CALML3

gene
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Also known as CLP

Summary

CALML3 (calmodulin like 3, HGNC:1452) is a protein-coding gene on chromosome 10p15.1, encoding Calmodulin-like protein 3 (P27482). May function as a specific light chain of unconventional myosin-10 (MYO10), also enhances MYO10 translation, possibly by acting as a chaperone for the emerging MYO10 heavy chain protein.

Predicted to enable calcium ion binding activity. Located in extracellular exosome.

Source: NCBI Gene 810 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 27 total
  • Druggable target: yes — 1 molecules with ChEMBL bioactivity
  • MANE Select transcript: NM_005185

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1452
Approved symbolCALML3
Namecalmodulin like 3
Location10p15.1
Locus typegene with protein product
StatusApproved
AliasesCLP
Ensembl geneENSG00000178363
Ensembl biotypeprotein_coding
OMIM114184
Entrez810

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000315238

RefSeq mRNA: 1 — MANE Select: NM_005185 NM_005185

CCDS: CCDS7069

Canonical transcript exons

ENST00000315238 — 1 exons

ExonStartEnd
ENSE0000123457055249615526771

Expression profiles

Bgee: expression breadth ubiquitous, 177 present calls, max score 99.33.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 6.5547 / max 1765.8783, expressed in 100 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1036446.5547100

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
lower esophagus mucosaUBERON:003583499.33gold quality
gingivaUBERON:000182899.27gold quality
gingival epitheliumUBERON:000194999.20gold quality
mammalian vulvaUBERON:000099799.00gold quality
tongue squamous epitheliumUBERON:000691998.73gold quality
esophagus mucosaUBERON:000246998.64gold quality
upper arm skinUBERON:000426398.47gold quality
pharyngeal mucosaUBERON:000035598.21gold quality
oral cavityUBERON:000016797.68gold quality
skin of legUBERON:000151196.92gold quality
skin of abdomenUBERON:000141696.60gold quality
cervix epitheliumUBERON:000480196.29gold quality
zone of skinUBERON:000001496.17gold quality
hair follicleUBERON:000207396.11gold quality
squamous epitheliumUBERON:000691496.09gold quality
epithelium of esophagusUBERON:000197696.01gold quality
esophagus squamous epitheliumUBERON:000692096.00gold quality
penisUBERON:000098994.04gold quality
body of tongueUBERON:001187693.61gold quality
nippleUBERON:000203093.28gold quality
upper leg skinUBERON:000426293.24gold quality
mouth mucosaUBERON:000372992.42gold quality
buccal mucosa cellCL:000233691.97gold quality
minor salivary glandUBERON:000183091.39gold quality
tongueUBERON:000172391.28gold quality
cervix squamous epitheliumUBERON:000692290.31gold quality
saliva-secreting glandUBERON:000104490.08gold quality
vaginaUBERON:000099689.88gold quality
tonsilUBERON:000237286.85gold quality
thymusUBERON:000237086.13gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

ExperimentMarker?Max mean expression
E-HCAD-1yes1897.61
E-MTAB-10855yes1548.79
E-CURD-79yes1430.64
E-CURD-114yes143.48
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

17 targeting CALML3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-504-3P99.3067.181745
HSA-MIR-939-3P98.9765.072347
HSA-MIR-465698.7966.221306
HSA-MIR-6801-3P98.0464.64805
HSA-MIR-6810-3P97.9664.571023
HSA-MIR-466997.9462.71224
HSA-MIR-66597.6065.641781
HSA-MIR-6894-3P96.7365.64798
HSA-MIR-423-3P95.9967.7562
HSA-MIR-6741-5P93.8663.06437
HSA-MIR-473090.1269.6564

Literature-anchored findings (GeneRIF, showing 8)

