CNNM1

gene
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Also known as SLC70A1

Summary

CNNM1 (cyclin and CBS domain divalent metal cation transport mediator 1, HGNC:102) is a protein-coding gene on chromosome 10q24.2, encoding Metal transporter CNNM1 (Q9NRU3). Probable metal transporter.

This gene encodes a member of the ancient conserved domain protein family. The encoded protein may bind copper. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 26507 — RefSeq curated summary.

At a glance

  • GWAS associations: 6
  • Clinical variants (ClinVar): 138 total
  • MANE Select transcript: NM_020348

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:102
Approved symbolCNNM1
Namecyclin and CBS domain divalent metal cation transport mediator 1
Location10q24.2
Locus typegene with protein product
StatusApproved
AliasesSLC70A1
Ensembl geneENSG00000119946
Ensembl biotypeprotein_coding
OMIM607802
Entrez26507

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000356713, ENST00000488090, ENST00000696687, ENST00000914274

RefSeq mRNA: 4 — MANE Select: NM_020348 NM_001345887, NM_001345888, NM_001345889, NM_020348

CCDS: CCDS7478, CCDS91317

Canonical transcript exons

ENST00000356713 — 11 exons

ExonStartEnd
ENSE000008112619936441799364516
ENSE000008112639937705599377218
ENSE000008112659938782099388003
ENSE000008112679938815299388301
ENSE000008112689939030699390407
ENSE000012374369936495599365002
ENSE000012374439936222799362396
ENSE000012374619932935699330960
ENSE000013532969936083599360975
ENSE000019140609939143799394330
ENSE000024900529935751299357655

Expression profiles

Bgee: expression breadth ubiquitous, 176 present calls, max score 84.16.

FANTOM5 (CAGE): breadth broad, TPM avg 1.8058 / max 52.4389, expressed in 439 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1064851.6181423
1064840.175498
1064860.01233

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
postcentral gyrusUBERON:000258184.16gold quality
prefrontal cortexUBERON:000045183.49gold quality
parietal lobeUBERON:000187283.34gold quality
lateral nuclear group of thalamusUBERON:000273683.14gold quality
right hemisphere of cerebellumUBERON:001489082.28gold quality
right frontal lobeUBERON:000281082.24gold quality
Brodmann (1909) area 46UBERON:000648382.23gold quality
frontal cortexUBERON:000187082.21gold quality
cerebellar hemisphereUBERON:000224582.13gold quality
cerebellar cortexUBERON:000212982.06gold quality
Brodmann (1909) area 9UBERON:001354081.96gold quality
spermCL:000001981.79silver quality
nucleus accumbensUBERON:000188281.47gold quality
superior frontal gyrusUBERON:000266181.47gold quality
caudate nucleusUBERON:000187381.44gold quality
male germ cellCL:000001581.32silver quality
lateral globus pallidusUBERON:000247681.29gold quality
cerebellumUBERON:000203781.24gold quality
neocortexUBERON:000195080.87gold quality
putamenUBERON:000187480.80gold quality
dorsolateral prefrontal cortexUBERON:000983480.79gold quality
cerebral cortexUBERON:000095679.02gold quality
anterior cingulate cortexUBERON:000983578.96gold quality
cingulate cortexUBERON:000302778.95gold quality
telencephalonUBERON:000189378.88gold quality
orbitofrontal cortexUBERON:000416778.02gold quality
forebrainUBERON:000189077.75gold quality
brainUBERON:000095577.47gold quality
occipital lobeUBERON:000202177.44gold quality
right testisUBERON:000453477.38gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-MTAB-5061yes229.21
E-ANND-3yes5.17
E-MTAB-8060no213.62

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

153 targeting CNNM1, 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-4455100.0065.481587
HSA-MIR-4425100.0067.591049
HSA-MIR-9-5P100.0072.282361
HSA-MIR-4682100.0068.891258
HSA-MIR-4673100.0066.641490
HSA-MIR-806899.9873.852376
HSA-MIR-4645-5P99.9865.811284
HSA-MIR-314899.9775.066478
HSA-MIR-50799.9770.111915
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-55799.9670.011640
HSA-MIR-4725-3P99.9669.532520
HSA-MIR-6780B-5P99.9669.602562
HSA-MIR-211099.9666.681930
HSA-MIR-6772-5P99.9467.01577
HSA-MIR-1236-3P99.9468.041695
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-552-5P99.9368.561583
HSA-MIR-314399.9371.963104
HSA-MIR-450B-5P99.9271.483175
HSA-MIR-6809-3P99.9171.453814
HSA-MIR-4753-3P99.9071.033786
HSA-MIR-627-3P99.9071.423316
HSA-MIR-129-5P99.8870.263273
HSA-MIR-6780A-5P99.8866.692776
HSA-MIR-1211999.8768.351653
HSA-MIR-612499.8769.783551
HSA-MIR-10395-5P99.8667.35676
HSA-MIR-3151-5P99.8663.831069
HSA-MIR-4728-5P99.8569.394718

