CLMN

gene
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Also known as FLJ12383KIAA1188KIAA0500

Summary

CLMN (calmin, HGNC:19972) is a protein-coding gene on chromosome 14q32.13, encoding Calmin (Q96JQ2).

Predicted to enable actin filament binding activity. Predicted to be involved in negative regulation of cell population proliferation. Predicted to act upstream of or within neuron projection development. Predicted to be located in membrane. Predicted to be part of meiotic nuclear membrane microtubule tethering complex. Predicted to be active in cytoplasm and nuclear outer membrane.

Source: NCBI Gene 79789 — RefSeq curated summary.

At a glance

  • GWAS associations: 10
  • Clinical variants (ClinVar): 220 total
  • MANE Select transcript: NM_024734

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:19972
Approved symbolCLMN
Namecalmin
Location14q32.13
Locus typegene with protein product
StatusApproved
AliasesFLJ12383, KIAA1188, KIAA0500
Ensembl geneENSG00000165959
Ensembl biotypeprotein_coding
OMIM611121
Entrez79789

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 6 protein_coding, 3 retained_intron, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000298912, ENST00000553733, ENST00000555336, ENST00000555615, ENST00000556416, ENST00000556441, ENST00000556454, ENST00000557215, ENST00000557696, ENST00000869560, ENST00000941995

RefSeq mRNA: 1 — MANE Select: NM_024734 NM_024734

CCDS: CCDS9933

Canonical transcript exons

ENST00000298912 — 13 exons

ExonStartEnd
ENSE000010984649521564195215733
ENSE000010984919522169195221774
ENSE000010985429521321995213409
ENSE000011689239521068695210879
ENSE000013125789518194095191732
ENSE000013271609531971195319908
ENSE000034639939523007295230133
ENSE000035070059522376095223855
ENSE000035269539519649895196694
ENSE000035313139519453695194596
ENSE000035763009520283895204463
ENSE000036284049520939595209477
ENSE000036298099519384995193919

Expression profiles

Bgee: expression breadth ubiquitous, 275 present calls, max score 98.86.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.9064 / max 291.2049, expressed in 1232 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1447838.14331180
1447821.5792610
1447840.183981

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
spermCL:000001998.86gold quality
male germ cellCL:000001596.79gold quality
lateral nuclear group of thalamusUBERON:000273696.54gold quality
bronchial epithelial cellCL:000232895.85gold quality
left testisUBERON:000453395.58gold quality
right testisUBERON:000453495.48gold quality
renal medullaUBERON:000036294.75gold quality
epithelium of bronchusUBERON:000203194.61gold quality
corpus callosumUBERON:000233694.35gold quality
sural nerveUBERON:001548894.14gold quality
bronchusUBERON:000218594.12gold quality
mucosa of paranasal sinusUBERON:000503093.28gold quality
testisUBERON:000047393.27gold quality
mucosa of sigmoid colonUBERON:000499392.81gold quality
colonic mucosaUBERON:000031792.37gold quality
body of pancreasUBERON:000115092.11gold quality
dorsal plus ventral thalamusUBERON:000189791.73gold quality
metanephros cortexUBERON:001053390.96gold quality
dorsal motor nucleus of vagus nerveUBERON:000287090.70gold quality
globus pallidusUBERON:000187590.58gold quality
inferior vagus X ganglionUBERON:000536390.44gold quality
medial globus pallidusUBERON:000247790.34gold quality
buccal mucosa cellCL:000233690.21gold quality
nephron tubuleUBERON:000123189.99gold quality
pancreasUBERON:000126489.70gold quality
inferior olivary complexUBERON:000212789.64gold quality
kidneyUBERON:000211389.20gold quality
adult mammalian kidneyUBERON:000008289.12gold quality
subthalamic nucleusUBERON:000190689.10gold quality
lateral globus pallidusUBERON:000247689.09gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 5.

