CALU

Summary

CALU (calumenin, HGNC:1458) is a protein-coding gene on chromosome 7q32.1, encoding Calumenin (O43852). Involved in regulation of vitamin K-dependent carboxylation of multiple N-terminal glutamate residues.

The product of this gene is a calcium-binding protein localized in the endoplasmic reticulum (ER) and it is involved in such ER functions as protein folding and sorting. This protein belongs to a family of multiple EF-hand proteins (CERC) that include reticulocalbin, ERC-55, and Cab45 and the product of this gene. Alternatively spliced transcript variants encoding different isoforms have been identified.

Source: NCBI Gene 813 — RefSeq curated summary.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 84 total — 1 likely-pathogenic
• Druggable target: yes
• MANE Select transcript: NM_001219

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1458
Approved symbol	CALU
Name	calumenin
Location	7q32.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000128595
Ensembl biotype	protein_coding
OMIM	603420
Entrez	813

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 25 protein_coding

ENST00000249364, ENST00000449187, ENST00000479257, ENST00000493278, ENST00000535011, ENST00000542996, ENST00000860033, ENST00000860034, ENST00000860035, ENST00000860036, ENST00000860037, ENST00000860038, ENST00000860039, ENST00000860040, ENST00000860041, ENST00000918180, ENST00000918181, ENST00000918182, ENST00000918183, ENST00000918184, ENST00000918185, ENST00000918186, ENST00000955246, ENST00000955247, ENST00000955248

RefSeq mRNA: 5 — MANE Select: NM_001219 NM_001130674, NM_001199671, NM_001199672, NM_001199673, NM_001219

CCDS: CCDS47703, CCDS56506, CCDS56507, CCDS56508, CCDS5805

Canonical transcript exons

ENST00000249364 — 7 exons

Exon	Start	End
ENSE00000882081	128754262	128754455
ENSE00001208337	128769063	128773400
ENSE00001550006	128739359	128739432
ENSE00003505852	128748573	128748804
ENSE00003542406	128767456	128767655
ENSE00003671449	128758871	128759037
ENSE00003687696	128759792	128759852

Expression profiles

Bgee: expression breadth ubiquitous, 303 present calls, max score 99.77.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 268.8713 / max 8021.8461, expressed in 1828 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
80934	242.8957	1828
80935	21.6155	1658
80944	1.9082	832
80943	0.7723	409
80937	0.7500	426
80945	0.7356	368
80936	0.1941	70

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
stromal cell of endometrium	CL:0002255	99.77	gold quality
smooth muscle tissue	UBERON:0001135	99.24	gold quality
tendon of biceps brachii	UBERON:0008188	98.94	gold quality
thoracic aorta	UBERON:0001515	98.58	gold quality
ascending aorta	UBERON:0001496	98.57	gold quality
tendon	UBERON:0000043	98.51	gold quality
right coronary artery	UBERON:0001625	98.48	gold quality
calcaneal tendon	UBERON:0003701	98.47	gold quality
descending thoracic aorta	UBERON:0002345	98.42	gold quality
aorta	UBERON:0000947	98.33	gold quality
left coronary artery	UBERON:0001626	98.24	gold quality
popliteal artery	UBERON:0002250	98.18	gold quality
tibial artery	UBERON:0007610	98.17	gold quality
artery	UBERON:0001637	98.12	gold quality
right atrium auricular region	UBERON:0006631	98.07	gold quality
coronary artery	UBERON:0001621	97.98	gold quality
adrenal tissue	UBERON:0018303	97.86	gold quality
gall bladder	UBERON:0002110	97.65	gold quality
lower esophagus muscularis layer	UBERON:0035833	97.57	gold quality
lower esophagus	UBERON:0013473	97.53	gold quality
heart left ventricle	UBERON:0002084	97.52	gold quality
ventricular zone	UBERON:0003053	97.51	gold quality
heart	UBERON:0000948	97.49	gold quality
cardiac ventricle	UBERON:0002082	97.49	gold quality
myometrium	UBERON:0001296	97.41	gold quality
heart right ventricle	UBERON:0002080	97.31	gold quality
islet of Langerhans	UBERON:0000006	97.30	gold quality
cardiac atrium	UBERON:0002081	97.27	gold quality
body of uterus	UBERON:0009853	97.20	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	97.20	gold quality

Single-cell (SCXA)

Detected in 16 experiment(s), a significant marker in 15.