  • CLP may be required during terminal differentiation to increase myosin-10 function as cells migrate toward the upper layers and establish new adhesive contacts. (PMID:17130134)
  • increased CLP expression and CLP-mediated Myo10 function are important for skin differentiation and wound reepithelialization (PMID:18818677)
  • expression was readily detected in areas of normal oral mucosa, while a notable downregulation of expression occurred in areas of malignant transformation (PMID:19166543)
  • Increased CALML3 expression in suprabasal layers is characteristic for differentiating keratinocytes in normal epidermis, and nuclear expression of CALML3 inversely correlates with expression of the proliferation marker Ki-67. (PMID:23638045)
  • We identified calmodulin-like protein 3 (CALML3) as a key sensor of this SNP and a coregulator of ERalpha, which contributes to differential gene transcription regulation in an estrogen and SERM-dependent fashion. Furthermore, using CRISPR/Cas9-engineered ZR75-1 breast cancer cells with different ZNF423 SNP genotypes, striking differences in cellular responses to SERMs and PARP inhibitors, alone or in combination (PMID:28821270)
  • UVB irradiation induced increase in apoptosis, Reactive Oxygen Species production and Ca2+ concentration of human lens epithelial cells , in part, by downregulating the expression of CALML3 and involved oxidative stress, Ca2+, JNK1/2 and ERK1/2 signaling pathways, suggesting that investigating CALML3 may useful for developing cataract treatment. (PMID:29436594)
  • Loss of CALML3 predicts shorter overall and relapse-free survival in postoperative hepatocellular carcinoma (HCC) patients, thus providing a prognostic biomarker and therapy target in HCC. (PMID:29445139)
  • Metformin suppresses gastric cancer through stimulating Calml3 secretion from TAFs. (PMID:30320344)

Cross-species orthologs

12 orthologs

OrganismSymbolGene ID
danio_reriocalm1aENSDARG00000021811
danio_reriocalm1bENSDARG00000034187
mus_musculusCalml3ENSMUSG00000063130
rattus_norvegicusCalml3ENSRNOG00000031955
drosophila_melanogasterTpnC4FBGN0033027
caenorhabditis_elegansWBGENE00000285
caenorhabditis_elegansWBGENE00000287
caenorhabditis_eleganspat-10WBGENE00003934
caenorhabditis_elegansWBGENE00006583
caenorhabditis_elegansWBGENE00008453
caenorhabditis_elegansF35C12.3WBGENE00009408
caenorhabditis_elegansWBGENE00015264

Paralogs (20): CABP7 (ENSG00000100314), CABP5 (ENSG00000105507), CALML4 (ENSG00000129007), CALM2 (ENSG00000143933), CETN2 (ENSG00000147400), CETN3 (ENSG00000153140), CABP1 (ENSG00000157782), CALM3 (ENSG00000160014), CABP2 (ENSG00000167791), CALML6 (ENSG00000169885), EFCAB3 (ENSG00000172421), EFCAB12 (ENSG00000172771), CABP4 (ENSG00000175544), CETN1 (ENSG00000177143), CALML5 (ENSG00000178372), CALN1 (ENSG00000183166), CALM1 (ENSG00000198668), EFCAB2 (ENSG00000203666), EFCAB7 (ENSG00000203965), EFCAB9 (ENSG00000214360)

Protein

Protein identifiers

Calmodulin-like protein 3P27482 (reviewed: P27482)

Alternative names: CaM-like protein, Calmodulin-related protein NB-1

All UniProt accessions (1): P27482

UniProt curated annotations — full annotation on UniProt →

Function. May function as a specific light chain of unconventional myosin-10 (MYO10), also enhances MYO10 translation, possibly by acting as a chaperone for the emerging MYO10 heavy chain protein. May compete with calmodulin by binding, with different affinities, to cellular substrates.

Subunit / interactions. Interacts with MYO10, the interaction is calcium-dependent and essential for MYO10 function in filopodial extension.

Tissue specificity. Expressed in normal mammary, prostate, cervical, and epidermal tissues. It is greatly reduced or undetectable in transformed cells.

Induction. By TGFB1.

Miscellaneous. Binds four calcium ions.

Similarity. Belongs to the calmodulin family.