Literature-anchored findings (GeneRIF, showing 1)

  • SNHG7 Facilitates Hepatocellular Carcinoma Occurrence by Sequestering miR-9-5p to Upregulate CNNM1 Expression. (PMID:32397799)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_reriocnnm1ENSDARG00000078087
mus_musculusCnnm1ENSMUSG00000025189
rattus_norvegicusCnnm1ENSRNOG00000016302
drosophila_melanogasteruexFBGN0262124
caenorhabditis_elegansWBGENE00011260
caenorhabditis_elegansWBGENE00016343
caenorhabditis_elegansWBGENE00016879

Paralogs (3): CNNM2 (ENSG00000148842), CNNM4 (ENSG00000158158), CNNM3 (ENSG00000168763)

Protein

Protein identifiers

Metal transporter CNNM1Q9NRU3 (reviewed: Q9NRU3)

Alternative names: Ancient conserved domain-containing protein 1, Cyclin-M1

All UniProt accessions (2): Q9NRU3, A0A8Q3SIV9

UniProt curated annotations — full annotation on UniProt →

Function. Probable metal transporter.

Subcellular location. Cell membrane.

Tissue specificity. Restricted to brain and testis.

Miscellaneous. Shares weak sequence similarity with the cyclin family, hence its name. However, it has no cyclin-like function in vivo.

Similarity. Belongs to the ACDP family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9NRU3-11yes
Q9NRU3-22

RefSeq proteins (4): NP_001332816, NP_001332817, NP_001332818, NP_065081* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000644CBS_domDomain
IPR002550CNNMDomain
IPR044751Ion_transp-like_CBSDomain
IPR045095ACDPFamily
IPR046342CBS_dom_sfHomologous_superfamily
IPR057492Ig_CNNM1/2/4_NDomain

Pfam: PF00571, PF01595, PF25511, PF25562

UniProt features (21 total): transmembrane region 4, region of interest 4, compositionally biased region 3, modified residue 3, domain 3, chain 1, splice variant 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NRU3-F167.070.24

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 (3): 821, 824, 850

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 100 (showing top): AHRARNT_01, BENPORATH_ES_WITH_H3K27ME3, AP2_Q3, USF_C, STARK_HYPPOCAMPUS_22Q11_DELETION_UP, MYCMAX_01, YY1_02, CAATGCA_MIR33, GATA2_01, RYTTCCTG_ETS2_B, GOBP_MONOATOMIC_ION_HOMEOSTASIS, GOCC_NEURON_PROJECTION, RGAGGAARY_PU1_Q6, NERF_Q2, GOBP_TRANSMEMBRANE_TRANSPORT

GO Biological Process (3): monoatomic ion transport (GO:0006811), magnesium ion homeostasis (GO:0010960), transmembrane transport (GO:0055085)

GO Molecular Function (2): transmembrane transporter activity (GO:0022857), protein binding (GO:0005515)

GO Cellular Component (4): plasma membrane (GO:0005886), dendrite (GO:0030425), neuronal cell body (GO:0043025), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
transport2
monoatomic cation homeostasis1
inorganic ion homeostasis1
cellular process1
transporter activity1
transmembrane transport1
binding1
membrane1
cell periphery1
neuron projection1
dendritic tree1
somatodendritic compartment1
cell body1
cellular anatomical structure1

Protein interactions and networks

STRING

808 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CNNM1H7C2H4H7C2H4911
CNNM1P0DN79P0DN79905
CNNM1COX11Q9Y6N1704
CNNM1TRPM6Q9BX84696
CNNM1SLC41A1Q8IVJ1676
CNNM1HPSE2Q8WWQ2649
CNNM1SLC41A2Q96JW4598
CNNM1TRPM7Q96QT4595
CNNM1NIPAL3Q6P499519
CNNM1SLC41A3Q96GZ6515
CNNM1MRS2Q9HD23505
CNNM1NIPAL2Q9H841495
CNNM1NIPAL1Q6NVV3494
CNNM1NIPAL4Q0D2K0463
CNNM1NIPA2Q8N8Q9451