Experiment	Marker?	Max mean expression
E-HCAD-1	yes	81.74
E-MTAB-8410	yes	39.48
E-HCAD-5	yes	32.92
E-HCAD-10	yes	30.06
E-HCAD-31	yes	28.00
E-CURD-122	yes	20.54
E-MTAB-6678	yes	16.57
E-CURD-112	yes	15.83
E-CURD-46	yes	13.60
E-MTAB-8142	yes	12.61
E-MTAB-5061	yes	12.22
E-HCAD-13	yes	11.75
E-GEOD-83139	yes	7.65
E-ENAD-27	yes	6.82
E-MTAB-6075	no	1399.36

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

182 targeting CALU, 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-6873-3P	100.00	71.42	2626
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-6798-5P	100.00	65.77	699
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790

Literature-anchored findings (GeneRIF, showing 14)

• Data show that calumenin in the presence of calcium binds specifically to thrombospondin-1, but closely-related reticulocalbin does not form a similar complex. (PMID:18688696)
• associated with arterial calcification and short-term prognosis of the outcome of patients with non-ST-elevation acute coronary syndrome (PMID:20673165)
• Quantitative PCR assays for VKORC1, CYP4F2, GGCX and CALU identified two copies in all populations. (PMID:22188360)
• Study found the secretion of calu-1/2-EGFP required microtubule integrity, and that calu-1/2-EGFP-containing vesicles were transported by the motor proteins Kif5b and cytoplasmic dynein. (PMID:22514732)
• Calumenin is a new CFTR chaperone. (PMID:22768251)
• Calu-15, a novel isoform of Calu with phosphorylation-dependent nuclear localization, has a critical role in promoting filopodia formation and cell migration by upregulating the GDF-15 transcription. (PMID:24136234)
• Calumenin is characterized as a charged protein exhibiting close similarity with intrinsically disordered proteins and is hypothesized to regulate F508del-CFTR folding by electrostatic effects. (PMID:25120007)
• CALU polymorphism A29809G affects calumenin availability involving vascular calcification (PMID:25823396)
• Results show that OSBPL5 and CALU were expressed at higher levels in the lung tissues of metastasis-positive cases than that in the metastasis-negative cases suggesting they can promote invasiveness of lung cancer cells. (PMID:25963840)
• Results provide direct evidence for the involvement of CALU and LGALS3BP as potential negative regulators in the virus-triggered induction of the typeI interferons. (PMID:26124285)
• irradiated tumor cells were observed to significantly up-regulate the expression of calcium-binding proteins CALM1, CALU, and RCN1, suggesting important roles for these mediators in promoting irradiated tumor cell survival during hypoxia (PMID:27790916)
• The Calumenin modulates Sarco/Endoplasmic reticulumCa2+ATPase (SERCA) pump activity without drastically affecting ER-Ca(2+) concentration. (PMID:28189267)
• Replacing Leu with Gly (L150G) in Calu1 enables the protein to adopt a structural fold even in the Ca(2+) free form. The fourth (of seven) EF-hand of HsCalu1 nucleates the structural fold of the protein depending on the switch residue (Gly or Leu). (PMID:29319298)
• Establishment of a CALU, AURKA, and MCM2 gene panel for discrimination of metastasis from primary colon and lung cancers. (PMID:32469983)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	calub	ENSDARG00000005115
danio_rerio	calua	ENSDARG00000045676
mus_musculus	Calu	ENSMUSG00000029767
rattus_norvegicus	Calu	ENSRNOG00000006197
drosophila_melanogaster	scf	FBGN0025682
caenorhabditis_elegans		WBGENE00019760

Paralogs (4): RCN1 (ENSG00000049449), SDF4 (ENSG00000078808), RCN2 (ENSG00000117906), RCN3 (ENSG00000142552)

Protein

Protein identifiers

Calumenin — O43852 (reviewed: O43852)

Alternative names: Crocalbin, IEF SSP 9302

All UniProt accessions (3): O43852, H0Y875, Q6IAW5

UniProt curated annotations — full annotation on UniProt →

Function. Involved in regulation of vitamin K-dependent carboxylation of multiple N-terminal glutamate residues. Seems to inhibit gamma-carboxylase GGCX. Binds 7 calcium ions with a low affinity.

