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RGD DISEASE ONTOLOGY - ANNOTATIONS

RGD uses the Human Disease Ontology (DO, https://disease-ontology.org/) for disease curation across species. RGD automatically downloads each new release of the ontology on a monthly basis. Some additional terms which are required for RGD's curation purposes but are not currently covered in the official version of DO have been added. As corresponding terms are added to DO, these custom terms are retired and the DO terms substituted in existing annotations and subsequently used for curation.

Term:vitamin B12 deficiency
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Accession:DOID:0050731 term browser browse the term
Definition:A vitamin metabolic disorder that results from low blood levels of vitamin B12. (DO)
Synonyms:exact_synonym: cobalamin deficiency;   hypocobalaminemia;   vitamin B12 deficiencies
 narrow_synonym: acquired cobalamin-deficient neuropathy;   vitamin B12 deficiency anemia
 primary_id: MESH:D014806
 alt_id: MIM:612542
 xref: EFO:0000734


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vitamin B12 deficiency term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Abcd4 ATP binding cassette subfamily D member 4 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22922874 NCBI chrNW_004936488:3,526,875...3,538,851
Ensembl chrNW_004936488:3,523,344...3,538,858
JBrowse link
G Amn amnion associated transmembrane protein ISO ClinVar Annotator: match by term: Vitamin B12 deficiency ClinVar PMID:25741868 NCBI chrNW_004936835:961,840...970,287
Ensembl chrNW_004936835:961,826...970,234
JBrowse link
G Calr calreticulin ISO protein:increased expression:kidney (rat) RGD PMID:25982389 RGD:11352764 NCBI chrNW_004936659:1,994,695...1,999,070
Ensembl chrNW_004936659:1,994,648...1,999,430
JBrowse link
G Cbs cystathionine beta-synthase ISO protein:decreased expression:liver (rat) RGD PMID:2732804 RGD:40903037 NCBI chrNW_004936500:976,043...1,003,559
Ensembl chrNW_004936500:987,128...1,003,388
JBrowse link
G Cd40lg CD40 ligand treatment ISO RGD PMID:16716410 RGD:2313422 NCBI chrNW_004936513:10,607,617...10,620,403
Ensembl chrNW_004936513:10,607,617...10,620,403
JBrowse link
G Cfl1 cofilin 1 ISO protein:increased expression:kidney (rat) RGD PMID:25982389 RGD:11352764 NCBI chrNW_004936599:3,678,724...3,682,314
Ensembl chrNW_004936599:3,677,804...3,682,307
JBrowse link
G Gpx3 glutathione peroxidase 3 treatment ISO RGD PMID:11115425 RGD:401827848 NCBI chrNW_004936647:3,904,787...3,914,223
Ensembl chrNW_004936647:3,906,113...3,913,498
JBrowse link
G Mtr 5-methyltetrahydrofolate-homocysteine methyltransferase ISO protein:decreased expression,decreased activity:liver: RGD PMID:14646334 RGD:8694080 NCBI chrNW_004936484:16,087,924...16,180,089
Ensembl chrNW_004936484:16,087,923...16,180,148
JBrowse link
G Pon1 paraoxonase 1 ISO protein:decreased activity:serum (human) RGD PMID:22568797 RGD:11553830 NCBI chrNW_004936585:4,954,871...4,979,560
Ensembl chrNW_004936585:4,954,869...4,979,591
JBrowse link
congenital intrinsic factor deficiency term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cblif cobalamin binding intrinsic factor ISO ClinVar Annotator: match by term: Congenital intrinsic factor deficiency | ClinVar Annotator: match by term: Hereditary intrinsic factor deficiency OMIM
ClinVar
PMID:9536098 PMID:14576042 PMID:14695536 PMID:15738392 PMID:16199547 More... NCBI chrNW_004936581:2,919,793...2,933,743
Ensembl chrNW_004936581:2,920,355...2,933,403
JBrowse link
