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Atlas / Gene / CA10

CA10

gene
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Also known as CARPXCA-RPXHUCEP-15

Summary

CA10 (carbonic anhydrase 10 (inactive), HGNC:1369) is a protein-coding gene on chromosome 17q21.33-q22, encoding Carbonic anhydrase-related protein 10 (Q9NS85). Does not have a catalytic activity.

This gene encodes a protein that belongs to the carbonic anhydrase family of zinc metalloenzymes, which catalyze the reversible hydration of carbon dioxide in various biological processes. The protein encoded by this gene is an acatalytic member of the alpha-carbonic anhydrase subgroup, and it is thought to play a role in the central nervous system, especially in brain development. Multiple transcript variants encoding the same protein have been found for this gene.

Source: NCBI Gene 56934 — RefSeq curated summary.

At a glance

  • GWAS associations: 22
  • Clinical variants (ClinVar): 46 total
  • MANE Select transcript: NM_020178

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1369
Approved symbolCA10
Namecarbonic anhydrase 10 (inactive)
Location17q21.33-q22
Locus typegene with protein product
StatusApproved
AliasesCARPX, CA-RPX, HUCEP-15
Ensembl geneENSG00000154975
Ensembl biotypeprotein_coding
OMIM604642
Entrez56934

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 8 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000285273, ENST00000442502, ENST00000451037, ENST00000570565, ENST00000571371, ENST00000571918, ENST00000573294, ENST00000575097, ENST00000575181, ENST00000897800, ENST00000897801

RefSeq mRNA: 3 — MANE Select: NM_020178 NM_001082533, NM_001082534, NM_020178

CCDS: CCDS32684

Canonical transcript exons

ENST00000451037 — 9 exons

ExonStartEnd
ENSE000016373825215772652158714
ENSE000026746475163032051631606
ENSE000034839735207231952072393
ENSE000034998705163585551636009
ENSE000035003335164918251649254
ENSE000035598375163347651633650
ENSE000035824665165364151653736
ENSE000036039855174763351747818
ENSE000036834375193099051931132

Expression profiles

Bgee: expression breadth ubiquitous, 167 present calls, max score 97.68.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.3147 / max 232.0860, expressed in 149 samples.

FANTOM5 promoters (14 alternative TSS)

Promoter IDTPM avgSamples expressed
1670480.4519108
1670450.152985
1670550.137674
1670560.131657
1670570.085047
1670530.079539
1670440.058130
1670460.055136
1670430.040322
1670470.037011

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cerebellar cortexUBERON:000212997.68gold quality
cerebellar hemisphereUBERON:000224597.66gold quality
cerebellumUBERON:000203797.46gold quality
right hemisphere of cerebellumUBERON:001489097.25gold quality
cerebellar vermisUBERON:000472096.43gold quality
middle temporal gyrusUBERON:000277194.83gold quality
prefrontal cortexUBERON:000045193.06gold quality
dorsolateral prefrontal cortexUBERON:000983492.95gold quality
ponsUBERON:000098892.32gold quality
right frontal lobeUBERON:000281092.30gold quality
Brodmann (1909) area 23UBERON:001355492.08gold quality
anterior cingulate cortexUBERON:000983591.98gold quality
cingulate cortexUBERON:000302791.91gold quality
endothelial cellCL:000011591.90gold quality
frontal cortexUBERON:000187091.69gold quality
frontal lobeUBERON:001652591.69gold quality
Brodmann (1909) area 9UBERON:001354091.67gold quality
amygdalaUBERON:000187691.03gold quality
neocortexUBERON:000195090.78gold quality
cerebral cortexUBERON:000095689.38gold quality
temporal lobeUBERON:000187188.92gold quality
superior frontal gyrusUBERON:000266188.64gold quality
primary visual cortexUBERON:000243687.17gold quality
hypothalamusUBERON:000189886.13gold quality
entorhinal cortexUBERON:000272885.67gold quality
orbitofrontal cortexUBERON:000416785.42silver quality
telencephalonUBERON:000189384.87gold quality
brainUBERON:000095584.53gold quality
renal glomerulusUBERON:000007484.37gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047384.04gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 8.