Subunit / interactions. Interacts with GGCX.

Subcellular location. Endoplasmic reticulum membrane. Golgi apparatus. Secreted. Melanosome. Sarcoplasmic reticulum lumen.

Tissue specificity. Ubiquitously expressed. Expressed at high levels in heart, placenta and skeletal muscle, at lower levels in lung, kidney and pancreas and at very low levels in brain and liver.

Similarity. Belongs to the CREC family.

Isoforms (15)

UniProt ID	Names	Canonical?
O43852-1	1	yes
O43852-2	2, Crocalbin
O43852-3	3
O43852-4	4
O43852-5	5
O43852-6	6
O43852-7	7
O43852-8	8
O43852-9	9
O43852-10	10
O43852-11	11
O43852-12	12
O43852-13	13
O43852-14	14
O43852-15	15

RefSeq proteins (5): NP_001124146, NP_001186600, NP_001186601, NP_001186602, NP_001210* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002048	EF_hand_dom	Domain
IPR011992	EF-hand-dom_pair	Homologous_superfamily
IPR018247	EF_Hand_1_Ca_BS	Binding_site

Pfam: PF13202

UniProt features (70 total): binding site 26, splice variant 15, sequence conflict 10, modified residue 8, domain 6, signal peptide 1, chain 1, glycosylation site 1, sequence variant 1, short sequence motif 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O43852-F1	79.82	0.33

Functional residue map

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

Ligand- & substrate-binding residues (26): 83; 85; 92; 117; 119; 121; 128; 164; 166; 168; 175; 201 …

Post-translational modifications (8): 44, 47, 65, 69, 165, 254, 261, 277

Glycosylation sites (1): 131

Function

Pathways and Gene Ontology

Reactome pathways

8 pathways

ID	Pathway
R-HSA-114608	Platelet degranulation
R-HSA-381426	Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)
R-HSA-8957275	Post-translational protein phosphorylation
R-HSA-109582	Hemostasis
R-HSA-392499	Metabolism of proteins
R-HSA-597592	Post-translational protein modification
R-HSA-76002	Platelet activation, signaling and aggregation
R-HSA-76005	Response to elevated platelet cytosolic Ca2+

MSigDB gene sets: 325 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, RNGTGGGC_UNKNOWN, TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP, MODULE_52, BORCZUK_MALIGNANT_MESOTHELIOMA_UP, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, REACTOME_PLATELET_ACTIVATION_SIGNALING_AND_AGGREGATION, ATACCTC_MIR202, GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP, GNF2_PTX3, KYNG_DNA_DAMAGE_DN, TGACCTY_ERR1_Q2, MODULE_16, DOANE_BREAST_CANCER_CLASSES_DN

GO Biological Process (0):

GO Molecular Function (3): calcium ion binding (GO:0005509), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (9): extracellular region (GO:0005576), endoplasmic reticulum (GO:0005783), endoplasmic reticulum lumen (GO:0005788), endoplasmic reticulum membrane (GO:0005789), Golgi apparatus (GO:0005794), membrane (GO:0016020), sarcoplasmic reticulum lumen (GO:0033018), melanosome (GO:0042470), sarcoplasmic reticulum (GO:0016529)

Reactome top-level categories

Rollup of top-5 pathways:

Category	Pathways
Metabolism of proteins	2
Response to elevated platelet cytosolic Ca2+	1
Post-translational protein modification	1
Hemostasis	1
Platelet activation, signaling and aggregation	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
cytoplasm	2
endomembrane system	2
intracellular membrane-bounded organelle	2
endoplasmic reticulum	2
metal ion binding	1
binding	1
cation binding	1
intracellular organelle lumen	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
endoplasmic reticulum lumen	1
sarcoplasmic reticulum	1
pigment granule	1
sarcoplasm	1