RefSeq proteins (1): NP_005176* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002048EF_hand_domDomain
IPR011992EF-hand-dom_pairHomologous_superfamily
IPR018247EF_Hand_1_Ca_BSBinding_site
IPR050230CALM/Myosin/TropC-likeFamily

Pfam: PF13499

UniProt features (35 total): binding site 19, helix 7, domain 4, strand 4, chain 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
1GGZX-RAY DIFFRACTION1.5

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P27482-F183.170.16

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 (19): 57; 59; 61; 63; 68; 94; 96; 98; 105; 130; 132; 134

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 117 (showing top): JAEGER_METASTASIS_DN, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, CREBP1_Q2, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_MONOATOMIC_CATION_TRANSPORT, GOBP_RESPONSE_TO_METAL_ION, SMITH_TERT_TARGETS_DN, GOBP_REGULATION_OF_CALCIUM_ION_TRANSMEMBRANE_TRANSPORT, GOBP_MAINTENANCE_OF_LOCATION, GOCC_CENTROSOME, GOBP_SARCOPLASMIC_RETICULUM_CALCIUM_ION_TRANSPORT, KEGG_OLFACTORY_TRANSDUCTION, GOBP_DETECTION_OF_STIMULUS, GOBP_MONOATOMIC_ION_HOMEOSTASIS, GOBP_REGULATION_OF_RELEASE_OF_SEQUESTERED_CALCIUM_ION_INTO_CYTOSOL

GO Biological Process (3): detection of calcium ion (GO:0005513), regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880), calcineurin-mediated signaling (GO:0097720)

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

GO Cellular Component (5): cytoplasm (GO:0005737), centrosome (GO:0005813), synaptic vesicle membrane (GO:0030672), myelin sheath (GO:0043209), extracellular exosome (GO:0070062)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
detection of chemical stimulus1
response to calcium ion1
release of sequestered calcium ion into cytosol by sarcoplasmic reticulum1
regulation of release of sequestered calcium ion into cytosol1
calcium-mediated signaling1
metal ion binding1
binding1
cation binding1
intracellular anatomical structure1
centriole1
microtubule organizing center1
synaptic vesicle1
exocytic vesicle membrane1
extracellular vesicle1

Protein interactions and networks

STRING

7352 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CALML3NOS3P29474996
CALML3CALD1Q05682996
CALML3NOS1P29475995
CALML3MARCKSP29966995
CALML3IQGAP1P46940994
CALML3MYLK2Q9H1R3994
CALML3CAMK2AQ9UQM7994
CALML3MYLKQ15746993
CALML3RYR2Q92736993
CALML3NRGNQ92686992
CALML3CACNA1CQ13936991
CALML3RYR1P21817990
CALML3TRPV1Q8NER1990
CALML3CAMK4Q16566987
CALML3MBPP02686987
CALML3GAP43P17677987

IntAct

194 interactions, top by confidence:

ABTypeScore
POC5CETN3psi-mi:“MI:0914”(association)0.920
POC5CETN3psi-mi:“MI:0914”(association)0.770
EIF4E2GIGYF1psi-mi:“MI:0914”(association)0.730
CFTRESYT2psi-mi:“MI:0914”(association)0.710
CALML3MYO10psi-mi:“MI:0915”(physical association)0.680
CALML3MYO10psi-mi:“MI:0407”(direct interaction)0.680
MYO10CALML3psi-mi:“MI:0407”(direct interaction)0.680
CALML3IQCNpsi-mi:“MI:0915”(physical association)0.670
IQCNCALML3psi-mi:“MI:0915”(physical association)0.670
ANXA9PPLpsi-mi:“MI:0914”(association)0.660
SINHCAFTNRC18psi-mi:“MI:0914”(association)0.640
RAB11BSH3BP5psi-mi:“MI:0914”(association)0.640
CAPZA2CNOT1psi-mi:“MI:0914”(association)0.640
CFTRHAX1psi-mi:“MI:0914”(association)0.610
CALML3KIAA1683psi-mi:“MI:0915”(physical association)0.560
MFICALML3psi-mi:“MI:0915”(physical association)0.560
CALML3MFIpsi-mi:“MI:0915”(physical association)0.560
IQCB1CALML3psi-mi:“MI:0915”(physical association)0.560
CALML3IQCB1psi-mi:“MI:0915”(physical association)0.560
ZSCAN12A2ML1psi-mi:“MI:0914”(association)0.530

