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HUMAN PHENOTYPE - ANNOTATIONS

The Human Phenotype Ontology (HPO) is downloaded weekly from http://compbio.charite.de/hudson/job/hpo/lastStableBuild/artifact/ontology/release/hp.obo. The file downloaded is considered the "last stable build" available for the ontology. For more about the HPO, view their website at http://www.human-phenotype-ontology.org/.
Term:Abnormal substantia nigra morphology
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Accession:HP:0045007 term browser browse the term
Definition:A structural anomaly of the substantia nigra, which is a midbrain dopaminergic nucleus which has a critical role in modulating motor movement and reward functions as part of the basal ganglia circuitry.
Synonyms:exact_synonym: Abnormality of the substantia nigra
 xref: UMLS:C4022403


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Abnormal substantia nigra morphology term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ATXN2 ataxin 2 IAGP ORPHA:98756 HPO NCBI chr12:111,452,214...111,599,673
Ensembl chr12:111,443,485...111,599,676 		JBrowse link
G C19orf12 chromosome 19 open reading frame 12 IAGP ORPHA:289560 HPO NCBI chr19:29,698,886...29,715,789
Ensembl chr19:29,698,937...29,715,789 		JBrowse link
G CACNA1A calcium voltage-gated channel subunit alpha1 A IAGP ClinVar Annotator: match by term: Abnormality of the substantia nigra ClinVar PMID:25741868 NCBI chr19:13,206,442...13,506,479
Ensembl chr19:13,206,442...13,633,025 		JBrowse link
G GCH1 GTP cyclohydrolase 1 IAGP ORPHA:98808 HPO NCBI chr14:54,842,017...54,902,826
Ensembl chr14:54,842,008...54,902,826 		JBrowse link
G IMPDH2 inosine monophosphate dehydrogenase 2 IAGP ORPHA:98808 HPO NCBI chr 3:49,024,325...49,029,398
Ensembl chr 3:49,024,325...49,029,447 		JBrowse link
G NR4A2 nuclear receptor subfamily 4 group A member 2 IAGP ORPHA:98808 HPO NCBI chr 2:156,324,437...156,332,721
Ensembl chr 2:156,324,437...156,342,348 		JBrowse link
G SPG11 SPG11 vesicle trafficking associated, spatacsin IAGP ORPHA:2822 HPO NCBI chr15:44,562,696...44,663,662
Ensembl chr15:44,554,818...44,663,688 		JBrowse link
Iron accumulation in substantia nigra term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G FTL ferritin light chain IAGP ORPHA:157846 HPO NCBI chr19:48,965,309...48,966,879
Ensembl chr19:48,965,309...48,966,879 		JBrowse link
G TBCE tubulin folding cofactor E IAGP ORPHA:496756 HPO NCBI chr 1:235,367,427...235,452,443
Ensembl chr 1:235,367,360...235,452,443
Ensembl chr 1:235,367,360...235,452,443 		JBrowse link
G VPS41 VPS41 subunit of HOPS complex IAGP OMIM:619389 HPO NCBI chr 7:38,722,974...38,909,191
Ensembl chr 7:38,722,974...38,932,394 		JBrowse link
G WDR45 WD repeat domain 45 IAGP ORPHA:329284 HPO NCBI chr  X:49,074,442...49,101,178
Ensembl chr  X:49,074,433...49,101,170 		JBrowse link
Substantia nigra gliosis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ADH1C alcohol dehydrogenase 1C (class I), gamma polypeptide IAGP OMIM:168600 HPO NCBI chr 4:99,336,497...99,352,746
Ensembl chr 4:99,336,497...99,352,746 		JBrowse link
G ATXN2 ataxin 2 IAGP OMIM:168600 HPO NCBI chr12:111,452,214...111,599,673
Ensembl chr12:111,443,485...111,599,676 		JBrowse link
G ATXN3 ataxin 3 IAGP ORPHA:276238 ORPHA:276241 ORPHA:276244 HPO NCBI chr14:92,058,552...92,106,582
Ensembl chr14:92,044,496...92,106,621 		JBrowse link
G ATXN8OS ATXN8 opposite strand lncRNA IAGP OMIM:168600 HPO NCBI chr13:70,107,213...70,139,753
Ensembl chr13:70,107,213...70,171,738 		JBrowse link
G BDNF brain derived neurotrophic factor no_association IAGP DNA:polymorphisms: :196G>A (p.V66M), 270C>T RGD PMID:16565926 RGD:10059346 NCBI chr11:27,654,893...27,722,030
Ensembl chr11:27,654,893...27,722,058 		JBrowse link
G FBXO7 F-box protein 7 IAGP ORPHA:171695 HPO NCBI chr22:32,474,811...32,498,829
Ensembl chr22:32,474,676...32,498,829 		JBrowse link