ExperimentMarker?Max mean expression
E-GEOD-98556yes399.51
E-HCAD-35yes93.01
E-MTAB-7316yes48.50
E-CURD-119yes47.30
E-HCAD-25yes24.59
E-GEOD-84465yes23.46
E-GEOD-137537yes17.99
E-ANND-3yes4.90

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

122 targeting CA10, 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-6867-5P100.0082.213464
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-340-5P100.0072.504437
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-3646100.0073.565283
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-3064-3P100.0070.091254
HSA-MIR-574-5P100.0066.01989
HSA-MIR-453499.9966.581907
HSA-MIR-366299.9973.825684
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-607799.9968.042299
HSA-MIR-511-3P99.9968.851467
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-548AN99.9770.912817
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-34C-5P99.9770.451577
HSA-MIR-449B-5P99.9770.261580
HSA-MIR-448799.9664.581252
HSA-MIR-570-3P99.9672.414910
HSA-MIR-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505
HSA-MIR-808299.9567.271170
HSA-MIR-391099.9571.132227
HSA-MIR-381-3P99.9371.872854

Literature-anchored findings (GeneRIF, showing 12)

  • The results suggest that the variations of CA8 and CA10 loci may be important determinants of osteoporosis in Japanese women. (PMID:19172221)
  • our results suggest that genes CA10 and also SGK493 may be an important risk factor for asthma development, especially for a nonatopic phenotype. (PMID:24407380)
  • Copy number deletion on CA10 was associated with a 1.69-fold decreased risk for osteoarthritis. (PMID:25880085)
  • Two African-ancestry specific variants were found to be significantly associated with metabolic syndrome S: SNP rs73989312[A] near CA10 that conferred increased risk; and SNP rs77244975[C] in CTNNA3 that conferred protection against this disease. (PMID:26507551)
  • CA10 directly binds in a cis configuration to a conserved membrane-proximal, extracellular sequence of alpha- and beta-neurexins. (PMID:28154140)
  • The changes in the ratios of mRNA levels and the respective proteins (HIF-1alpha, HIF-2, NF-kB, VEGF, VEGFR2, and carboanhydrase IX) may contribute to kidney-cancer metastasis. (PMID:28537244)
  • Total heterogeneous methylation of CA10 conferred a significantly higher risk of Colorectal Cancer.The gene methylation status of blood leukocytes may be associated with CRC risk. (PMID:29291617)
  • results suggest that CA11 and CA10 negatively regulate neuronal activity-dependent glioma growth and inhibit glioma aggression. Thus, CA11/CA10 may represent a potential therapeutic target for the treatment of gliomas. (PMID:30636076)
  • Glycolysis, via NADH-dependent dimerisation of CtBPs, regulates hypoxia-induced expression of CAIX and stem-like breast cancer cell survival. (PMID:32618367)
  • Methylation of WT1, CA10 in peripheral blood leukocyte is associated with breast cancer risk: a case-control study. (PMID:32736539)
  • Carbonic anhydrase 10 functions as a tumor suppressor in renal cell carcinoma and its methylation is a risk factor for survival outcome. (PMID:34980544)
  • Identifies a string of seven CCG repeats in the 5’ UTR of a carbonic anhydrase X cDNA from human brain. (PMID:9921901)

Cross-species orthologs

12 orthologs

OrganismSymbolGene ID
danio_rerioca10bENSDARG00000009568
mus_musculusCar10ENSMUSG00000056158
rattus_norvegicusCar10ENSRNOG00000002626
drosophila_melanogasterCAH13FBGN0033542
drosophila_melanogasterCAH14FBGN0034554
drosophila_melanogasterCAH15FBGN0034560
drosophila_melanogasterCAH7FBGN0037788
drosophila_melanogasterCAH4FBGN0039235
drosophila_melanogasterCARPBFBGN0052698
caenorhabditis_elegansWBGENE00000279
caenorhabditis_elegansWBGENE00000283
caenorhabditis_eleganscah-6WBGENE00000284