ExperimentMarker?Max mean expression
E-HCAD-35yes72.68
E-ANND-3yes14.73
E-CURD-119yes14.03
E-GEOD-134144yes7.93
E-ENAD-27yes7.08
E-CURD-11no113.86

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

306 targeting CLMN, 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-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-4533100.0069.482758
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-4283100.0066.422097
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-340-5P100.0072.504437
HSA-MIR-5692A100.0074.406850
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-3925-3P100.0069.951237
HSA-MIR-4262100.0073.263931
HSA-MIR-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-3646100.0073.565283
HSA-MIR-5193100.0067.261744
HSA-MIR-3120-5P100.0065.56965
HSA-MIR-4682100.0068.891258
HSA-MIR-188-3P100.0068.761240
HSA-MIR-366299.9973.825684
HSA-MIR-548AW99.9972.573559
HSA-MIR-453199.9969.703181
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioclmnbENSDARG00000043667
danio_rerioclmnaENSDARG00000096867
mus_musculusClmnENSMUSG00000021097
rattus_norvegicusClmnENSRNOG00000011044

Paralogs (36): SYNE2 (ENSG00000054654), SPTB (ENSG00000070182), ACTN1 (ENSG00000072110), ACTN2 (ENSG00000077522), DSP (ENSG00000096696), DRP2 (ENSG00000102385), SPTBN1 (ENSG00000115306), MACF1 (ENSG00000127603), FLNC (ENSG00000128591), ACTN4 (ENSG00000130402), SYNE1 (ENSG00000131018), MICAL2 (ENSG00000133816), DTNA (ENSG00000134769), MICAL1 (ENSG00000135596), FLNB (ENSG00000136068), SPTBN5 (ENSG00000137877), DTNB (ENSG00000138101), GAS2L3 (ENSG00000139354), DST (ENSG00000151914), UTRN (ENSG00000152818), SPTBN4 (ENSG00000160460), SPTA1 (ENSG00000163554), PKHD1 (ENSG00000170927), SPTBN2 (ENSG00000173898), SYNE3 (ENSG00000176438), PLEC (ENSG00000178209), SMTNL2 (ENSG00000188176), FLNA (ENSG00000196924), SPTAN1 (ENSG00000197694), DMD (ENSG00000198947), PKHD1L1 (ENSG00000205038), DYTN (ENSG00000232125), MICAL3 (ENSG00000243156), ACTN3 (ENSG00000248746), EPPK1 (ENSG00000261150), GAS2L2 (ENSG00000270765)

Protein

Protein identifiers

CalminQ96JQ2 (reviewed: Q96JQ2)

Alternative names: Calponin-like transmembrane domain protein

All UniProt accessions (5): Q96JQ2, G3V3D8, G3V4C0, G3V5E0, G3V5U3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Tissue specificity. Widely expressed at intermediate level.

RefSeq proteins (1): NP_079010* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001589Actinin_actin-bd_CSConserved_site
IPR001715CH_domDomain
IPR036872CH_dom_sfHomologous_superfamily
IPR047826CLMN_CH_secondDomain
IPR047827CLMN_CH_firstDomain
IPR052403LINC-complex_assocFamily

Pfam: PF00307

UniProt features (35 total): compositionally biased region 13, modified residue 9, region of interest 6, domain 2, sequence conflict 2, chain 1, transmembrane region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96JQ2-F152.840.18

Functional residue map

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

Post-translational modifications (9): 301, 402, 619, 699, 713, 769, 838, 841, 907

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 187 (showing top): TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_6HR_DN, GOBP_NEUROGENESIS, DELYS_THYROID_CANCER_DN, GOBP_NUCLEUS_LOCALIZATION, CAIRO_HEPATOBLASTOMA_UP, GFI1_01, GOMF_ACTIN_BINDING, NRF2_01, GOBP_CELL_PROJECTION_ORGANIZATION, ROSS_AML_WITH_PML_RARA_FUSION, GOBP_ORGANELLE_LOCALIZATION, chr14q32, YNGTTNNNATT_UNKNOWN, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, MULLIGHAN_MLL_SIGNATURE_2_DN

GO Biological Process (3): nuclear migration (GO:0007097), negative regulation of cell population proliferation (GO:0008285), neuron projection development (GO:0031175)

