LRCOL1

Summary

LRCOL1 (leucine rich colipase like 1, HGNC:44160) is a protein-coding gene on chromosome 12q24.33, encoding Leucine-rich colipase-like protein 1 (A6NCL2).

Predicted to enable enzyme activator activity. Predicted to be involved in digestion and lipid catabolic process. Predicted to be located in extracellular region.

Source: NCBI Gene 100507055 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 29 total
• MANE Select transcript: NM_001195520

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:44160
Approved symbol	LRCOL1
Name	leucine rich colipase like 1
Location	12q24.33
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000204583
Ensembl biotype	protein_coding
Entrez	100507055

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 3 protein_coding, 3 nonsense_mediated_decay, 2 retained_intron

ENST00000376608, ENST00000536100, ENST00000544018, ENST00000545517, ENST00000616042, ENST00000622710, ENST00000880637, ENST00000880638

RefSeq mRNA: 1 — MANE Select: NM_001195520 NM_001195520

CCDS: CCDS73547

Canonical transcript exons

ENST00000376608 — 6 exons

Exon	Start	End
ENSE00001616099	132606147	132606264
ENSE00002220581	132603151	132603404
ENSE00002283583	132604706	132604831
ENSE00003589582	132604462	132604584
ENSE00003651166	132604254	132604376
ENSE00003850351	132610323	132610582

Expression profiles

Bgee: expression breadth ubiquitous, 120 present calls, max score 89.32.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1420 / max 95.4458, expressed in 38 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
134220	0.0566	17
134217	0.0443	7
134218	0.0386	8
134219	0.0026	1

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	89.32	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.07	silver quality
right uterine tube	UBERON:0001302	85.34	gold quality
liver	UBERON:0002107	83.87	gold quality
right lung	UBERON:0002167	77.73	gold quality
upper lobe of left lung	UBERON:0008952	76.99	gold quality
metanephros cortex	UBERON:0010533	71.45	gold quality
fallopian tube	UBERON:0003889	70.73	gold quality
lung	UBERON:0002048	70.04	gold quality
left uterine tube	UBERON:0001303	68.65	gold quality
spleen	UBERON:0002106	68.42	gold quality
lower esophagus mucosa	UBERON:0035834	65.65	gold quality
lymph node	UBERON:0000029	65.51	gold quality
placenta	UBERON:0001987	65.09	gold quality
ectocervix	UBERON:0012249	65.06	gold quality
right lobe of thyroid gland	UBERON:0001119	64.90	gold quality
endocervix	UBERON:0000458	64.70	gold quality
left lobe of thyroid gland	UBERON:0001120	62.59	gold quality
thyroid gland	UBERON:0002046	62.57	gold quality
small intestine Peyer’s patch	UBERON:0003454	62.42	gold quality
small intestine	UBERON:0002108	61.30	gold quality
body of uterus	UBERON:0009853	61.07	gold quality
lower esophagus	UBERON:0013473	60.76	gold quality
lower esophagus muscularis layer	UBERON:0035833	60.73	gold quality
uterine cervix	UBERON:0000002	60.49	gold quality
right adrenal gland cortex	UBERON:0035827	60.47	gold quality
right adrenal gland	UBERON:0001233	60.38	gold quality
myometrium	UBERON:0001296	59.50	gold quality
subcutaneous adipose tissue	UBERON:0002190	59.47	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	59.06	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.95

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

5 targeting LRCOL1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-7156-5P	99.64	68.81	1369
HSA-MIR-4273	99.45	67.93	1206
HSA-MIR-661	99.09	65.94	2062
HSA-MIR-1292-3P	72.98	63.40	23

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Lrcol1	ENSMUSG00000072754
rattus_norvegicus	Lrcol1	ENSRNOG00000037466

Paralogs (3): CLPS (ENSG00000137392), CLPSL2 (ENSG00000196748), CLPSL1 (ENSG00000204140)

Protein

Protein identifiers

Leucine-rich colipase-like protein 1 — A6NCL2 (reviewed: A6NCL2)

All UniProt accessions (4): A0A087WT69, A0A087WYD7, A0A087WZ94, A6NCL2

RefSeq proteins (1): NP_001182449* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001981	Colipase	Family

Pfam: PF15083

UniProt features (5 total): sequence conflict 2, signal peptide 1, chain 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NCL2-F1	82.05	0.19

Functional residue map

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

Glycosylation sites (1): 31

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 18 (showing top): GOBP_DIGESTION, GOBP_LIPID_METABOLIC_PROCESS, GOBP_LIPID_CATABOLIC_PROCESS, chr12q24, GOMF_ENZYME_ACTIVATOR_ACTIVITY, GOMF_ENZYME_REGULATOR_ACTIVITY, CHEN_METABOLIC_SYNDROM_NETWORK, MIKKELSEN_MEF_LCP_WITH_H3K27ME3, MIKKELSEN_IPS_LCP_WITH_H3K4ME3, MIKKELSEN_ES_LCP_WITH_H3K4ME3, FOSTER_KDM1A_TARGETS_UP, ZNF331_TARGET_GENES, MIR661, DESCARTES_FETAL_LUNG_LYMPHATIC_ENDOTHELIAL_CELLS, MYOCD_TARGET_GENES

GO Biological Process (2): digestion (GO:0007586), lipid catabolic process (GO:0016042)

GO Molecular Function (1): enzyme activator activity (GO:0008047)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
multicellular organismal process	1
lipid metabolic process	1
catabolic process	1
catalytic activity	1
enzyme regulator activity	1
molecular function activator activity	1
cellular anatomical structure	1

