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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:spina bifida
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Accession:DOID:0080016 term browser browse the term
Definition:A neural tube defect that is characterized by incomplete closing of the spine and membranes around the spinal cord during early development. (DO)
Synonyms:exact_synonym: Spina Bifidas;   cleft spine;   open spine;   rachischises;   rachischisis;   schistorrhachis;   spinal dysraphia;   spinal dysraphias;   spinal dysraphism;   spinal dysraphisms;   status dysraphicus
 related_synonym: Spina Bifida, Susceptibility To
 primary_id: MESH:D016135
 alt_id: OMIA:000938
 xref: EFO:0003105;   GARD:7673;   ICD9CM:741;   NCI:C101214


show annotations for term's descendants           Sort by:
spina bifida term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Apex1 apurinic/apyrimidinic endodeoxyribonuclease 1 susceptibility ISO DNA:polymorphism: :p.D148E (human) RGD PMID:15887293 RGD:2315675 NCBI chr15:24,144,595...24,146,785
Ensembl chr15:24,144,362...24,146,785 		JBrowse link
G Ccl2 C-C motif chemokine ligand 2 ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Spina bifida, susceptibility to		 CTD
ClinVar		 PMID:11500196 PMID:15466648 PMID:16352737 PMID:16596675 PMID:18940815 More... NCBI chr10:67,005,424...67,007,222
Ensembl chr10:67,005,424...67,007,226 		JBrowse link
G Cfl1 cofilin 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:17352815 NCBI chr 1:202,796,012...202,801,337
Ensembl chr 1:202,786,627...202,817,587 		JBrowse link
G Chka choline kinase alpha ISO CTD Direct Evidence: marker/mechanism CTD PMID:17184542 NCBI chr 1:201,076,804...201,125,517
Ensembl chr 1:201,076,860...201,125,516 		JBrowse link
G Cyp26a1 cytochrome P450, family 26, subfamily a, polypeptide 1 ISO RGD PMID:11953746 RGD:737785 NCBI chr 1:235,471,368...235,475,204
Ensembl chr 1:235,471,298...235,475,204 		JBrowse link
G Fgfr2 fibroblast growth factor receptor 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:9605588 NCBI chr 1:184,745,418...184,850,655
Ensembl chr 1:184,745,420...184,850,626 		JBrowse link
G Fkbp8 FKBP prolyl isomerase 8 ISS MouseDO NCBI chr16:18,895,608...18,902,648
Ensembl chr16:18,893,576...18,902,612 		JBrowse link
G Gli1 GLI family zinc finger 1 ISO protein:increased expression:brain RGD PMID:26446020 RGD:12801432 NCBI chr 7:63,156,926...63,169,579
Ensembl chr 7:63,156,926...63,169,251 		JBrowse link
G Gli2 GLI family zinc finger 2 ISO DNA, protein:hypermethylation, decreased expression:promoter, brain RGD PMID:26446020 RGD:12801432 NCBI chr13:29,946,882...30,163,589
Ensembl chr13:29,946,809...30,163,574 		JBrowse link
G Mthfd1 methylenetetrahydrofolate dehydrogenase, cyclohydrolase and formyltetrahydrofolate synthetase 1 ISO RGD PMID:9611072 RGD:1600190 NCBI chr 6:94,977,862...95,045,375
Ensembl chr 6:94,977,862...95,045,372 		JBrowse link
G Mthfr methylenetetrahydrofolate reductase susceptibility
no_association
severity		 ISO DNA:transition:cds:g.677C>T (human)
CTD Direct Evidence: marker/mechanism
DNA:polymorphism: :677C>T(human) 		CTD
RGD		 PMID:27713094 PMID:10791559 PMID:15022402 PMID:12797455 RGD:6893455, RGD:11565178, RGD:11565104 NCBI chr 5:158,465,248...158,484,999
Ensembl chr 5:158,465,296...158,483,797 		JBrowse link
G Mtr 5-methyltetrahydrofolate-homocysteine methyltransferase ISO DNA:polymorphism: :2756A>G(human) RGD PMID:12375236 RGD:1302512 NCBI chr17:58,219,998...58,308,560
Ensembl chr17:58,220,071...58,304,822 		JBrowse link
G Mtrr 5-methyltetrahydrofolate-homocysteine methyltransferase reductase susceptibility ISO DNA:polymorphism: :66A>G(human) RGD PMID:12590188 PMID:12375236 RGD:5508199, RGD:1302512 NCBI chr 1:34,866,991...34,899,425
Ensembl chr 1:34,867,089...34,899,425 		JBrowse link
G Nkx2-8 NK2 homeobox 8 ISO Spinal dysraphism OMIA PMID:375559 PMID:1641930 PMID:4434313 PMID:4732250 PMID:5023160 More... NCBI chr 6:74,086,274...74,087,977