Paralogs (14): CA11 (ENSG00000063180), CA12 (ENSG00000074410), CA2 (ENSG00000104267), CA9 (ENSG00000107159), CA14 (ENSG00000118298), CA6 (ENSG00000131686), CA1 (ENSG00000133742), CA3 (ENSG00000164879), CA4 (ENSG00000167434), CA7 (ENSG00000168748), CA5B (ENSG00000169239), CA5A (ENSG00000174990), CA8 (ENSG00000178538), CA13 (ENSG00000185015)

Protein

Protein identifiers

Carbonic anhydrase-related protein 10 — Q9NS85 (reviewed: Q9NS85)

Alternative names: Carbonic anhydrase-related protein X, Cerebral protein 15

All UniProt accessions (5): Q9NS85, A0A384MTY8, I3L0J7, I3L375, I3NI54

UniProt curated annotations — full annotation on UniProt →

Function. Does not have a catalytic activity.

Tissue specificity. Strong expression in brain and central nervous system.

Similarity. Belongs to the alpha-carbonic anhydrase family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9NS85-11yes
Q9NS85-22

RefSeq proteins (3): NP_001076002, NP_001076003, NP_064563* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001148CA_domDomain
IPR023561Carbonic_anhydrase_a-classFamily
IPR036398CA_dom_sfHomologous_superfamily
IPR041878Alpha_CARP_X/XIFamily

Pfam: PF00194

UniProt features (3 total): chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NS85-F185.650.74

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 160 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_DN, BENPORATH_ES_WITH_H3K27ME3, GOMF_CARBONATE_DEHYDRATASE_ACTIVITY, TGCACTT_MIR519C_MIR519B_MIR519A, GGGTGGRR_PAX4_03, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5, MYOD_01, TGCTGAY_UNKNOWN, CCTGTGA_MIR513, ZIC1_01, GOBP_HEAD_DEVELOPMENT, AACTTT_UNKNOWN, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, GOMF_HYDRO_LYASE_ACTIVITY, IK3_01

GO Biological Process (1): brain development (GO:0007420)

GO Molecular Function (3): carbonate dehydratase activity (GO:0004089), zinc ion binding (GO:0008270), hydro-lyase activity (GO:0016836)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
central nervous system development1
animal organ development1
head development1
hydro-lyase activity1
transition metal ion binding1
carbon-oxygen lyase activity1

Protein interactions and networks

STRING

2498 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CA10BSCL2Q96G97762
CA10ALBP02768593
CA10BGLAPP02818589
CA10SPP1P10451550
CA10PYGMP11217547
CA10BMP2P12643510
CA10WDR64B1ANS9508
CA10AGPAT2O15120490
CA10RUNX2Q13950489
CA10IBSPP21815482
CA10AHSGP02765481
CA10MGPP08493453
CA10PTHP01270438
CA10ENAMQ9NRM1424
CA10CBLN1P02682422

IntAct

9 interactions, top by confidence:

ABTypeScore
CA10WDHD1psi-mi:“MI:0914”(association)0.640
CA10FXR1psi-mi:“MI:0915”(physical association)0.370
CA10SHANK3psi-mi:“MI:0915”(physical association)0.370
PARLH2AC21psi-mi:“MI:0914”(association)0.350
MSI2ANXA13psi-mi:“MI:0914”(association)0.350
CA10ENTPD5psi-mi:“MI:0914”(association)0.350

BioGRID (90): CA10 (Affinity Capture-MS), MTHFD1 (Affinity Capture-MS), WDHD1 (Affinity Capture-MS), TSC22D1 (Affinity Capture-MS), IMPACT (Affinity Capture-MS), ASS1 (Affinity Capture-MS), CALCOCO1 (Affinity Capture-MS), TOR1AIP1 (Affinity Capture-MS), PHYHIP (Affinity Capture-MS), COL6A2 (Affinity Capture-MS), ABT1 (Affinity Capture-MS), INO80 (Affinity Capture-MS), ACTR10 (Affinity Capture-MS), MTERF4 (Affinity Capture-MS), G6PD (Affinity Capture-MS)

