CLPSL2

Summary

CLPSL2 (colipase like 2, HGNC:21250) is a protein-coding gene on chromosome 6p21.31, encoding Colipase-like protein 2 (Q6UWE3).

Predicted to enable enzyme activator activity. Predicted to be involved in response to food. Predicted to be located in extracellular region.

Source: NCBI Gene 389383 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 17 total
• MANE Select transcript: NM_207409

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21250
Approved symbol	CLPSL2
Name	colipase like 2
Location	6p21.31
Locus type	gene with protein product
Status	Approved
Aliases	dJ510O8.5, UNQ3045
Ensembl gene	ENSG00000196748
Ensembl biotype	protein_coding
Entrez	389383

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000360454, ENST00000403376, ENST00000467122, ENST00000481904, ENST00000924056

RefSeq mRNA: 2 — MANE Select: NM_207409 NM_001286550, NM_207409

CCDS: CCDS4810, CCDS69095

Canonical transcript exons

ENST00000403376 — 3 exons

Exon	Start	End
ENSE00001831078	35776598	35776702
ENSE00003462023	35779355	35779552
ENSE00003680785	35777459	35777581

Expression profiles

Bgee: expression breadth broad, 71 present calls, max score 83.32.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1222 / max 64.0492, expressed in 49 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
67467	0.1222	49

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.32	silver quality
body of pancreas	UBERON:0001150	74.62	gold quality
pancreas	UBERON:0001264	62.70	gold quality
anterior cingulate cortex	UBERON:0009835	56.33	gold quality
Ammon’s horn	UBERON:0001954	51.68	gold quality
superior frontal gyrus	UBERON:0002661	50.17	gold quality
cerebral cortex	UBERON:0000956	48.58	gold quality
prefrontal cortex	UBERON:0000451	48.36	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	47.54	gold quality
cortical plate	UBERON:0005343	47.13	gold quality
frontal cortex	UBERON:0001870	46.37	gold quality
Brodmann (1909) area 9	UBERON:0013540	46.34	gold quality
right frontal lobe	UBERON:0002810	43.57	gold quality
tonsil	UBERON:0002372	43.29	silver quality
ventricular zone	UBERON:0003053	41.67	gold quality
islet of Langerhans	UBERON:0000006	41.20	gold quality
pituitary gland	UBERON:0000007	40.70	gold quality
bone marrow cell	CL:0002092	38.98	gold quality
metanephros cortex	UBERON:0010533	38.96	silver quality
right lobe of thyroid gland	UBERON:0001119	38.72	gold quality
brain	UBERON:0000955	37.79	gold quality
primary visual cortex	UBERON:0002436	37.67	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
amygdala	UBERON:0001876	37.12	gold quality
temporal lobe	UBERON:0001871	37.03	gold quality
thoracic mammary gland	UBERON:0005200	36.79	gold quality
adenohypophysis	UBERON:0002196	36.55	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
bone marrow	UBERON:0002371	35.42	gold quality
cortex of kidney	UBERON:0001225	33.71	silver quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-HCAD-38	no	1807.34
E-ANND-3	no	1.65

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

7 targeting CLPSL2, 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-4487	99.96	64.58	1252
HSA-MIR-6081	99.48	66.07	1446
HSA-MIR-3164	99.02	68.39	1071
HSA-MIR-6820-3P	99.02	68.50	1035
HSA-MIR-3664-3P	97.85	67.62	1452
HSA-MIR-874-5P	96.93	63.92	1014
HSA-MIR-1287-5P	96.80	65.30	743

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Clpsl2	ENSMUSG00000024224
rattus_norvegicus	Clpsl2	ENSRNOG00000038807

Paralogs (3): CLPS (ENSG00000137392), CLPSL1 (ENSG00000204140), LRCOL1 (ENSG00000204583)

Protein

Protein identifiers

Colipase-like protein 2 — Q6UWE3 (reviewed: Q6UWE3)

All UniProt accessions (1): Q6UWE3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Similarity. Belongs to the colipase family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6UWE3-1	1	yes
Q6UWE3-2	2

RefSeq proteins (2): NP_001273479, NP_997292* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001981	Colipase	Family

UniProt features (9 total): disulfide bond 5, signal peptide 1, chain 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6UWE3-F1	83.50	0.55

Functional residue map

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

Disulfide bonds (5): 34–45, 40–56, 44–78, 66–86, 80–97

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 11 (showing top): GOBP_DIGESTION, GOBP_LIPID_METABOLIC_PROCESS, GOBP_LIPID_CATABOLIC_PROCESS, GOMF_ENZYME_ACTIVATOR_ACTIVITY, GOMF_ENZYME_REGULATOR_ACTIVITY, PEDRIOLI_MIR31_TARGETS_UP, ZNF561_TARGET_GENES, MIR3164, MIR6820_3P, GOMF_MOLECULAR_FUNCTION_ACTIVATOR_ACTIVITY, chr6p21

GO Biological Process (3): digestion (GO:0007586), lipid catabolic process (GO:0016042), response to food (GO:0032094)

GO Molecular Function (2): enzyme activator activity (GO:0008047), protein binding (GO:0005515)

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
response to nutrient levels	1
response to chemical	1
catalytic activity	1
enzyme regulator activity	1
molecular function activator activity	1
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

134 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CLPSL2	PATE3	B3GLJ2	524
CLPSL2	GLB1L3	Q8NCI6	507
CLPSL2	PATE2	Q6UY27	448
CLPSL2	GLB1L	Q6UWU2	447
CLPSL2	GLB1L2	Q8IW92	447
CLPSL2	UBTD1	Q9HAC8	437
CLPSL2	PATE1	Q8WXA2	435
CLPSL2	MCFD2	Q8NI22	408
CLPSL2	MRPL54	Q6P161	399
CLPSL2	GNG10	P50151	399
CLPSL2	RPRD2	Q5VT52	393
CLPSL2	RNASE13	Q5GAN3	391
CLPSL2	RASL11A	Q6T310	370
CLPSL2	DDA1	Q9BW61	358
CLPSL2	MTARC1	Q5VT66	358