Ensembl chr 6:74,086,274...74,087,977 		JBrowse link
G Pax3 paired box 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:3902948 PMID:6385329 PMID:12854658 PMID:17149730 NCBI chr 9:79,567,455...79,664,042
Ensembl chr 9:79,568,634...79,664,042 		JBrowse link
G Pcmt1 protein-L-isoaspartate (D-aspartate) O-methyltransferase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:16256389 NCBI chr 1:2,111,756...2,160,354
Ensembl chr 1:2,111,763...2,159,201 		JBrowse link
G Pcyt1a phosphate cytidylyltransferase 1A, choline ISO CTD Direct Evidence: marker/mechanism CTD PMID:17184542 NCBI chr11:68,313,860...68,357,828
Ensembl chr11:68,313,882...68,357,357 		JBrowse link
G Pdgfra platelet derived growth factor receptor alpha ISO CTD Direct Evidence: marker/mechanism CTD PMID:11023856 NCBI chr14:33,005,838...33,054,347
Ensembl chr14:33,005,839...33,054,335 		JBrowse link
G Pon1 paraoxonase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:21031563 NCBI chr 4:33,294,737...33,325,759
Ensembl chr 4:33,294,722...33,321,360 		JBrowse link
G Ptch1 patched 1 ISO protein:decreased expression:brain RGD PMID:26446020 RGD:12801432 NCBI chr17:1,542,705...1,607,730
Ensembl chr17:1,542,877...1,607,333 		JBrowse link
G Rnf2 ring finger protein 2 IEP RGD PMID:20515739 RGD:9491842 NCBI chr13:63,553,964...63,584,047
Ensembl chr13:63,554,862...63,583,099 		JBrowse link
G Suz12 SUZ12 polycomb repressive complex 2 subunit IEP RGD PMID:20515739 RGD:9491842 NCBI chr10:64,967,035...65,012,916
Ensembl chr10:64,966,967...65,012,738 		JBrowse link
G Txn2 thioredoxin 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:19165900 NCBI chr 7:109,496,772...109,510,378
Ensembl chr 7:109,496,761...109,510,359 		JBrowse link
G Vangl2 VANGL planar cell polarity protein 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:21404367 NCBI chr13:84,462,731...84,489,404
Ensembl chr13:84,465,527...84,489,378 		JBrowse link
caudal regression syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Casq2 calsequestrin 2 ISO ClinVar Annotator: match by term: Caudal regression sequence | ClinVar Annotator: match by term: Sacral defect with anterior meningocele ClinVar PMID:24033266 PMID:25741868 PMID:26196381 PMID:28492532 NCBI chr 2:189,526,003...189,582,276
Ensembl chr 2:189,525,960...189,582,267 		JBrowse link
G Cdx2 caudal type homeo box 2 ISO ClinVar Annotator: match by term: Sirenomelia ClinVar PMID:25741868 NCBI chr12:7,726,798...7,733,142
Ensembl chr12:7,726,798...7,733,142 		JBrowse link
G Pcsk5 proprotein convertase subtilisin/kexin type 5 ISO CTD Direct Evidence: marker/mechanism CTD PMID:18519639 NCBI chr 1:214,837,847...215,267,626
Ensembl chr 1:214,837,927...215,267,600 		JBrowse link
G Ryr1 ryanodine receptor 1 ISO ClinVar Annotator: match by term: Agenesis of sacrum ClinVar PMID:18564 PMID:9497245 PMID:10484775 PMID:11575529 PMID:12059893 More... NCBI chr 1:84,292,578...84,423,824
Ensembl chr 1:84,292,578...84,423,812 		JBrowse link
G Vangl1 VANGL planar cell polarity protein 1 ISO ClinVar Annotator: match by term: Caudal regression sequence | ClinVar Annotator: match by term: Sacral defect with anterior meningocele
CTD Direct Evidence: marker/mechanism		 ClinVar
OMIM
CTD		 PMID:17409324 PMID:19319979 PMID:22892949 PMID:24033266 PMID:24307374 More... NCBI chr 2:189,586,681...189,637,609
Ensembl chr 2:189,589,229...189,637,619 		JBrowse link
G Zbtb16 zinc finger and BTB domain containing 16 IAGP RGD PMID:27727328 RGD:40924666 NCBI chr 8:48,989,376...49,177,011
Ensembl chr 8:48,994,566...49,177,011 		JBrowse link
lateral meningocele syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Notch3 notch receptor 3 ISO ClinVar Annotator: match by term: Lateral meningocele syndrome | ClinVar Annotator: match by term: Lehman syndrome
CTD Direct Evidence: marker/mechanism		 OMIM
ClinVar
CTD		 PMID:3484396 PMID:8878478 PMID:9188658 PMID:9388399 PMID:10227618 More... NCBI chr 7:11,132,984...11,184,025