BioGRID (264): KIAA1683 (Two-hybrid), C11orf65 (Two-hybrid), CALML3 (Affinity Capture-MS), CALML3 (Affinity Capture-MS), CALML3 (Affinity Capture-MS), CALML3 (Affinity Capture-MS), CALML3 (Affinity Capture-MS), CALML3 (Affinity Capture-MS), CALML3 (Affinity Capture-MS), CALML3 (Affinity Capture-MS), CALML3 (Affinity Capture-MS), CALML3 (Affinity Capture-MS), CALML3 (Affinity Capture-MS), CALML3 (Affinity Capture-MS), CALML3 (Affinity Capture-MS)

ESM2 similar proteins: A0A125YHX7, A0A125YZN2, J9W034, O15182, O23184, O35648, O74435, O82659, P02597, P02599, P04352, P05434, P05933, P06704, P27163, P27164, P27482, P41041, P41208, P41209, P41210, P43645, P43646, P49258, P53440, P53441, P54213, P60204, P60205, P60206, P61859, P61860, P61861, Q06827, Q12798, Q24956, Q27177, Q27178, Q27179, Q2TBN3

Diamond homologs: A4IF97, B7SNI3, F1SSF9, O14950, O23320, O93409, O96081, O97341, P02597, P02608, P02609, P02610, P02611, P02612, P02613, P04112, P04113, P04464, P04466, P05419, P05932, P05933, P05944, P05963, P07461, P08051, P08052, P08733, P10916, P11118, P11121, P13543, P13832, P13833, P14533, P18061, P18432, P18666, P19105, P19625

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance26
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

55 predictions. Top by Δscore:

VariantEffectΔscore
10:5525525:TGTCC:Tdonor_gain0.8700
10:5525149:AAG:Aacceptor_gain0.8100
10:5525148:CA:Cacceptor_gain0.7200
10:5525149:AA:Aacceptor_gain0.7200
10:5525145:TGACA:Tacceptor_gain0.6600
10:5525070:C:CAacceptor_gain0.6300
10:5525497:A:AGdonor_gain0.5900
10:5525498:A:Gdonor_gain0.5900
10:5525495:TG:Tdonor_gain0.5800
10:5525526:GTCCA:Gdonor_gain0.5700
10:5525706:A:AGacceptor_gain0.5700
10:5525082:T:TAacceptor_gain0.4700
10:5525150:A:Gacceptor_gain0.4600
10:5525149:A:AGacceptor_gain0.4500
10:5525496:G:Adonor_gain0.4400
10:5525145:T:TAacceptor_gain0.4300
10:5525690:C:Aacceptor_gain0.4100
10:5525505:G:GTdonor_gain0.3900
10:5525531:A:Gdonor_gain0.3700
10:5525679:ATCCC:Aacceptor_gain0.3600
10:5525683:C:Aacceptor_gain0.3400
10:5525124:C:CTacceptor_gain0.3200
10:5525703:T:Aacceptor_gain0.3200
10:5525086:AT:Aacceptor_gain0.3100
10:5525707:C:Gacceptor_gain0.3100
10:5525532:G:GGdonor_gain0.3000
10:5525581:C:Tdonor_gain0.3000
10:5525070:C:Gacceptor_gain0.2900
10:5525714:C:Aacceptor_gain0.2800
10:5525739:T:Gacceptor_gain0.2700

AlphaMissense

1000 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
10:5525134:T:CF17L0.993
10:5525136:C:AF17L0.993
10:5525136:C:GF17L0.993
10:5525290:T:CF69L0.991
10:5525292:C:AF69L0.991
10:5525292:C:GF69L0.991
10:5525168:T:AI28N0.988
10:5525353:T:CF90L0.988
10:5525355:C:AF90L0.988
10:5525355:C:GF90L0.988
10:5525387:T:AV101D0.988
10:5525231:T:CL49P0.985
10:5525291:T:CF69S0.985
10:5525198:G:CR38P0.984
10:5525402:T:CL106P0.983
10:5525200:T:CS39P0.982
10:5525168:T:CI28T0.981
10:5525362:T:CF93L0.980
10:5525364:C:AF93L0.980
10:5525364:C:GF93L0.980
10:5525143:T:CF20L0.979
10:5525145:T:AF20L0.979
10:5525145:T:GF20L0.979
10:5525192:T:AV36D0.979
10:5525509:T:CF142L0.979
10:5525511:T:AF142L0.979
10:5525511:T:GF142L0.979
10:5525168:T:GI28S0.978
10:5525354:T:CF90S0.978
10:5525291:T:GF69C0.976