GO Molecular Function (3): actin filament binding (GO:0051015), actin binding (GO:0003779), protein binding (GO:0005515)

GO Cellular Component (4): nuclear outer membrane (GO:0005640), cytoplasm (GO:0005737), meiotic nuclear membrane microtubule tethering complex (GO:0034993), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
intracellular transport1
nucleus localization1
establishment of organelle localization1
cell population proliferation1
regulation of cell population proliferation1
negative regulation of cellular process1
neuron development1
plasma membrane bounded cell projection organization1
actin binding1
protein-containing complex binding1
cytoskeletal protein binding1
binding1
nuclear membrane1
organelle outer membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
intracellular anatomical structure1
microtubule organizing center attachment site1
nuclear membrane microtubule tethering complex1

Protein interactions and networks

STRING

850 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CLMNKIF6Q6ZMV9447
CLMNEFL1Q7Z2Z2426
CLMNEMDP50402423
CLMNAFAP1L2Q8N4X5414
CLMNERICH6BQ5W0A0409
CLMNNRAPQ86VF7409
CLMNLRRIQ3A6PVS8402
CLMNUBXN7O94888396
CLMNCYP24A1Q07973392
CLMNCOPB1P53618384
CLMNTESCQ96BS2380
CLMNSTRBPQ96SI9378
CLMNA1CFQ9NQ94377
CLMNSERPINB1P30740375
CLMNFAM234BA2RU67372

IntAct

31 interactions, top by confidence:

ABTypeScore
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
ANXA9PPLpsi-mi:“MI:0914”(association)0.660
YWHAGBLTP3Bpsi-mi:“MI:2364”(proximity)0.640
ADCY9NEMP1psi-mi:“MI:0914”(association)0.640
YWHAHBLTP3Bpsi-mi:“MI:2364”(proximity)0.570
DYNLT2BSNX2psi-mi:“MI:0914”(association)0.530
HSCBRBP5psi-mi:“MI:0914”(association)0.350
COPB2ESYT2psi-mi:“MI:0914”(association)0.350
CTNNB1TCERG1psi-mi:“MI:0914”(association)0.350
RTN4ESYT2psi-mi:“MI:0914”(association)0.350
UBBRNF40psi-mi:“MI:0914”(association)0.350
AP2M1C1orf226psi-mi:“MI:0914”(association)0.350
FPR1GPR89Apsi-mi:“MI:0914”(association)0.350
PPLUBR5psi-mi:“MI:0914”(association)0.350
UBL4BFECHpsi-mi:“MI:0914”(association)0.350
CLMNUQCC4psi-mi:“MI:0914”(association)0.350
GPR182SLC12A8psi-mi:“MI:0914”(association)0.350
AP2M1PER1psi-mi:“MI:0914”(association)0.350
SLC67A1LTN1psi-mi:“MI:0914”(association)0.350
SLC2A2ESYT2psi-mi:“MI:0914”(association)0.350
SLC7A11PSMD9psi-mi:“MI:0914”(association)0.350
SLC7A9CDC7psi-mi:“MI:0914”(association)0.350
CANXESYT2psi-mi:“MI:2364”(proximity)0.270
CDH1ESYT2psi-mi:“MI:2364”(proximity)0.270
SFNBLTP3Bpsi-mi:“MI:2364”(proximity)0.270
CLMNFHL1psi-mi:“MI:0915”(physical association)0.000

BioGRID (101): CLMN (Proximity Label-MS), CLMN (Affinity Capture-MS), CLMN (Affinity Capture-RNA), CLMN (Affinity Capture-MS), CLMN (Proximity Label-MS), CLMN (Affinity Capture-RNA), CLMN (Protein-RNA), CLMN (Proximity Label-MS), CLMN (Proximity Label-MS), CLMN (Proximity Label-MS), CLMN (Proximity Label-MS), CLMN (Proximity Label-MS), CLMN (Proximity Label-MS), CLMN (Proximity Label-MS), CLMN (Two-hybrid)

