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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 nutritional condition produced by a deficiency of VITAMIN B 12 in the diet, characterized by megaloblastic anemia. Since vitamin B 12 is not present in plants, humans have obtained their supply from animal products, from multivitamin supplements in the form of pills, and as additives to food preparations. A wide variety of neuropsychiatric abnormalities is also seen in vitamin B 12 deficiency and appears to be due to an undefined defect involving myelin synthesis. (From Cecil Textbook of Medicine, 19th ed, p848)
Synonyms:exact_synonym: Cobalamin deficiency;   Vitamin B12 Deficiencies;   hypocobalaminemia
 narrow_synonym: acquired cobalamin-deficient neuropathy;   vitamin B12 deficiency anemia
 related_synonym: B12QTL1;   VITAMIN B12 PLASMA LEVEL QUANTITATIVE TRAIT LOCUS 1
 primary_id: MESH:D014806
 alt_id: OMIM:612542;   RDO:0004498
For additional species annotation, visit the Alliance of Genome Resources.


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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 chr 6:108,315,026...108,329,550
Ensembl chr 6:108,315,035...108,329,464
JBrowse link
G Amn amnion associated transmembrane protein ISO ClinVar Annotator: match by term: Cobalamin deficiency ClinVar PMID:25741868 NCBI chr 6:135,724,455...135,731,896
Ensembl chr 6:135,724,455...135,731,896
JBrowse link
G Calr calreticulin IEP protein:increased expression:kidney (rat) RGD PMID:25982389 RGD:11352764 NCBI chr19:25,956,771...25,961,666
Ensembl chr19:25,956,771...25,961,666
JBrowse link
G Cbs cystathionine beta synthase IEP protein:decreased expression:liver (rat) RGD PMID:2732804 RGD:40903037 NCBI chr20:10,361,987...10,386,663
Ensembl chr20:10,361,988...10,386,751
JBrowse link
G Cd40lg CD40 ligand treatment IDA RGD PMID:16716410 RGD:2313422 NCBI chr  X:159,703,703...159,714,886
Ensembl chr  X:159,703,578...159,716,562
JBrowse link
G Cfl1 cofilin 1 IEP protein:increased expression:kidney (rat) RGD PMID:25982389 RGD:11352764 NCBI chr 1:220,869,805...220,873,337
Ensembl chr 1:220,869,805...220,873,337
JBrowse link
G Fut2 fucosyltransferase 2 ISO ClinVar Annotator: match by term: Vitamin b12 plasma level quantitative trait locus 1 OMIM
ClinVar
PMID:7876234 PMID:7876235 PMID:8755920 PMID:8928486 PMID:12692541 PMID:18776911 PMID:25741868 PMID:30401457 NCBI chr 1:101,631,633...101,651,668
Ensembl chr 1:101,631,635...101,651,668
JBrowse link
G Mtr 5-methyltetrahydrofolate-homocysteine methyltransferase IEP protein:decreased expression,decreased activity:liver: RGD PMID:14646334 RGD:8694080 NCBI chr17:66,210,444...66,295,014
Ensembl chr17:66,210,461...66,295,014
JBrowse link
G Pon1 paraoxonase 1 ISO protein:decreased activity:serum (human) RGD PMID:22568797 RGD:11553830 NCBI chr 4:30,249,749...30,276,297
Ensembl chr 4:30,249,742...30,276,372
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: Intrinsic factor deficiency
ClinVar Annotator: match by OMIM:261000
DNA:mutations:cds:c.68A>G,67C>G, deletion,p.Q5R,p.Q5G(human)
OMIM
ClinVar
PMID:14576042 PMID:14695536 PMID:15738392 PMID:19036097 PMID:20408840 PMID:22854512 PMID:22929189 PMID:24033266 PMID:25308559 PMID:25741868 PMID:27577878 PMID:28492532, PMID:14695536 RGD:11049582 NCBI chr 1:228,118,048...228,132,296
Ensembl chr 1:228,118,048...228,132,404
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:12590260 PMID:13852753 PMID:15024727 PMID:17114957 PMID:17285242 PMID:18181028 PMID:21750092 PMID:22078000 PMID:22631584 PMID:22929189 PMID:24156255 PMID:28492532 PMID:30691194 NCBI chr 6:135,724,455...135,731,896
Ensembl chr 6:135,724,455...135,731,896