Protein interactions and networks

STRING

60 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRCOL1	SPMIP4	Q8N865	705
LRCOL1	FAM229B	Q4G0N7	703
LRCOL1	NYAP1	Q6ZVC0	665
LRCOL1	FSCB	Q5H9T9	595
LRCOL1	LELP1	Q5T871	582
LRCOL1	CABS1	Q96KC9	581
LRCOL1	SPATA24	Q86W54	581
LRCOL1	EDDM3B	P56851	568
LRCOL1	TMEM114	B3SHH9	533
LRCOL1	DRC11	Q86XH1	520
LRCOL1	NAB2	Q15742	512
LRCOL1	MYH15	Q9Y2K3	462
LRCOL1	ABTB1	Q969K4	448
LRCOL1	IFT56	A0AVF1	446
LRCOL1	RNF13	O43567	412

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A6NCL2, D3ZTT2, O19131, O46655, O70280, P01177, P01178, P01179, P01180, P01183, P01185, P01186, P03973, P13389, P19438, P22298, P22934, P25118, P35454, P35455, P50555, P58658, P58659, Q02509, Q14AE4, Q32LD3, Q3URS3, Q5T700, Q68US5, Q6UWE3, Q6UWL2, Q6V9X0, Q6WN34, Q76LW6, Q86Y78, Q8BPP5, Q8BVP6, Q8N6Q3, Q8VEA6, Q8WXA2

Diamond homologs: A6NCL2, Q3URS3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	26
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1072 predictions. Top by Δscore:

Variant	Effect	Δscore
12:132607206:T:TA	donor_gain	1.0000
12:132604580:TTGGG:T	acceptor_gain	0.9800
12:132604585:C:CC	acceptor_gain	0.9800
12:132604708:T:TA	donor_gain	0.9800
12:132604581:TGGG:T	acceptor_gain	0.9700
12:132605014:CGGGG:C	acceptor_gain	0.9700
12:132605287:G:GT	donor_gain	0.9700
12:132606262:GACCT:G	acceptor_loss	0.9700
12:132606263:ACCTG:A	acceptor_loss	0.9700
12:132606265:C:CA	acceptor_loss	0.9700
12:132606266:T:A	acceptor_loss	0.9700
12:132606267:G:C	acceptor_loss	0.9700
12:132607219:T:TA	donor_gain	0.9600
12:132610282:C:A	donor_gain	0.9600
12:132605019:C:CC	acceptor_gain	0.9500
12:132610319:CTACC:C	donor_loss	0.9500
12:132610320:TAC:T	donor_loss	0.9500
12:132610321:ACC:A	donor_loss	0.9500
12:132610322:C:A	donor_loss	0.9500
12:132604377:C:CC	acceptor_gain	0.9400
12:132606265:C:CC	acceptor_gain	0.9400
12:132610317:CCCTA:C	donor_loss	0.9400
12:132610318:CCTAC:C	donor_loss	0.9400
12:132604582:GGG:G	acceptor_gain	0.9300
12:132605016:GGGC:G	acceptor_loss	0.9300
12:132605018:GCTGA:G	acceptor_loss	0.9300
12:132605019:C:CA	acceptor_loss	0.9300
12:132605020:T:G	acceptor_loss	0.9300
12:132606139:GCAC:G	donor_loss	0.9300
12:132606140:CACC:C	donor_loss	0.9300

AlphaMissense

1039 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:132604294:C:G	C146S	0.992
12:132604295:A:T	C146S	0.992
12:132604468:C:A	W116C	0.992
12:132604468:C:G	W116C	0.992
12:132604550:C:G	C89S	0.992
12:132604551:A:T	C89S	0.992
12:132604712:C:A	W75C	0.991
12:132604712:C:G	W75C	0.991
12:132604342:C:G	C130S	0.990
12:132604343:A:T	C130S	0.990
12:132604505:C:G	C104S	0.989
12:132604506:A:T	C104S	0.989
12:132604265:A:G	C156R	0.988
12:132604360:C:G	C124S	0.987
12:132604361:A:T	C124S	0.987
12:132604568:C:G	C83S	0.987
12:132604569:A:T	C83S	0.987
12:132604295:A:G	C146R	0.986
12:132604293:G:C	C146W	0.985
12:132604359:G:C	C124W	0.985
12:132604360:C:T	C124Y	0.985
12:132604478:C:G	C113S	0.985
12:132604479:A:T	C113S	0.985
12:132604264:C:G	C156S	0.984
12:132604265:A:T	C156S	0.984
12:132604797:C:G	C47S	0.984
12:132604798:A:T	C47S	0.984
12:132604504:G:C	C104W	0.982
12:132604506:A:G	C104R	0.982
12:132604551:A:G	C89R	0.982

dbSNP variants (sampled 300 via entrez): RS1000252968 (12:132605140 CAGG>C), RS1000479696 (12:132610307 C>T), RS1000549715 (12:132604110 G>A,C,T), RS1000663519 (12:132608726 C>T), RS1000735287 (12:132608978 C>T), RS1000783799 (12:132611042 G>A), RS1000988948 (12:132606133 T>C,G), RS1001318102 (12:132610658 C>T), RS1001824927 (12:132605740 CTCTCTT>C), RS1001877904 (12:132608313 G>A), RS1001985301 (12:132603708 G>A,C), RS1002246960 (12:132608106 A>G), RS1002548763 (12:132606134 G>C), RS1002635901 (12:132610771 C>T), RS1003257523 (12:132611375 C>T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST005951_3	Body mass index	6.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aflatoxin B2	increases methylation	1
Silicon Dioxide	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Propofol	decreases expression	1

Clinical trials (associated diseases)

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