ESM2 similar proteins: A0A7H0DN92, A0JN41, A7MAQ2, F4HUC4, F4IHR4, F4JIK2, O04846, O43570, O57211, P04195, P08060, P0DO50, P0DSY1, P0DSY2, P10731, P12890, P18761, P18915, P19021, P20508, P23280, P28651, P35219, P48284, P61215, P97467, Q10462, Q18932, Q20781, Q5PPN4, Q5R4U0, Q5TZ24, Q64444, Q68CI2, Q6RZI9, Q75N34, Q75N35, Q84UV8, Q865C0, Q866X6

Diamond homologs: A0A7H0DN92, A0JN41, B0BNN3, O57211, P00915, P00916, P00917, P00918, P00919, P00920, P00921, P04195, P07450, P07451, P07452, P07630, P0DSY1, P0DSY2, P13634, P14141, P16015, P20508, P23470, P23471, P23589, P27139, P35217, P35218, P43165, P43166, P48282, P48283, P61215, P83299, Q05909, Q1LZA1, Q3SZX4, Q5R4U0, Q5S1S4, Q66HG6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance40
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2999 predictions. Top by Δscore:

VariantEffectΔscore
17:51631603:TTTA:Tacceptor_gain1.0000
17:51631604:TTA:Tacceptor_gain1.0000
17:51631605:TA:Tacceptor_gain1.0000
17:51631607:C:CCacceptor_gain1.0000
17:51633646:TGCAT:Tacceptor_gain1.0000
17:51633648:CAT:Cacceptor_gain1.0000
17:51633649:ATC:Aacceptor_loss1.0000
17:51633650:TCT:Tacceptor_loss1.0000
17:51633651:C:CCacceptor_gain1.0000
17:51633652:T:Gacceptor_loss1.0000
17:51649180:A:ACdonor_gain1.0000
17:51649181:C:CCdonor_gain1.0000
17:51653639:A:ACdonor_gain1.0000
17:51653640:C:CCdonor_gain1.0000
17:51653658:C:CTdonor_gain1.0000
17:51653659:T:TTdonor_gain1.0000
17:51747629:ATAC:Adonor_loss1.0000
17:51747631:ACCT:Adonor_gain1.0000
17:51747631:ACCTC:Adonor_gain1.0000
17:51747632:C:CAdonor_loss1.0000
17:51747632:CCTC:Cdonor_gain1.0000
17:51747632:CCTCC:Cdonor_gain1.0000
17:51747634:T:TAdonor_gain1.0000
17:51747635:C:Adonor_gain1.0000
17:51747814:CTGAC:Cacceptor_gain1.0000
17:51747817:ACC:Aacceptor_loss1.0000
17:51930985:CTTA:Cdonor_loss1.0000
17:51930986:TTACC:Tdonor_loss1.0000
17:51930987:TACCT:Tdonor_loss1.0000
17:51930988:ACCTT:Adonor_gain1.0000

AlphaMissense

2182 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:51633580:C:AR287M1.000
17:51633580:C:GR287T1.000
17:51633637:C:GR268P1.000
17:51635912:G:CC244W1.000
17:51635913:C:TC244Y1.000
17:51635914:A:GC244R1.000
17:51635934:C:TG237E1.000
17:51635935:C:AG237W1.000
17:51747798:G:CN100K1.000
17:51747798:G:TN100K1.000
17:51931089:G:CC60W1.000
17:51931090:C:TC60Y1.000
17:51931091:A:GC60R1.000
17:51931100:A:GW57R1.000
17:51931100:A:TW57R1.000
17:51931119:C:AW50C1.000
17:51931119:C:GW50C1.000
17:51931121:A:GW50R1.000
17:51931121:A:TW50R1.000
17:51633547:C:GR298P0.999
17:51633556:C:GR295P0.999
17:51633557:G:TR295S0.999
17:51633579:C:AR287S0.999
17:51633579:C:GR287S0.999
17:51633581:T:CR287G0.999
17:51633631:A:GL270P0.999
17:51633634:A:GL269P0.999
17:51635896:A:GW250R0.999
17:51635896:A:TW250R0.999
17:51635913:C:AC244F0.999