G GBA1 glucosylceramidase beta 1 IAGP OMIM:168600 HPO NCBI chr 1:155,234,452...155,244,627
Ensembl chr 1:155,234,452...155,244,699 		JBrowse link
G GLUD2 glutamate dehydrogenase 2 IAGP OMIM:168600 HPO NCBI chr  X:121,047,610...121,050,094
Ensembl chr  X:121,047,610...121,050,094 		JBrowse link
G LRRK2 leucine rich repeat kinase 2 IAGP OMIM:607060 HPO NCBI chr12:40,224,997...40,369,285
Ensembl chr12:40,196,744...40,369,285 		JBrowse link
G MAPT microtubule associated protein tau IAGP OMIM:168600 HPO NCBI chr17:45,894,554...46,028,334
Ensembl chr17:45,894,527...46,028,334 		JBrowse link
G MT-TT mitochondrially encoded tRNA-Thr (ACN) IAGP OMIM:168600 HPO NCBI chr MT:15,888...15,953
Ensembl chr MT:15,888...15,953 		JBrowse link
G NR4A2 nuclear receptor subfamily 4 group A member 2 IAGP OMIM:168600 HPO NCBI chr 2:156,324,437...156,332,721
Ensembl chr 2:156,324,437...156,342,348 		JBrowse link
G PRKN parkin RBR E3 ubiquitin protein ligase IAGP OMIM:600116 HPO NCBI chr 6:161,347,417...162,727,766
Ensembl chr 6:161,347,417...162,727,775 		JBrowse link
G SNCA synuclein alpha IAGP ORPHA:171695 HPO NCBI chr 4:89,724,099...89,838,304
Ensembl chr 4:89,700,345...89,838,315 		JBrowse link
G SNCAIP synuclein alpha interacting protein IAGP OMIM:168600 HPO NCBI chr 5:122,311,353...122,464,219
Ensembl chr 5:122,311,354...122,464,219 		JBrowse link
G TBP TATA-box binding protein IAGP OMIM:168600 HPO NCBI chr 6:170,554,369...170,572,859
Ensembl chr 6:170,554,302...170,572,870 		JBrowse link
Substantia nigra hypointensity on susceptibility-weighted imaging term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G GTPBP2 GTP binding protein 2 IAGP OMIM:617988 HPO NCBI chr 6:43,620,494...43,631,333
Ensembl chr 6:43,605,316...43,629,264 		JBrowse link
G SLC44A1 solute carrier family 44 member 1 IAGP OMIM:618868 HPO NCBI chr 9:105,244,651...105,438,504
Ensembl chr 9:105,244,622...105,439,171 		JBrowse link
Thinning of the substantia nigra pars compacta term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G NR4A2 nuclear receptor subfamily 4 group A member 2 IAGP OMIM:619911 HPO NCBI chr 2:156,324,437...156,332,721
Ensembl chr 2:156,324,437...156,342,348 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  Human phenotype 15292
    Phenotypic abnormality 15290
      Abnormality of the nervous system 10551
        Abnormal nervous system morphology 4209
          Morphological central nervous system abnormality 4062
            Abnormality of brain morphology 3010
              Abnormal midbrain morphology 86
                Abnormal substantia nigra morphology 27
                  Focal substantia nigra T2 hyperintensity 0
                  Iron accumulation in substantia nigra 4
                  Substantia nigra gliosis 16
                  Substantia nigra hypointensity on susceptibility-weighted imaging 2
                  Thinning of the substantia nigra pars compacta 1
Path 2
Term Annotations click to browse term
  Human phenotype 15292
    Phenotypic abnormality 15290
      Abnormality of the nervous system 10551
        Abnormal nervous system morphology 4209
          Morphological central nervous system abnormality 4062
            Abnormality of brain morphology 3010
              Abnormal forebrain morphology 2130
                Abnormal cerebral morphology 2103
                  Abnormal cerebral subcortex morphology 1169
                    Abnormal basal ganglia morphology 209
                      Abnormal substantia nigra morphology 27
                        Focal substantia nigra T2 hyperintensity 0
                        Iron accumulation in substantia nigra 4
                        Substantia nigra gliosis 16
                        Substantia nigra hypointensity on susceptibility-weighted imaging 2
                        Thinning of the substantia nigra pars compacta 1
paths to the root