IntAct

89 interactions, top by confidence:

ABTypeScore
PTP4A1CNNM1psi-mi:“MI:0915”(physical association)0.850
MAPK14OBSL1psi-mi:“MI:0914”(association)0.790
CNNM1PTP4A2psi-mi:“MI:0915”(physical association)0.760
PTP4A2CNNM1psi-mi:“MI:0915”(physical association)0.760
PTP4A2PTP4A3psi-mi:“MI:0914”(association)0.640
HSF2BPCNNM1psi-mi:“MI:0915”(physical association)0.560
GPR21TMEM120Bpsi-mi:“MI:0914”(association)0.530
ARL15SLC25A20psi-mi:“MI:0914”(association)0.530
CHRNDTPST2psi-mi:“MI:0914”(association)0.530
FUT3C1QL1psi-mi:“MI:0914”(association)0.530
SLC22A15ZFPL1psi-mi:“MI:0914”(association)0.530
PTP4A1ATE1psi-mi:“MI:0914”(association)0.530
SCGB1D4EGFRpsi-mi:“MI:0914”(association)0.530
PTP4A1PSMD3psi-mi:“MI:0914”(association)0.420
PTP4A2USP11psi-mi:“MI:2364”(proximity)0.420
PTP4A1PSMD3psi-mi:“MI:2364”(proximity)0.420
PTP4A1FDFT1psi-mi:“MI:0914”(association)0.350
PCDHA4TMEM223psi-mi:“MI:0914”(association)0.350
TTYH1TMEM223psi-mi:“MI:0914”(association)0.350
HLA-DRATMEM223psi-mi:“MI:0914”(association)0.350
CHRNA3TMEM223psi-mi:“MI:0914”(association)0.350
ZDHHC12NBASpsi-mi:“MI:0914”(association)0.350
BTNL8TMEM131Lpsi-mi:“MI:0914”(association)0.350
TCTN2TMEM131Lpsi-mi:“MI:0914”(association)0.350
CHRNB2TMEM131Lpsi-mi:“MI:0914”(association)0.350
PCDHA12KLRG2psi-mi:“MI:0914”(association)0.350
SIDT2KLRG2psi-mi:“MI:0914”(association)0.350

BioGRID (112): CNNM1 (Affinity Capture-MS), CNNM1 (Affinity Capture-MS), CNNM1 (Affinity Capture-MS), CNNM1 (Affinity Capture-MS), CNNM1 (Affinity Capture-MS), CNNM1 (Affinity Capture-MS), CNNM1 (Affinity Capture-MS), CNNM1 (Affinity Capture-MS), CNNM1 (Affinity Capture-MS), CNNM1 (Affinity Capture-MS), CNNM1 (Affinity Capture-MS), CNNM1 (Affinity Capture-MS), CNNM1 (Affinity Capture-MS), CNNM1 (Affinity Capture-MS), CNNM1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0B4J1F4, A0A0G2JXN2, A2AWP8, A2RRH5, C9J798, O43374, O70277, O95294, P04629, P59926, Q0GA42, Q13368, Q14318, Q16512, Q29RM4, Q2HY40, Q2T9P3, Q2TBA3, Q5BIM1, Q5M7W1, Q5R5M3, Q5R811, Q5T7P8, Q5XIS9, Q62746, Q6PFQ7, Q6PFY8, Q7TNM2, Q7TP90, Q7Z4K8, Q8BG60, Q8BHT7, Q8BQC3, Q8C6N3, Q8CIW5, Q8IZ69, Q8NCT1, Q920N2, Q92546, Q925B4

Diamond homologs: A0A0B7P9G0, A0A131MCZ8, A0JPA0, A3QM97, A8EZU0, A8F2M1, A8GPR9, A8GTI4, A8GUH1, O05961, P0C588, Q0GA42, Q12296, Q1RGX2, Q32NY4, Q3TWN3, Q4UK99, Q4V3C7, Q54318, Q57368, Q5U2P1, Q67XQ0, Q68W10, Q69ZF7, Q6P4Q7, Q8NE01, Q8RY60, Q8VZI2, Q92GI2, Q9GYL2, Q9H8M5, Q9LTD8, Q9NRU3, Q9USJ3, Q9ZQR4, Q9ZVS8, Q9CM13, Q9LK65, P75586, Q49399