Imerslund-Grasbeck Syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Amn amnion associated transmembrane protein ISO ClinVar Annotator: match by term: Imerslund-Grasbeck syndrome ClinVar PMID:6741523 PMID:9536098 PMID:12590260 PMID:13852753 PMID:15024727 More... NCBI chrNW_004936835:961,840...970,287
Ensembl chrNW_004936835:961,826...970,234
JBrowse link
G Cacnb2 calcium voltage-gated channel auxiliary subunit beta 2 ISO ClinVar Annotator: match by term: Imerslund-Grasbeck syndrome ClinVar PMID:28492532 NCBI chrNW_004936520:8,951,994...9,164,039
Ensembl chrNW_004936520:8,955,164...9,295,331
JBrowse link
G Cdc42bpb CDC42 binding protein kinase beta ISO ClinVar Annotator: match by term: Imerslund-Grasbeck syndrome ClinVar PMID:12590260 PMID:15024727 PMID:16199547 PMID:17114957 PMID:17285242 More... NCBI chrNW_004936835:975,941...1,026,046
Ensembl chrNW_004936835:975,960...1,026,025
JBrowse link
G Cubn cubilin ISO ClinVar Annotator: match by term: Imerslund-Grasbeck syndrome ClinVar PMID:9536098 PMID:10080186 PMID:10887099 PMID:15024727 PMID:15963748 More... NCBI chrNW_004936520:10,140,784...10,410,082
Ensembl chrNW_004936520:10,140,784...10,409,851
JBrowse link
G Hacd1 3-hydroxyacyl-CoA dehydratase 1 ISO ClinVar Annotator: match by term: Imerslund-Grasbeck syndrome ClinVar PMID:28492532 NCBI chrNW_004936520:9,716,178...9,725,949
Ensembl chrNW_004936520:9,716,224...9,727,841
JBrowse link
G Slc39a12 solute carrier family 39 member 12 ISO ClinVar Annotator: match by term: Imerslund-Grasbeck syndrome ClinVar PMID:28492532 NCBI chrNW_004936520:9,380,723...9,444,146
Ensembl chrNW_004936520:9,380,650...9,444,152
JBrowse link
G St8sia6 ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6 ISO ClinVar Annotator: match by term: Imerslund-Grasbeck syndrome ClinVar PMID:28492532 NCBI chrNW_004936520:9,869,166...9,990,205
Ensembl chrNW_004936520:9,869,195...9,988,541
JBrowse link
G Stam signal transducing adaptor molecule ISO ClinVar Annotator: match by term: Imerslund-Grasbeck syndrome ClinVar PMID:28492532 NCBI chrNW_004936520:9,627,674...9,689,658
Ensembl chrNW_004936520:9,624,628...9,689,686
JBrowse link
G Traf3 TNF receptor associated factor 3 ISO ClinVar Annotator: match by term: Imerslund-Grasbeck syndrome ClinVar PMID:28492532 NCBI chrNW_004936835:844,747...955,900
Ensembl chrNW_004936835:844,727...950,664
JBrowse link
G Trdmt1 tRNA aspartic acid methyltransferase 1 ISO ClinVar Annotator: match by term: Imerslund-Grasbeck syndrome ClinVar PMID:28492532 NCBI chrNW_004936520:10,104,050...10,122,057 JBrowse link
G Vim vimentin ISO ClinVar Annotator: match by term: Imerslund-Grasbeck syndrome ClinVar PMID:28492532 NCBI chrNW_004936520:10,051,692...10,059,324
Ensembl chrNW_004936520:10,052,012...10,059,182
JBrowse link
Imerslund-Grasbeck Syndrome 1 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Amn amnion associated transmembrane protein ISO ClinVar Annotator: match by term: Enterocyte cobalamin malabsorption | ClinVar Annotator: match by term: Enterocyte intrinsic factor receptor, defect of | ClinVar Annotator: match by term: Imerslund-Gräsbeck syndrome 1 | ClinVar Annotator: match by term: Megaloblastic anemia 1, Finnish type ClinVar PMID:6741523 PMID:9536098 PMID:12590260 PMID:13852753 PMID:15024727 More... NCBI chrNW_004936835:961,840...970,287
Ensembl chrNW_004936835:961,826...970,234
JBrowse link
G Cblif cobalamin binding intrinsic factor ISO DNA:polymorphisms, missense mutations, splice sites:exon,intron:
protein:increased excretion:urine:
RGD PMID:10435666 PMID:15738392 RGD:11049583 RGD:11049586 NCBI chrNW_004936581:2,919,793...2,933,743
