic process (GO:0006629), lipid catabolic process (GO:0016042), cornification (GO:0070268)

GO Molecular Function (5): lipoprotein lipase activity (GO:0004465), lipase activity (GO:0016298), hydrolase activity (GO:0016787), hydrolase activity, acting on ester bonds (GO:0016788), carboxylic ester hydrolase activity (GO:0052689)

GO Cellular Component (1): extracellular region (GO:0005576)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Keratinization	1
Developmental Biology	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
hydrolase activity, acting on ester bonds	2
primary metabolic process	1
lipid metabolic process	1
catabolic process	1
programmed cell death	1
keratinization	1
cornified envelope assembly	1
triacylglycerol lipase activity	1
catalytic activity	1
hydrolase activity	1
cellular anatomical structure	1

Protein interactions and networks

STRING

964 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LIPM	TFEB	P19484	457
LIPM	LIPG	Q9Y5X9	433
LIPM	LIPT2	A6NK58	432
LIPM	LIPT1	Q9Y234	428
LIPM	SCGB1D2	O95969	403
LIPM	PLA2G15	Q8NCC3	399
LIPM	TEX30	Q5JUR7	377
LIPM	IGSF22	Q8N9C0	372
LIPM	AASDH	Q4L235	368
LIPM	GPR82	Q96P67	361
LIPM	ABHD13	Q7L211	353
LIPM	LIPI	Q6XZB0	352
LIPM	ABHD12B	Q7Z5M8	351
LIPM	MYBPH	Q13203	348
LIPM	FAM135A	Q9P2D6	346

IntAct

2 interactions, top by confidence:

A	B	Type	Score
LIPM	CNOT8	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (1): LIPM (Negative Genetic)

ESM2 similar proteins: A2AIR5, A5D7I4, A8MXE2, A9X1C8, B4F753, B9EKX1, O60242, O60656, O75077, O77485, O77486, O77487, O95803, P16442, P23945, P25291, P97464, Q10981, Q14246, Q16394, Q4R766, Q5GJ04, Q5IGR7, Q5IGR8, Q5M7U7, Q5RBC3, Q5VYY2, Q62452, Q64633, Q64634, Q6AYT7, Q6ZQM8, Q704V6, Q7ZTV5, Q80ZF8, Q8TCU5, Q99LR1, Q9D4Y8, Q9D806, Q9DGB6

Diamond homologs: J3SDX8, O16956, O46107, O46108, O61866, O74430, P04634, P07098, P34163, P38571, P78898, P80035, Q29458, Q3U4B4, Q3YBN2, Q4R4S5, Q5VXI9, Q5VXJ0, Q5VYY2, Q5W064, Q64194, Q67ZU1, Q8BM14, Q8K2A6, Q93789, Q94252, Q9CPP7, Q9Z0M5, Q07950, Q71DJ5, O60095, Q07804

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

45 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	41
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1223 predictions. Top by Δscore:

Variant	Effect	Δscore
10:88803044:G:GG	donor_gain	1.0000
10:88813093:GCA:G	acceptor_loss	1.0000
10:88813095:A:AG	acceptor_gain	1.0000
10:88813095:A:G	acceptor_loss	1.0000
10:88813096:G:GG	acceptor_gain	1.0000
10:88813276:GA:G	donor_gain	1.0000
10:88813277:A:G	donor_gain	1.0000
10:88815083:TGCA:T	acceptor_loss	1.0000
10:88815084:GCAG:G	acceptor_loss	1.0000
10:88815086:A:AG	acceptor_gain	1.0000
10:88815086:AG:A	acceptor_gain	1.0000
10:88815087:G:GA	acceptor_gain	1.0000
10:88815087:GG:G	acceptor_gain	1.0000
10:88815087:GGCT:G	acceptor_gain	1.0000
10:88817824:GGCA:G	acceptor_gain	1.0000
10:88803039:ATATT:A	donor_gain	0.9900
10:88803040:TATT:T	donor_gain	0.9900
10:88803041:ATT:A	donor_gain	0.9900
10:88803041:ATTG:A	donor_loss	0.9900
10:88803042:TT:T	donor_gain	0.9900
10:88803042:TTGT:T	donor_loss	0.9900
10:88803044:GTAA:G	donor_loss	0.9900
10:88803046:AA:A	donor_loss	0.9900
10:88812919:T:A	acceptor_gain	0.9900
10:88813095:AG:A	acceptor_gain	0.9900
10:88813096:GG:G	acceptor_gain	0.9900
10:88813096:GGTT:G	acceptor_gain	0.9900
10:88813277:A:AG	donor_gain	0.9900
10:88813292:TCAG:T	donor_loss	0.9900
10:88813293:CAGGT:C	donor_loss	0.9900

AlphaMissense

2825 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:88813291:T:C	F154L	0.990
10:88813293:C:A	F154L	0.990
10:88813293:C:G	F154L	0.990
10:88813282:T:C	F151L	0.986
10:88813284:C:A	F151L	0.986
10:88813284:C:G	F151L	0.986
10:88813213:T:A	W128R	0.985
10:88813213:T:C	W128R	0.985
10:88820283:T:A	W352R	0.984
10:88820283:T:C	W352R	0.984
10:88813174:A:C	S115R	0.976
10:88813176:C:A	S115R	0.976
10:88813176:C:G	S115R	0.976
10:88813294:A:C	S155R	0.975
10:88814530:T:A	S155R	0.975
10:88814530:T:G	S155R	0.975
10:88820277:G:C	A350P	0.971
10:88820394:T:C	F389L	0.971
10:88820396:C:A	F389L	0.971
10:88820396:C:G	F389L	0.971
10:88813230:G:C	R133S	0.969
10:88813230:G:T	R133S	0.969
10:88820379:T:A	W384R	0.968
10:88820379:T:C	W384R	0.968
10:88813150:T:A	W107R	0.967
10:88813150:T:C	W107R	0.967
10:88816820:G:C	R288P	0.965
10:88820298:G:C	D357H	0.964
10:88808383:T:C	I78T	0.962
10:88813183:T:C	F118L	0.962

dbSNP variants (sampled 300 via entrez): RS1000067367 (10:88812580 T>A), RS1000354405 (10:88818048 T>A), RS1000423386 (10:88812264 T>C), RS1000465223 (10:88811399 A>G), RS1000922087 (10:88806746 G>A), RS1001583893 (10:88809079 C>T), RS1001794499 (10:88803669 T>C), RS1001795641 (10:88817074 G>T), RS1001910256 (10:88817365 G>A), RS1001983039 (10:88804865 A>G), RS1002196308 (10:88819456 G>T), RS1002206127 (10:88819751 G>A), RS1002591386 (10:88810553 T>C), RS1002786187 (10:88804626 C>T), RS1002916679 (10:88815877 C>T)

Disease associations

OMIM: gene MIM:613923 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression	1
sodium arsenate	increases abundance, decreases expression	1
CGP 52608	affects binding, increases reaction	1
Arsenic	decreases expression, increases abundance	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.