ESM2 similar proteins: A0A1B0GVH6, A0A1L8H8C0, A0A1L8HFX9, A0A2R6X6S3, A0JM08, A0MS83, A2BIL8, A2RUV4, E9Q309, F1MCY2, F1QIC4, P46012, Q08D57, Q1LY77, Q498L0, Q4KMC9, Q501J7, Q52KW0, Q5DTJ9, Q5F3P8, Q5RAU1, Q5SW79, Q5T5U3, Q5VT06, Q62417, Q62770, Q66J90, Q69Z38, Q6A065, Q6DFG0, Q6DFV3, Q6FWU4, Q71M21, Q80TN7, Q86TC9, Q8AV28, Q8C5W0, Q8IVL0, Q8IZ21, Q8K0T7

Diamond homologs: A5D7D1, D3ZEN0, D3ZHA0, D3ZHV2, D3ZQL6, E1BBG2, F1MF74, F1RA39, F6QZ15, G3MWR8, G3V7L1, L7UZ85, M9MRD1, O13728, O15020, O43707, O75369, O76329, O88990, O94851, O97592, P05094, P05095, P07751, P11277, P11530, P11531, P11532, P11533, P12814, P13395, P13466, P15508, P16086, P16546, P18091, P20111, P21333, P30427, P35609

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 41 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.

Reactome pathways:

PathwayPartnersFoldFDR
G2/M Checkpoints521.0×8e-04
SARS-CoV Infections58.7×7e-03
Infectious disease75.4×7e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance153
Likely benign29
Benign15

Top pathogenic / likely-pathogenic (0)

SpliceAI

2897 predictions. Top by Δscore:

VariantEffectΔscore
14:95193321:T:Adonor_gain1.0000
14:95193330:T:TAdonor_gain1.0000
14:95194530:A:ACdonor_gain1.0000
14:95194531:C:CCdonor_gain1.0000
14:95194531:CTAA:Cdonor_gain1.0000
14:95194532:TAA:Tdonor_loss1.0000
14:95194533:AAC:Adonor_loss1.0000
14:95194534:A:ACdonor_gain1.0000
14:95194534:A:Cdonor_loss1.0000
14:95194535:C:Adonor_loss1.0000
14:95194535:C:CCdonor_gain1.0000
14:95194592:TAGTC:Tacceptor_gain1.0000
14:95194594:GTC:Gacceptor_gain1.0000
14:95194595:TC:Tacceptor_gain1.0000
14:95194596:CC:Cacceptor_gain1.0000
14:95194596:CCTGA:Cacceptor_loss1.0000
14:95194597:C:CCacceptor_gain1.0000
14:95196495:TACCT:Tdonor_loss1.0000
14:95196496:AC:Adonor_loss1.0000
14:95196497:C:Gdonor_loss1.0000
14:95196690:TGGGA:Tacceptor_gain1.0000
14:95196691:GGGA:Gacceptor_gain1.0000
14:95196692:GGA:Gacceptor_gain1.0000
14:95196693:GA:Gacceptor_gain1.0000
14:95196695:C:CCacceptor_gain1.0000
14:95209393:A:ACdonor_gain1.0000
14:95209394:C:CCdonor_gain1.0000
14:95209394:CGG:Cdonor_gain1.0000
14:95209399:T:TAdonor_gain1.0000
14:95209478:C:CCacceptor_gain1.0000

AlphaMissense

6681 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
14:95191620:A:GW985R0.999
14:95191620:A:TW985R0.999
14:95210845:A:GW215R0.999
14:95210845:A:TW215R0.999
14:95215669:A:GL130P0.999
14:95221713:A:GL101P0.999
14:95221739:A:CF92L0.999
14:95221739:A:TF92L0.999
14:95221741:A:GF92L0.999
14:95230095:A:GW41R0.999
14:95230095:A:TW41R0.999
14:95210836:C:AG218W0.998
14:95215664:A:GW132R0.998
14:95215664:A:TW132R0.998
14:95221704:A:GL104S0.998
14:95221734:A:GL94S0.998
14:95223806:C:AG65V0.998
14:95210835:C:TG218E0.997
14:95210843:C:AW215C0.997
14:95210843:C:GW215C0.997
14:95215702:A:CI119R0.997
14:95215702:A:TI119K0.997
14:95221706:A:CF103L0.997
14:95221706:A:TF103L0.997
14:95221708:A:GF103L0.997
14:95221725:A:TI97K0.997
14:95221727:G:CN96K0.997
14:95221727:G:TN96K0.997
14:95221740:A:GF92S0.997
14:95223806:C:TG65D0.997