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 PMID:16199547 PMID:17576681 PMID:22277662 PMID:22495309 PMID:22929189 PMID:24033266 PMID:24156255 PMID:25349199 PMID:25525159 PMID:25741868 PMID:26040326 PMID:27197912 PMID:28492532 PMID:31497480 PMID:31613795 PMID:33532864 NCBI chr17:80,584,921...80,807,181
Ensembl chr17:80,584,878...80,807,243
JBrowse link
G Traf3 Tnf receptor-associated factor 3 ISO ClinVar Annotator: match by term: Imerslund-Grasbeck syndrome ClinVar PMID:28492532 NCBI chr 6:135,610,698...135,720,247
Ensembl chr 6:135,610,743...135,718,564
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 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:12590260 PMID:13852753 PMID:15024727 PMID:17114957 PMID:17285242 PMID:18181028 PMID:21750092 PMID:22078000 PMID:22631584 PMID:22929189 PMID:24156255 PMID:25741868 PMID:28492532 PMID:30691194 NCBI chr 6:135,724,455...135,731,896
Ensembl chr 6:135,724,455...135,731,896
JBrowse link
G Cblif cobalamin binding intrinsic factor ISO DNA:polymorphisms, missense mutations, splice sites:exon,intron:
protein:increased excretion:urine:
RGD PMID:15738392, PMID:10435666 RGD:11049583, RGD:11049586 NCBI chr 1:228,118,048...228,132,296
Ensembl chr 1:228,118,048...228,132,404
JBrowse link
G Cubn cubilin ISO DNA:missense mutation:cds:p.P1297L (human)
ClinVar Annotator: match by term: Enterocyte intrinsic factor receptor, defect of
ClinVar Annotator: match by term: Megaloblastic anemia 1, Finnish type
ClinVar Annotator: match by term: Imerslund-Gräsbeck syndrome 1
ClinVar
OMIM
PMID:9536098 PMID:10080186 PMID:10887099 PMID:15024727 PMID:15963748 PMID:16199547 PMID:17576681 PMID:17668238 PMID:21208123 PMID:22277662 PMID:22495309 PMID:22929189 PMID:24033266 PMID:24156255 PMID:25349199 PMID:25525159 PMID:25741868 PMID:26040326 PMID:27197912 PMID:28492532 PMID:31497480 PMID:31613795 PMID:33532864, PMID:10080186 RGD:61796 NCBI chr17:80,584,921...80,807,181
Ensembl chr17:80,584,878...80,807,243
JBrowse link
G Traf3 Tnf receptor-associated factor 3 ISO ClinVar Annotator: match by term: Enterocyte intrinsic factor receptor, defect of ClinVar PMID:28492532 NCBI chr 6:135,610,698...135,720,247
Ensembl chr 6:135,610,743...135,718,564
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 DNA:mutation:splice site:
ClinVar Annotator: match by term: IMERSLUND-GRASBECK SYNDROME 2
ClinVar Annotator: match by term: MEGALOBLASTIC ANEMIA, NORWEGIAN TYPE
ClinVar
OMIM
PMID:6741523 PMID:12590260 PMID:13852753 PMID:15024727 PMID:17114957 PMID:17285242 PMID:22078000 PMID:24156255 PMID:26040326, PMID:17114957 RGD:11071839 NCBI chr 6:135,724,455...135,731,896
Ensembl chr 6:135,724,455...135,731,896
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 Dcdc2c doublecortin domain containing 2C ISO ClinVar Annotator: match by term: Methylmalonic acidemia with homocystinuria ClinVar PMID:25741868 NCBI chr 6:47,737,814...47,812,219
Ensembl chr 6:47,774,060...47,848,075
JBrowse link
G Hcfc1 host cell factor C1 ISO ClinVar Annotator: match by term: Methylmalonic acidemia with homocystinuria ClinVar PMID:24011988 PMID:25167861 PMID:25281006 PMID:25741868 PMID:26893841 PMID:27403441 NCBI chr  X:156,812,012...156,837,227
Ensembl chr  X:156,812,064...156,837,227
JBrowse link
G Mmachc metabolism of cobalamin associated C ISO ClinVar Annotator: match by term: methylmalonic aciduria and homocystinuria type cblC
ClinVar Annotator: match by term: Methylmalonic aciduria with homocystinuria cblC type
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 acidemia with homocystinuria
CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA, cblC TYPE, DIGENIC
ClinVar Annotator: match by OMIM:277400
OMIM
ClinVar
CTD