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 124 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
R-HSA-425366512.8×2e-03
Neurotransmitter receptors and postsynaptic signal transmission79.9×5e-04
Transmission across Chemical Synapses77.5×2e-03
SLC-mediated transmembrane transport86.7×1e-03
Neuronal System85.0×5e-03
Transport of small molecules103.5×1e-02

GO biological processes:

GO termPartnersFoldFDR
acetylcholine receptor signaling pathway529.2×2e-04
membrane depolarization523.9×3e-04
monoatomic ion transmembrane transport815.6×3e-05
monoatomic ion transport68.8×6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance111
Likely benign2
Benign13

Top pathogenic / likely-pathogenic (0)

SpliceAI

2024 predictions. Top by Δscore:

VariantEffectΔscore
10:99330948:GAGTT:Gdonor_gain1.0000
10:99330956:GAAGG:Gdonor_gain1.0000
10:99330958:AGGG:Adonor_loss1.0000
10:99330959:GG:Gdonor_gain1.0000
10:99330959:GGGT:Gdonor_loss1.0000
10:99330960:GG:Gdonor_gain1.0000
10:99357507:TCTA:Tacceptor_loss1.0000
10:99357508:CTA:Cacceptor_loss1.0000
10:99357509:TAG:Tacceptor_loss1.0000
10:99357510:A:AGacceptor_gain1.0000
10:99357510:A:Tacceptor_loss1.0000
10:99357510:AG:Aacceptor_gain1.0000
10:99357511:G:GAacceptor_gain1.0000
10:99357511:GG:Gacceptor_gain1.0000
10:99357511:GGA:Gacceptor_gain1.0000
10:99357511:GGAA:Gacceptor_gain1.0000
10:99357511:GGAAA:Gacceptor_gain1.0000
10:99357656:G:GGdonor_gain1.0000
10:99360822:T:TAacceptor_gain1.0000
10:99360824:T:TAacceptor_gain1.0000
10:99360831:ACAGC:Aacceptor_loss1.0000
10:99360832:CAGC:Cacceptor_loss1.0000
10:99360833:A:AGacceptor_gain1.0000
10:99360833:AGCT:Aacceptor_gain1.0000
10:99360834:G:GTacceptor_gain1.0000
10:99360834:GC:Gacceptor_gain1.0000
10:99360834:GCT:Gacceptor_gain1.0000
10:99360834:GCTG:Gacceptor_gain1.0000
10:99360834:GCTGA:Gacceptor_gain1.0000
10:99362211:A:AGacceptor_gain1.0000

AlphaMissense

6095 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
10:99330730:T:AL448H1.000
10:99330730:T:CL448P1.000
10:99330781:C:AP465Q1.000
10:99330838:T:CL484S1.000
10:99330952:T:CF522S1.000
10:99330956:G:CK523N1.000
10:99330956:G:TK523N1.000
10:99357520:C:GH528D1.000
10:99357524:T:CL529P1.000
10:99357526:G:CA530P1.000
10:99357533:T:AV532D1.000
10:99357583:G:CG549R1.000
10:99357584:G:TG549V1.000
10:99357590:T:AV551D1.000
10:99357599:A:TE554V1.000
10:99357602:A:CD555A1.000
10:99357612:G:CE558D1.000
10:99357612:G:TE558D1.000
10:99357632:T:CI565T1.000
10:99357632:T:GI565S1.000
10:99362386:T:CL673P1.000
10:99364417:G:CG677R1.000
10:99364456:T:CF690L1.000
10:99364458:T:AF690L1.000
10:99364458:T:GF690L1.000
10:99364471:T:CF695L1.000
10:99364473:T:AF695L1.000
10:99364473:T:GF695L1.000
10:99364484:G:AG699D1.000
10:99377187:T:AV770D1.000

dbSNP variants (sampled 300 via entrez): RS1000066093 (10:99359937 CAAAA>C,CAAA,CAAAAA), RS1000078270 (10:99369037 A>G), RS1000140994 (10:99378371 T>A), RS1000146473 (10:99360131 A>C), RS1000170379 (10:99373718 G>A), RS1000182556 (10:99328294 T>C,G), RS1000193442 (10:99378614 G>A), RS1000314133 (10:99335727 G>A,C), RS1000319875 (10:99380316 A>G), RS1000377364 (10:99384994 G>A,T), RS1000394716 (10:99340606 G>A), RS1000512897 (10:99335171 T>C), RS1000517219 (10:99379838 A>C,T), RS1000521198 (10:99380247 A>G), RS1000603093 (10:99378897 G>A)