Ensembl chrNW_004936581:2,920,355...2,933,403
JBrowse link
G Cdc42bpb CDC42 binding protein kinase beta ISO ClinVar Annotator: match by term: Megaloblastic anemia 1, Finnish type ClinVar PMID:12590260 PMID:15024727 PMID:16199547 PMID:17114957 PMID:17285242 More... NCBI chrNW_004936835:975,941...1,026,046
Ensembl chrNW_004936835:975,960...1,026,025
JBrowse link
G Cubn cubilin ISO ClinVar Annotator: match by term: Enterocyte intrinsic factor receptor, defect of | ClinVar Annotator: match by term: Imerslund-Gräsbeck syndrome 1 | ClinVar Annotator: match by term: Megaloblastic anemia 1, Finnish type OMIM
ClinVar
PMID:9536098 PMID:10080186 PMID:10887099 PMID:15024727 PMID:15963748 More... NCBI chrNW_004936520:10,140,784...10,410,082
Ensembl chrNW_004936520:10,140,784...10,409,851
JBrowse link
Imerslund-Grasbeck Syndrome 2 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Amn amnion associated transmembrane protein ISO ClinVar Annotator: match by term: MEGALOBLASTIC ANEMIA, NORWEGIAN TYPE | ClinVar Annotator: match by term: Megaloblastic anemia 1, Norwegian type OMIM
ClinVar
PMID:6741523 PMID:9536098 PMID:12590260 PMID:13852753 PMID:15024727 More... NCBI chrNW_004936835:961,840...970,287
Ensembl chrNW_004936835:961,826...970,234
JBrowse link
G Cdc42bpb CDC42 binding protein kinase beta ISO ClinVar Annotator: match by term: MEGALOBLASTIC ANEMIA, NORWEGIAN TYPE ClinVar PMID:12590260 PMID:15024727 PMID:16199547 PMID:17114957 PMID:17285242 More... NCBI chrNW_004936835:975,941...1,026,046
Ensembl chrNW_004936835:975,960...1,026,025
JBrowse link
methylmalonic aciduria and homocystinuria type cblC term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Abcd4 ATP binding cassette subfamily D member 4 ISO ClinVar Annotator: match by term: methylmalonic aciduria and homocystinuria type cblC ClinVar PMID:22922874 PMID:23141461 PMID:25234635 PMID:25741868 PMID:28492532 More... NCBI chrNW_004936488:3,526,875...3,538,851
Ensembl chrNW_004936488:3,523,344...3,538,858
JBrowse link
G Dcdc2c doublecortin domain containing 2C ISO ClinVar Annotator: match by term: methylmalonic aciduria and homocystinuria type cblC ClinVar PMID:25741868 NCBI chrNW_004936532:1,816,573...1,866,029
Ensembl chrNW_004936532:1,816,573...1,861,250
JBrowse link
G Hcfc1 host cell factor C1 ISO ClinVar Annotator: match by term: Vitamin B12 metabolic defect with combined deficiency of methylmalonyl-CoA mutase and homocysteine:methyltetrahydrofolate methyltransferase ClinVar PMID:24011988 PMID:25167861 PMID:25281006 PMID:25741868 PMID:26893841 More... NCBI chrNW_004936809:827,008...853,689
Ensembl chrNW_004936809:827,031...853,644
JBrowse link
G Lmbrd1 LMBR1 domain containing 1 ISO ClinVar Annotator: match by term: methylmalonic aciduria and homocystinuria type cblC ClinVar PMID:16199547 PMID:19136951 PMID:21303734 PMID:23776111 PMID:24664876 More... NCBI chrNW_004936618:1,694,886...1,792,586
Ensembl chrNW_004936618:1,689,646...1,792,802
JBrowse link
G Mmachc metabolism of cobalamin associated C ISO ClinVar Annotator: match by term: Cobalamin-C methylmalonic acidemia and homocystinuria | ClinVar Annotator: match by term: Methylmalonic acidemia and homocystinuria cblC type | ClinVar Annotator: match by term: Methylmalonic aciduria and homocystinuria, Vitamin B12-responsive | ClinVar Annotator: match by term: Methylmalonic aciduria with homocystinuria cblC type | ClinVar Annotator: match by term: Vitamin B12 metabolic defect with combined deficiency of methylmalonyl-CoA mutase and homocysteine:methyltetrahydrofolate methyltransferase | ClinVar Annotator: match by term: methylmalonic aciduria and homocystinuria type cblC OMIM