PMID:9536098 PMID:11261516 PMID:11320193 PMID:16199547 PMID:16311595 PMID:16714133 PMID:17431913 PMID:17576681 PMID:17768669 PMID:17853453 PMID:18164228 PMID:18245139 PMID:19370762 PMID:19700356 PMID:19760748 PMID:19767224 PMID:19836982 PMID:19914430 PMID:20219402 PMID:20549364 PMID:20610126 PMID:20631720 PMID:20652818 PMID:20924684 PMID:21055272 PMID:21114891 PMID:21228398 PMID:21835369 PMID:22447314 PMID:22560872 PMID:22642810 PMID:23580368 PMID:23757202 PMID:23825108 PMID:23837176 PMID:23954310 PMID:24033266 PMID:24126030 PMID:24210589 PMID:24577983 PMID:24599607 PMID:25388550 PMID:25398587 PMID:25511120 PMID:25668207 PMID:25672861 PMID:25687216 PMID:25689098 PMID:25741868 PMID:25772322 PMID:25809485 PMID:25894566 PMID:26149271 PMID:26270766 PMID:26283149 PMID:26287336 PMID:26412180 PMID:26563984 PMID:26658511 PMID:26825575 PMID:26979128 PMID:26990548 PMID:27252276 PMID:27383490 PMID:27751223 PMID:28151490 PMID:28218226 PMID:28327205 PMID:28454995 PMID:28481040 PMID:28492532 PMID:28693988 PMID:28835862 PMID:29042959 PMID:29294253 PMID:29379858 PMID:29396438 PMID:29453417 PMID:30157807 PMID:31279840 PMID:31470807 PMID:32164588 PMID:32943488 NCBI chr 5:135,555,587...135,561,723
Ensembl chr 5:135,555,565...135,561,914
JBrowse link
G Mmadhc metabolism of cobalamin associated D ISO ClinVar Annotator: match by term: methylmalonic aciduria and homocystinuria type cblC ClinVar NCBI chr 3:35,783,511...35,801,474
Ensembl chr 3:35,783,623...35,801,614
JBrowse link
G Prdx1 peroxiredoxin 1 ISO ClinVar Annotator: match by term: METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA, cblC TYPE, DIGENIC ClinVar
OMIM
PMID:29396438 NCBI chr 5:135,536,413...135,551,986
Ensembl chr 5:135,536,413...135,551,990
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:4434116, PMID:167441 RGD:11049584, RGD:11049587 NCBI chr 1:228,118,048...228,132,296
Ensembl chr 1:228,118,048...228,132,404
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 IMP
IDA
RGD PMID:16716410, PMID:16716410 RGD:2313422, RGD:2313422 NCBI chr 3:161,519,789...161,534,943
Ensembl chr 3:161,519,743...161,534,704
JBrowse link
G Cd40lg CD40 ligand treatment IEP
IDA
protein:increased expression:cerebrospinal fluid RGD PMID:16716410, PMID:16716410 RGD:2313422, RGD:2313422 NCBI chr  X:159,703,703...159,714,886
Ensembl chr  X:159,703,578...159,716,562
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
ClinVar Annotator: match by term: TCN2 DEFICIENCY
ClinVar Annotator: match by OMIM:275350
OMIM
ClinVar
PMID:7849710 PMID:7980584 PMID:10518276 PMID:12091374 PMID:12194912 PMID:12707225 PMID:14632784 PMID:17220211 PMID:19373259 PMID:20352340 PMID:22188304 PMID:24033266 PMID:25741868 PMID:27155006 PMID:28492532 NCBI chr14:84,173,992...84,189,299
Ensembl chr14:84,174,138...84,189,266
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 17129
    Nutritional and Metabolic Diseases 5514
      disease of metabolism 5514
        inherited metabolic disorder 2607
          vitamin metabolic disorder 37
            vitamin B12 deficiency 19
              Imerslund-Grasbeck Syndrome + 4
              Subacute Combined Degeneration 2
              congenital intrinsic factor deficiency 1
              methylmalonic aciduria and homocystinuria type cblC 5
              pernicious anemia + 1
              transcobalamin II deficiency 1
Path 2
Term Annotations click to browse term
  disease 17129
    Nutritional and Metabolic Diseases 5514
      disease of metabolism 5514
        acquired metabolic disease 2884
          nutrition disease 915
            Malnutrition 220
              nutritional deficiency disease 211
                Avitaminosis 120
                  Vitamin B Deficiency 70
                    vitamin B12 deficiency 19
                      Imerslund-Grasbeck Syndrome + 4
                      Subacute Combined Degeneration 2
                      congenital intrinsic factor deficiency 1
                      methylmalonic aciduria and homocystinuria type cblC 5
                      pernicious anemia + 1
                      transcobalamin II deficiency 1
paths to the root