Ensembl chr 7:11,133,706...11,184,025 		JBrowse link
myelomeningocele term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Aldh1a2 aldehyde dehydrogenase 1 family, member A2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:16237707 NCBI chr 8:71,877,850...71,957,107
Ensembl chr 8:71,877,850...71,957,107 		JBrowse link
G Mthfr methylenetetrahydrofolate reductase ISO CTD Direct Evidence: marker/mechanism CTD PMID:16602021 NCBI chr 5:158,465,248...158,484,999
Ensembl chr 5:158,465,296...158,483,797 		JBrowse link
G Slc2a1 solute carrier family 2 member 1 ISO DNA:deletion:intron:rs35565219 (human)
DNA:SNPs, haplotype: :rs710218, rs2229682 (human)		 RGD PMID:21135204 PMID:23427181 RGD:11070819, RGD:12879498 NCBI chr 5:132,717,196...132,745,416
Ensembl chr 5:132,717,196...132,745,416 		JBrowse link
G Sod1 superoxide dismutase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22972774 NCBI chr11:29,456,673...29,462,249
Ensembl chr11:29,456,558...29,462,249 		JBrowse link
G Sod2 superoxide dismutase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22972774 NCBI chr 1:47,638,318...47,645,163
Ensembl chr 1:47,636,528...47,645,189 		JBrowse link
Spina Bifida Cystica term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Actl6a actin-like 6A IEP RGD PMID:23677776 RGD:9587760 NCBI chr 2:115,492,374...115,508,401
Ensembl chr 2:115,492,285...115,508,401 		JBrowse link
G Actl6b actin-like 6B IEP RGD PMID:23677776 RGD:9587760 NCBI chr12:19,124,887...19,141,419
Ensembl chr12:19,124,916...19,141,376 		JBrowse link
G Chrna7 cholinergic receptor nicotinic alpha 7 subunit ISO CTD Direct Evidence: marker/mechanism CTD PMID:22473653 NCBI chr 1:116,711,559...116,837,269
Ensembl chr 1:116,714,711...116,837,240 		JBrowse link
G Gfap glial fibrillary acidic protein ISO CTD Direct Evidence: marker/mechanism CTD PMID:8422324 NCBI chr10:87,852,891...87,861,631
Ensembl chr10:87,852,890...87,861,589 		JBrowse link
G Runx1 RUNX family transcription factor 1 treatment IDA RGD PMID:26172505 RGD:11251712 NCBI chr11:31,839,880...32,074,427
Ensembl chr11:31,843,764...32,074,542 		JBrowse link
tethered spinal cord syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Braf B-Raf proto-oncogene, serine/threonine kinase ISO ClinVar Annotator: match by term: Occult spinal dysraphism sequence ClinVar PMID:4386970 PMID:5771505 PMID:16372351 PMID:16523510 PMID:16804887 More... NCBI chr 4:68,375,484...68,510,652
Ensembl chr 4:68,384,649...68,510,463 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 19050
    physical disorder 5170
      neural tube defect 136
        spina bifida 41
          Anencephaly and Spina Bifida X-Linked 0
          Camptodactyly Syndrome Guadalajara Type 2 0
          Camptodactyly Syndrome Guadalajara Type 3 0
          Spina Bifida Cystica + 5
          Spina Bifida, Folate-Sensitive 0
          Spina Bifida, X-Linked 0
          Split-Hand with Obstructive Uropathy, Spina Bifida, and Diaphragmatic Defects 0
          meningocele + 7
          myelomeningocele + 5
          spina bifida occulta + 1
Path 2
Term Annotations click to browse term
  disease 19050
    Developmental Disease 14522
      Congenital, Hereditary, and Neonatal Diseases and Abnormalities 13536
        Congenital Abnormalities 7762
          Nervous System Malformations 2450
            neural tube defect 136
              spina bifida 41
                Anencephaly and Spina Bifida X-Linked 0
                Camptodactyly Syndrome Guadalajara Type 2 0
                Camptodactyly Syndrome Guadalajara Type 3 0
                Spina Bifida Cystica + 5
                Spina Bifida, Folate-Sensitive 0
                Spina Bifida, X-Linked 0
                Split-Hand with Obstructive Uropathy, Spina Bifida, and Diaphragmatic Defects 0
                meningocele + 7
                myelomeningocele + 5
                spina bifida occulta + 1
paths to the root