ClinVar
PMID:9536098 PMID:11261516 PMID:11320193 PMID:14568819 PMID:16199547 More... NCBI chrNW_004936474:26,636,277...26,641,486
Ensembl chrNW_004936474:26,636,245...26,641,486
JBrowse link
G Mmadhc metabolism of cobalamin associated D ISO ClinVar Annotator: match by term: methylmalonic aciduria and homocystinuria type cblC ClinVar PMID:16199547 PMID:18385497 PMID:22156578 PMID:25155779 PMID:25741868 More... NCBI chrNW_004936469:27,771,741...27,804,324
Ensembl chrNW_004936469:27,771,937...27,787,233
JBrowse link
G Prdx1 peroxiredoxin 1 ISO ClinVar Annotator: match by term: Methylmalonic aciduria and homocystinuria, Vitamin B12-responsive | ClinVar Annotator: match by term: methylmalonic aciduria and homocystinuria type cblC OMIM
ClinVar
PMID:9536098 PMID:16311595 PMID:17576681 PMID:20631720 PMID:23954310 More... NCBI chrNW_004936474:26,641,776...26,653,291
Ensembl chrNW_004936474:26,639,259...26,653,328
JBrowse link
G Thap11 THAP domain containing 11 ISO OMIM:277400 MouseDO NCBI chrNW_004936475:18,209,683...18,212,294
Ensembl chrNW_004936475:18,210,732...18,211,634
JBrowse link
pernicious anemia term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cblif cobalamin binding intrinsic factor ISO RGD PMID:167441 PMID:4434116 RGD:11049584 RGD:11049587 NCBI chrNW_004936581:2,919,793...2,933,743
Ensembl chrNW_004936581:2,920,355...2,933,403
JBrowse link
Subacute Combined Degeneration term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cd40 CD40 molecule treatment ISO RGD PMID:16716410 RGD:2313422 NCBI chrNW_004936514:6,936,915...6,947,246
Ensembl chrNW_004936514:6,936,572...6,947,280
JBrowse link
G Cd40lg CD40 ligand treatment ISO protein:increased expression:cerebrospinal fluid RGD PMID:16716410 RGD:2313422 NCBI chrNW_004936513:10,607,617...10,620,403
Ensembl chrNW_004936513:10,607,617...10,620,403
JBrowse link
transcobalamin II deficiency term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Tcn2 transcobalamin 2 ISO ClinVar Annotator: match by term: Transcobalamin II deficiency OMIM
ClinVar
PMID:2430590 PMID:7849710 PMID:7980584 PMID:9536098 PMID:10518276 More... NCBI chrNW_004936904:97,535...113,886
Ensembl chrNW_004936904:95,542...113,985
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 14573
    Nutritional and Metabolic Diseases 7049
      disease of metabolism 7049
        inherited metabolic disorder 5583
          vitamin metabolic disorder 49
            vitamin B12 deficiency 29
              Imerslund-Grasbeck Syndrome + 12
              Subacute Combined Degeneration 2
              congenital intrinsic factor deficiency 1
              methylmalonic aciduria and homocystinuria type cblC 8
              pernicious anemia + 1
              transcobalamin II deficiency 1
Path 2
Term Annotations click to browse term
  disease 14573
    Nutritional and Metabolic Diseases 7049
      disease of metabolism 7049
        acquired metabolic disease 2137
          nutrition disease 774
            Malnutrition 236
              nutritional deficiency disease 221
                Avitaminosis 185
                  Vitamin B Deficiency 139
                    vitamin B12 deficiency 29
                      Imerslund-Grasbeck Syndrome + 12
                      Subacute Combined Degeneration 2
                      congenital intrinsic factor deficiency 1
                      methylmalonic aciduria and homocystinuria type cblC 8
                      pernicious anemia + 1
                      transcobalamin II deficiency 1
paths to the root