Protein interactions and networks

STRING

1434 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CALU	VKORC1	Q9BQB6	809
CALU	GGCX	P38435	714
CALU	CALR	P27797	708
CALU	SEC63	Q9UGP8	671
CALU	CYP4F2	P78329	646
CALU	HSPA5	P11021	633
CALU	PDIA3	P30101	586
CALU	EPHX1	P07099	566
CALU	CYP2C9	P11712	541
CALU	CALM1	P02593	528
CALU	CALML3	P27482	511
CALU	APCS	P02743	508
CALU	HSPA4	P34932	507
CALU	CALML5	Q9NZT1	504
CALU	CALML6	Q8TD86	502
CALU	CALML4	Q96GE6	502

IntAct

154 interactions, top by confidence:

A	B	Type	Score
CFTR	XPO1	psi-mi:“MI:0914”(association)	0.710
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
RAF1	CALU	psi-mi:“MI:0914”(association)	0.640
IRS4	PIK3R2	psi-mi:“MI:0914”(association)	0.640
UBQLN1	CALU	psi-mi:“MI:0915”(physical association)	0.560
CALU	UBQLN1	psi-mi:“MI:0915”(physical association)	0.560
ILK	HAX1	psi-mi:“MI:0914”(association)	0.530
IRAK1	SEC16A	psi-mi:“MI:0914”(association)	0.530
RAF1	EEF1E1	psi-mi:“MI:0914”(association)	0.530
	XPO1	psi-mi:“MI:0914”(association)	0.530
rep	CALU	psi-mi:“MI:0915”(physical association)	0.510
COL1A1	GOLIM4	psi-mi:“MI:0914”(association)	0.500
FAM20C	CALU	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
CALU	MFHAS1	psi-mi:“MI:0407”(direct interaction)	0.440
TUBA1A	TUBAL3	psi-mi:“MI:0914”(association)	0.420
TGOLN2	PGRMC1	psi-mi:“MI:0914”(association)	0.420
MET	NDUFA4	psi-mi:“MI:2364”(proximity)	0.420

BioGRID (425): UBQLN1 (Two-hybrid), CALU (Biochemical Activity), CALU (Affinity Capture-MS), CALU (Affinity Capture-MS), CALU (Affinity Capture-MS), CALU (Affinity Capture-MS), CALU (Affinity Capture-MS), CALU (Affinity Capture-MS), OBSL1 (Affinity Capture-MS), CALR (Co-fractionation), CALU (Co-fractionation), CALU (Co-fractionation), CALU (Co-fractionation), CALU (Co-fractionation), CALU (Co-fractionation)

ESM2 similar proteins: A4IG32, B1H2N3, B5X186, B5X4E0, D2HZB0, I6L9G5, J3S9D9, O35783, O35887, O43852, O93390, O93434, P06813, P07090, P07214, P09486, P13213, P16975, P20112, P22676, P47728, Q05186, Q08331, Q14257, Q15293, Q28BT4, Q2KJ39, Q3T0K1, Q3ZBY3, Q4U471, Q5R767, Q5R8Z6, Q5RDD8, Q62703, Q659X0, Q6EV76, Q6EV77, Q6IP82, Q6IQP3, Q6P8Y1

Diamond homologs: B5X186, B5X4E0, I6L9G5, J3S9D9, O35783, O35887, O43852, O93434, P02597, P04464, Q05186, Q14257, Q15293, Q28BT4, Q2KJ39, Q3T0K1, Q4U471, Q5RDD8, Q62703, Q66JA6, Q6IP82, Q6IQP3, Q6XLQ7, Q7SXV9, Q8BH97, Q8BP92, Q96D15, Q9FKW4, P42529, Q5ZKE5, Q03975, Q9M7R0

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
CALU	“down-regulates activity”	GGCX	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 163 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO term	Partners	Fold	FDR
insulin receptor signaling pathway	7	11.3×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	56
Likely benign	12
Benign	1