dbSNP variants (sampled 300 via entrez): RS1000036213 (14:95186546 G>A), RS1000057528 (14:95185419 C>T), RS1000063679 (14:95243977 T>C), RS1000089567 (14:95289743 TG>T), RS1000095017 (14:95193252 A>G), RS1000103571 (14:95306732 A>T), RS1000134013 (14:95214187 A>G,T), RS1000153544 (14:95321038 T>C), RS1000154858 (14:95267655 C>A), RS1000161869 (14:95210914 G>A), RS1000204315 (14:95257164 C>T), RS1000262012 (14:95248624 T>C), RS1000284180 (14:95285560 G>A), RS1000330687 (14:95259241 T>C), RS1000332195 (14:95317476 G>A)

Disease associations

OMIM: gene MIM:611121 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

10 associations (top):

StudyTraitp-value
GCST000618_26Response to antipsychotic treatment2.000000e-07
GCST000635_26Response to statin therapy2.000000e-08
GCST001585_36Breast size8.000000e-07
GCST001915_33Alzheimer’s disease (cognitive decline)2.000000e-08
GCST002805_2Body mass index9.000000e-07
GCST003854_23Gut microbiota (functional units)4.000000e-08
GCST004068_36Venous thromboembolism adjusted for sickle cell variant rs77121243-T5.000000e-06
GCST006190_65Diastolic blood pressure x smoking status (ever vs never) interaction (2df test)9.000000e-10
GCST009391_416Metabolite levels7.000000e-06
GCST010396_152Gut microbiota (bacterial taxa, hurdle binary method)2.000000e-06

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0005937longitudinal BMI measurement
EFO:0007874gut microbiome measurement
EFO:0006336diastolic blood pressure
EFO:0006527smoking status measurement
EFO:0010387phosphatidylcholine 38:5 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs8014194CLMN0.000

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases expression, affects expression, decreases methylation, increases expression, affects cotreatment5
sodium arsenitedecreases expression, increases expression5
Benzo(a)pyrenedecreases methylation, increases expression, affects methylation, decreases expression5
Estradioldecreases expression, increases reaction, affects cotreatment, increases expression5
Valproic Aciddecreases methylation, increases expression, affects expression4
bisphenol Sincreases expression, affects cotreatment, decreases expression3
Air Pollutantsincreases abundance, increases expression, decreases expression3
Calcitriolaffects cotreatment, increases expression, increases reaction3
Smokeincreases abundance, increases expression, decreases expression3
Tobacco Smoke Pollutiondecreases expression, affects expression3
Tretinoindecreases reaction, increases expression, decreases expression3
trichostatin Aincreases expression, affects expression2
potassium chromate(VI)affects cotreatment, decreases expression2
Fulvestrantaffects cotreatment, increases methylation, increases expression2
Acetaminophendecreases expression2
Dexamethasoneincreases expression, affects cotreatment, decreases expression2
Nickeldecreases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Cyclosporinedecreases expression2
Aflatoxin B1affects expression, increases methylation2
Particulate Matterdecreases expression, increases abundance, increases expression2
aristolochic acid Idecreases expression1
FR900359increases phosphorylation1
bisphenol Faffects cotreatment, increases methylation1
bufotalindecreases expression1
methylmercuric chloridedecreases expression1
2,5,2’,5’-tetrachlorobiphenyldecreases expression1
tris(2-butoxyethyl) phosphatedecreases expression1
mono-(2-ethylhexyl)phthalateincreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): venous thromboembolism