dbSNP variants (sampled 300 via entrez): RS1000009372 (10:5523959 G>A,C,T), RS1001699674 (10:5527125 G>A), RS1002170992 (10:5526905 TGG>T), RS1002503067 (10:5525777 C>CCTCCCCA), RS1002555584 (10:5525999 T>C), RS1002749925 (10:5526008 G>A), RS1003107383 (10:5525783 C>A,G,T), RS1003683207 (10:5524719 G>A), RS1004143521 (10:5524913 G>A,C,T), RS1004460541 (10:5523066 A>G), RS1005148926 (10:5527250 T>C), RS1005262012 (10:5527083 C>A), RS1006113818 (10:5523917 G>A), RS1006547061 (10:5526542 T>G), RS1006597448 (10:5526387 C>T)

Disease associations

OMIM: gene MIM:114184 | 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):

StudyTraitp-value
GCST012046_5Fasting insulin3.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5169127 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 27,339 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL126LINEZOLID427,339

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

ChEMBL bioactivities

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

pChemblTypeValueUnitMolecule
6.30IC50500nMCHEMBL5183837
5.89IC501300nMCHEMBL5202730
5.70IC502000nMCHEMBL5189056
5.03IC509300nMLINEZOLID

PubChem BioAssay actives

4 with measured affinity, of 5 total; 4 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
(5R)-3-[3-fluoro-4-[4-(1-methylpyridin-1-ium-4-yl)phenyl]phenyl]-5-(hydroxymethyl)-1,3-oxazolidin-2-one chloride1852696: Inhibition of CALML3 (unknown origin) assessed as apparent protein translation inhibition constant incubated for 5 hrs by SDS gel electrophoresisic500.5000uM
(5R)-3-(3-fluoro-4-pyridin-4-ylphenyl)-5-(hydroxymethyl)-1,3-oxazolidin-2-one1852696: Inhibition of CALML3 (unknown origin) assessed as apparent protein translation inhibition constant incubated for 5 hrs by SDS gel electrophoresisic501.3000uM
(5R)-3-[3-fluoro-4-[3-(hydroxymethyl)phenyl]phenyl]-5-(hydroxymethyl)-1,3-oxazolidin-2-one1852696: Inhibition of CALML3 (unknown origin) assessed as apparent protein translation inhibition constant incubated for 5 hrs by SDS gel electrophoresisic502.0000uM
Linezolid1852696: Inhibition of CALML3 (unknown origin) assessed as apparent protein translation inhibition constant incubated for 5 hrs by SDS gel electrophoresisic509.3000uM

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

ChemicalActions (top 5)PubMed papers
Air Pollutantsincreases abundance, increases expression, decreases expression2
Benzo(a)pyrenedecreases expression, increases methylation, affects methylation2
Tobacco Smoke Pollutionincreases expression, affects expression, decreases expression2
Particulate Matterdecreases expression, increases abundance2
sodium arsenatedecreases expression, increases abundance1
beta-lapachonedecreases expression1
arseniteincreases methylation1
hydroquinonedecreases expression1
seocalcitolincreases expression1
2-palmitoylglycerolincreases expression1
Arsenicdecreases expression, increases abundance1
Cadmiumincreases abundance, decreases expression1
Calcitriolincreases expression1
Estradiolaffects cotreatment, decreases expression1
Smokeincreases expression, increases abundance1
Valproic Acidincreases methylation1
Isotretinoindecreases expression1
Cadmium Chloridedecreases expression, increases abundance1
Simvastatinincreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5107418BindingInhibition of CALML3 (unknown origin) assessed as apparent protein translation inhibition constant incubated for 5 hrs by SDS gel electrophoresisStructure-Uptake Relationship Studies of Oxazolidinones in Gram-Negative ESKAPE Pathogens. — J Med Chem

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.