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
2430106	NM_001219.5(CALU):c.700C>T (p.Arg234Ter)	Likely pathogenic

SpliceAI

1186 predictions. Top by Δscore:

Variant	Effect	Δscore
7:128739430:AAGG:A	donor_loss	1.0000
7:128748795:A:T	donor_gain	1.0000
7:128748799:GCT:G	donor_gain	1.0000
7:128754259:C:G	acceptor_gain	1.0000
7:128754260:A:AG	acceptor_gain	1.0000
7:128754261:G:GT	acceptor_gain	1.0000
7:128754261:GA:G	acceptor_gain	1.0000
7:128754261:GAAA:G	acceptor_gain	1.0000
7:128754453:TAGG:T	donor_loss	1.0000
7:128754454:AGGTA:A	donor_loss	1.0000
7:128754457:T:A	donor_loss	1.0000
7:128758869:A:AG	acceptor_gain	1.0000
7:128758869:AGAT:A	acceptor_gain	1.0000
7:128758870:G:A	acceptor_loss	1.0000
7:128758870:G:GT	acceptor_gain	1.0000
7:128758870:GA:G	acceptor_gain	1.0000
7:128758870:GAT:G	acceptor_gain	1.0000
7:128758870:GATG:G	acceptor_gain	1.0000
7:128758870:GATGA:G	acceptor_gain	1.0000
7:128758975:G:GT	donor_gain	1.0000
7:128759004:G:GT	donor_gain	1.0000
7:128759004:GGA:G	donor_gain	1.0000
7:128759005:GAG:G	donor_gain	1.0000
7:128759007:G:GG	donor_gain	1.0000
7:128759030:T:TA	donor_gain	1.0000
7:128759031:A:AA	donor_gain	1.0000
7:128759034:ACAG:A	donor_loss	1.0000
7:128759035:CAG:C	donor_loss	1.0000
7:128759036:AG:A	donor_loss	1.0000
7:128759037:GG:G	donor_loss	1.0000

AlphaMissense

2156 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:128758996:C:G	H181D	1.000
7:128767497:T:A	W229R	1.000
7:128767497:T:C	W229R	1.000
7:128767499:G:C	W229C	1.000
7:128767499:G:T	W229C	1.000
7:128767581:T:A	W257R	1.000
7:128767581:T:C	W257R	1.000
7:128767583:G:C	W257C	1.000
7:128767583:G:T	W257C	1.000
7:128767620:G:C	A270P	1.000
7:128767626:C:G	H272D	1.000
7:128767630:T:C	L273P	1.000
7:128769132:T:C	F305L	1.000
7:128769133:T:G	F305C	1.000
7:128769134:T:A	F305L	1.000
7:128769134:T:G	F305L	1.000
7:128769135:G:T	G306W	1.000
7:128769136:G:A	G306E	1.000
7:128769136:G:T	G306V	1.000
7:128748774:T:C	L64P	0.999
7:128748801:T:A	L73H	0.999
7:128748801:T:C	L73P	0.999
7:128754303:T:A	V88D	0.999
7:128754318:T:C	L93P	0.999
7:128754411:T:A	V124D	0.999
7:128754416:T:A	W126R	0.999
7:128754416:T:C	W126R	0.999
7:128754418:G:C	W126C	0.999
7:128754418:G:T	W126C	0.999
7:128758921:G:C	D156H	0.999

dbSNP variants (sampled 300 via entrez): RS1000052259 (7:128756839 G>A,C), RS1000137861 (7:128762596 G>A), RS1000144053 (7:128751892 C>G), RS1000173665 (7:128744503 T>G), RS1000470796 (7:128739463 A>G), RS1000521340 (7:128739789 T>G), RS1001100510 (7:128758098 C>T), RS1001196775 (7:128753213 A>T), RS1001203082 (7:128766124 A>C,G), RS1001281417 (7:128766348 C>G,T), RS1001312624 (7:128766605 T>G), RS1001533353 (7:128758401 T>A), RS1001636879 (7:128753658 C>G), RS1001746141 (7:128739715 C>T), RS1001832911 (7:128759961 C>G,T)

Disease associations

OMIM: gene MIM:603420 | disease phenotypes: MIM:608423

GenCC curated gene-disease

Mondo (1): autosomal dominant limb-girdle muscular dystrophy type 1F (MONDO:0012034)

Orphanet (1): TNP03-related limb-girdle muscular dystrophy D2 (Orphanet:55595)

HPO phenotypes

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

GWAS associations

8 associations (top):

Study	Trait	p-value
GCST002030_2	Primary tooth development (time to first tooth eruption)	9.000000e-07
GCST002031_2	Primary tooth development (number of teeth)	4.000000e-09
GCST004401_3	Reading disability or specific language impairment (pleiotropy)	4.000000e-07
GCST004402_3	Reading disability or specific language impairment adjusted for intelligence quotient (pleiotropy)	3.000000e-07
GCST005316_14	Intelligence (MTAG)	3.000000e-10
GCST006097_9	Moderate to vigorous physical activity levels	4.000000e-09
GCST006414_126	Atrial fibrillation	5.000000e-09
GCST010732_12	Sensory peripheral neuropathy in microtubule targeting agent-treated breast cancer	3.000000e-06

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004337	intelligence
EFO:0008002	physical activity measurement
EFO:0005260	response to antimicrotubule agent

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C564242	Muscular Dystrophy, Limb-Girdle, Type 1F (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067027 (SINGLE PROTEIN)

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

PharmGKB clinical annotations

2 annotations.

Variant	Type	Level	Drugs	Phenotypes
rs1043550	Dosage	3	acenocoumarol
rs339097	Dosage	3	warfarin

PharmGKB variants

5 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs11653	CALU, OPN1SW		0.00	0
rs339097	CALU	3	4.25	1	warfarin
rs1043550	CALU	3	3.00	1	acenocoumarol
rs2290228	CALU		0.00	0
rs2307040	CALU		0.00	0

ChEMBL bioactivities

4 potent at pChembl≥5 of 4 total, top 4 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
5.76	Kd	1725	nM	CHEMBL3752910
5.76	ED50	1725	nM	CHEMBL3752910
5.47	Kd	3406	nM	CHEMBL5653589
5.47	ED50	3406	nM	CHEMBL5653589

PubChem BioAssay actives

2 with measured affinity, of 4 total; 2 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2147982: Binding affinity to human CALU incubated for 45 mins by Kinobead based pull down assay	kd	1.7248	uM
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2147982: Binding affinity to human CALU incubated for 45 mins by Kinobead based pull down assay	kd	3.4059	uM

CTD chemical–gene interactions

75 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, increases expression	3
Cyclosporine	decreases expression, increases expression, increases methylation	3
Resveratrol	affects cotreatment, increases expression, affects secretion	2
Air Pollutants	decreases expression, affects expression, increases abundance	2
Caffeine	decreases expression, increases phosphorylation	2
Nickel	increases expression	2
Tobacco Smoke Pollution	affects expression, increases expression	2
Valproic Acid	increases expression, affects expression	2
Warfarin	affects response to substance	2
Thapsigargin	decreases expression, increases expression	2
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
TAK-243	increases sumoylation	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
lead acetate	increases expression	1
potassium perchlorate	increases expression	1
sodium arsenate	decreases expression	1
trichostatin A	increases expression	1
tetrahydropalmatine	decreases expression	1
sodium arsenite	increases expression	1
cobaltous chloride	decreases expression	1
perfluorooctanoic acid	decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	increases expression, affects cotreatment	1
cupric oxide	increases expression	1
CGP 52608	affects binding, increases reaction	1
chloropicrin	decreases expression	1
deguelin	decreases expression	1
azaspiracid	increases expression	1
K 7174	increases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5651024	Binding	Binding affinity to human CALU incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_D1LT	Abcam K-562 CALU KO	Cancer cell line	Female
CVCL_D2IE	Abcam Raji CALU KO	Cancer cell line	Male
CVCL_UQ25	Abcam Jurkat CALU KO	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT05989620	Not specified	RECRUITING	Long-Term Development of Muscular Dystrophy Outcome Assessments