Disease associations

OMIM: gene MIM:607802 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): breast ductal adenocarcinoma (MONDO:0005590)

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

StudyTraitp-value
GCST001438_10Crohn’s disease5.000000e-07
GCST004482_104Peripheral arterial disease (traffic-related air pollution interaction)9.000000e-08
GCST005999_19Aspartate aminotransferase levels1.000000e-25
GCST007856_1Colorectal cancer or advanced adenoma4.000000e-06
GCST007856_18Colorectal cancer or advanced adenoma7.000000e-15
GCST011351_17Aspartate aminotransferase levels5.000000e-24

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0007908traffic air pollution measurement
EFO:0004736aspartate aminotransferase measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
D018270Carcinoma, Ductal, BreastC04.557.470.200.025.232.500; C04.557.470.615.132.500; C04.588.180.390; C17.800.090.500.390

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
potassium chromate(VI)decreases expression, increases expression, affects cotreatment2
aristolochic acid Idecreases expression1
FR900359increases phosphorylation1
dicrotophosincreases expression1
tris(2-butoxyethyl) phosphateaffects expression1
sodium arseniteaffects expression1
butyraldehydedecreases expression1
nickel sulfatedecreases expression1
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, affects response to substance, increases expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
chromium hexavalent ionaffects expression1
CGP 52608affects binding, increases reaction1
abrinedecreases expression1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amidedecreases expression, affects cotreatment1
bisphenol Saffects cotreatment, increases methylation1
Resveratrolaffects cotreatment, decreases expression1
Sunitinibincreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Leflunomideincreases expression1
Benzo(a)pyreneaffects methylation1
Copperaffects cotreatment, decreases expression1
Estradiolincreases expression1
Lipopolysaccharidesaffects response to substance, increases expression, affects cotreatment1
Phthalic Acidsdecreases methylation1
Testosteronedecreases expression1
Tetrachlorodibenzodioxindecreases expression, affects cotreatment1
Tobacco Smoke Pollutionincreases expression1
Triclosandecreases expression1
Urethanedecreases expression1
Valproic Acidincreases methylation1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT03414970PHASE3ACTIVE_NOT_RECRUITINGHypofractionated Radiation Therapy After Mastectomy in Preventing Recurrence in Patients With Stage IIa-IIIa Breast Cancer
NCT00461344PHASE2TERMINATEDDocetaxel + Doxorubicin as Neoadjuvant Chemotherapy in Patients With Breast Cancer
NCT07499999PHASE2NOT_YET_RECRUITINGRandomized Double-Blind Phase II Trial of Baby Exemestane Versus Baby Tamoxifen in Post-Menopausal Women at High Risk for Breast Cancer
NCT00637364PHASE1/PHASE2SUSPENDEDHigh Intensity Focused Ultrasound Tumor Treatment for Pancreatic Cancer Pain
NCT02779855PHASE1/PHASE2COMPLETEDTalimogene Laherparepvec in Combination With Neoadjuvant Chemotherapy in Triple Negative Breast Cancer
NCT01753908EARLY_PHASE1COMPLETEDBroccoli Sprout Extract in Treating Patients With Breast Cancer
NCT01796041EARLY_PHASE1COMPLETEDIntraoperative Imaging of Breast Cancer With Indocyanine Green
NCT01208974Not specifiedACTIVE_NOT_RECRUITINGNipple-Areola Complex (NAC) Irradiation After Nipple-Sparing Mastectomy and Reconstruction
NCT01875198Not specifiedTERMINATEDOncologic Impact of Splenectomy-omitting Radical Pancreatectomy in Well-selected Left-sided Pancreatic Cancer
NCT03543397Not specifiedUNKNOWNMRI in Ductal Carcinoma in Situ (DCIS)
NCT03834532Not specifiedCOMPLETEDLiving Well After Breast Surgery