IntAct

7 interactions, top by confidence:

A	B	Type	Score
CLPSL2	UBQLN2	psi-mi:“MI:0915”(physical association)	0.560
CLPSL2	UBQLN2	psi-mi:“MI:0915”(physical association)	0.000
UBQLN2	CLPSL2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (2): CLPSL2 (Two-hybrid), CLPSL2 (Affinity Capture-MS)

ESM2 similar proteins: A0A384E0Y8, A0JNQ7, A9JSD6, A9XFZ7, D2Y2C0, D2Y2E1, D2Y2E2, D2Y2E3, D2Y2E4, D2Y2E5, D3ZVN1, O75711, O96049, P02703, P02704, P02705, P04118, P08162, P0CJ14, P0DQT9, P0DQU0, P0DQU1, P0DRJ0, P11858, P17084, P19090, P42889, P42890, P80407, P83668, Q07663, Q27023, Q3UW21, Q5BQU9, Q5BQX9, Q5D231, Q5D232, Q5D233, Q5W280, Q6UWE3

Diamond homologs: D3ZVN1, P02703, P04118, P42889, Q3UW21, Q6UWE3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	16
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

481 predictions. Top by Δscore:

Variant	Effect	Δscore
6:35776699:AAAGG:A	donor_loss	0.9900
6:35776700:AAGG:A	donor_loss	0.9900
6:35776701:AGGT:A	donor_loss	0.9900
6:35776703:GTG:G	donor_loss	0.9900
6:35776704:T:A	donor_loss	0.9900
6:35777457:A:AG	acceptor_gain	0.9900
6:35777458:G:GG	acceptor_gain	0.9900
6:35777458:GAAA:G	acceptor_gain	0.9900
6:35777458:GA:G	acceptor_gain	0.9800
6:35777458:GAA:G	acceptor_gain	0.9800
6:35777913:C:G	donor_gain	0.9800
6:35777455:ACAG:A	acceptor_loss	0.9600
6:35777456:CA:C	acceptor_loss	0.9600
6:35777457:A:T	acceptor_loss	0.9600
6:35777458:G:A	acceptor_loss	0.9600
6:35777930:G:GG	donor_gain	0.9500
6:35776705:GA:G	donor_loss	0.9400
6:35777448:T:A	acceptor_loss	0.9400
6:35779353:A:AG	acceptor_gain	0.9400
6:35779354:G:GG	acceptor_gain	0.9400
6:35777458:GAAAA:G	acceptor_gain	0.9300
6:35779320:T:TA	acceptor_gain	0.9300
6:35776799:G:GT	donor_gain	0.9200
6:35777577:CCCAG:C	donor_loss	0.9200
6:35777578:CCAGG:C	donor_loss	0.9200
6:35777579:CAG:C	donor_loss	0.9200
6:35777580:AGGT:A	donor_loss	0.9200
6:35777581:GG:G	donor_loss	0.9200
6:35777582:G:GG	donor_loss	0.9200
6:35777583:T:A	donor_loss	0.9200

AlphaMissense

654 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:35777540:T:A	C56S	0.997
6:35777541:G:C	C56S	0.997
6:35777570:T:C	C66R	0.997
6:35777541:G:A	C56Y	0.996
6:35777570:T:A	C66S	0.996
6:35777571:G:C	C66S	0.996
6:35779379:T:C	C78R	0.996
6:35777492:T:A	C40S	0.995
6:35777493:G:C	C40S	0.995
6:35777507:T:A	C45S	0.995
6:35777508:G:C	C45S	0.995
6:35777540:T:C	C56R	0.995
6:35777571:G:A	C66Y	0.995
6:35779403:T:A	C86S	0.995
6:35779403:T:C	C86R	0.995
6:35779404:G:C	C86S	0.995
6:35777474:T:A	C34S	0.994
6:35777475:G:C	C34S	0.994
6:35777542:T:G	C56W	0.994
6:35777572:C:G	C66W	0.994
6:35779379:T:A	C78S	0.994
6:35779380:G:C	C78S	0.994
6:35779385:T:A	C80S	0.994
6:35779386:G:A	C80Y	0.994
6:35779386:G:C	C80S	0.994
6:35779404:G:A	C86Y	0.994
6:35779405:C:G	C86W	0.994
6:35779436:T:A	C97S	0.994
6:35779437:G:C	C97S	0.994
6:35777492:T:C	C40R	0.993

dbSNP variants (sampled 300 via entrez): RS1000061537 (6:35775395 A>G), RS1000255306 (6:35775654 C>G,T), RS1001672311 (6:35777093 C>T), RS1001767047 (6:35777315 G>A,T), RS1001824197 (6:35776232 C>G,T), RS1002585946 (6:35779881 G>A), RS1002807330 (6:35778753 A>G), RS1003144823 (6:35778582 C>T), RS1003728565 (6:35779585 G>A,T), RS1003737331 (6:35779858 G>A), RS1004046770 (6:35776219 C>G,T), RS1006022747 (6:35775464 G>T), RS1006403765 (6:35774735 G>A), RS1007336310 (6:35776181 T>C,G), RS1007987326 (6:35779928 T>G)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
ethyl-p-hydroxybenzoate	decreases expression	1
butyraldehyde	increases expression	1
pentanal	increases expression	1
jinfukang	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	increases methylation	1
Methylcholanthrene	affects binding, increases reaction	1
Plant Extracts	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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