dbSNP variants (sampled 300 via entrez): RS1000000005 (17:51974497 AAAAC>A), RS1000000243 (17:51813198 T>A,C), RS1000007518 (17:51972550 G>T), RS1000010830 (17:51725676 C>A,T), RS1000015708 (17:52082799 A>C), RS1000025394 (17:51884359 C>T), RS1000039800 (17:51691699 G>A,T), RS1000046144 (17:52143938 T>C), RS1000046335 (17:51851223 C>T), RS1000051954 (17:51709013 G>C), RS1000053877 (17:52147615 AACAGGAATGAAACTTGTT>A), RS1000062116 (17:51890252 T>C), RS1000069739 (17:51927230 C>T), RS1000070588 (17:51968102 T>C), RS1000077549 (17:51850993 C>A,G)

Disease associations

OMIM: gene MIM:604642 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

22 associations (top):

StudyTraitp-value
GCST000880_15Menarche (age at onset)7.000000e-13
GCST001859_50Thiazide-induced adverse metabolic effects in hypertensive patients6.000000e-06
GCST002541_112Menarche (age at onset)2.000000e-24
GCST002638_2Gastritis2.000000e-06
GCST002927_5Mercury levels6.000000e-06
GCST003993_14Menarche (age at onset)1.000000e-10
GCST005010_14Bacterial meningitis1.000000e-08
GCST006585_1702Blood protein levels5.000000e-10
GCST007327_115Smoking status (ever vs never smokers)2.000000e-09
GCST007327_161Smoking status (ever vs never smokers)6.000000e-11
GCST007327_83Smoking status (ever vs never smokers)6.000000e-10
GCST007576_133Chronotype5.000000e-11
GCST007831_2Anti-thyroglobulin (TgAb) levels in Hashimoto’s thyroiditis6.000000e-07
GCST007851_5Anti-thyroid peroxidase (TPOAb) and anti-thyroglobulin (TgAb) levels in Hashimoto’s thyroiditis4.000000e-06
GCST008832_4Gastroesophageal reflux disease1.000000e-11
GCST009391_1959Metabolite levels6.000000e-06
GCST010456_5Anthracycline-induced cardiotoxicity in early breast cancer1.000000e-06
GCST011365_154Myocardial infarction3.000000e-06
GCST011703_27Smoking initiation3.000000e-08
GCST012334_10Multisite chronic pain5.000000e-09
GCST012490_515Femur bone mineral density x serum urate levels interaction5.000000e-08
GCST90000514_24Gastroesophageal reflux disease2.000000e-09

EFO canonical traits (9, from GWAS)

EFO IDTrait name
EFO:0004703age at menarche
EFO:0008411susceptibility to bacterial meningitis measurement
EFO:0004318smoking behavior
EFO:0008328chronotype measurement
EFO:0005257response to anthracycline-based chemotherapy
EFO:1001482cardiotoxicity
EFO:0005670smoking initiation
EFO:0010100multisite chronic pain
EFO:0004531urate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB clinical annotations

1 annotations.

VariantTypeLevelDrugsPhenotypes
rs967676Efficacy3fluticasone propionate;montelukastAsthma

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs967676CA1032.001fluticasone propionate;montelukast

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

ChemicalActions (top 5)PubMed papers
methylmercuric chloridedecreases expression, increases expression2
Vorinostataffects cotreatment, increases expression2
Phenylmercuric Acetateaffects cotreatment, increases expression2
arseniteincreases methylation1
ochratoxin Aincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinaffects cotreatment, increases expression1
bisphenol Sdecreases methylation1
Benzo(a)pyreneaffects methylation, increases methylation1
Thimerosalincreases expression1
Tretinoinincreases expression1
Tunicamycindecreases expression1
Aflatoxin B1decreases methylation1
Antirheumatic Agentsincreases expression1
Thapsigargindecreases expression1

Clinical trials (associated diseases)

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

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.2
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot