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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:nephrocalcinosis
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Accession:DOID:12679 term browser browse the term
Definition:A condition characterized by calcification of the renal tissue itself. It is usually seen in distal RENAL TUBULAR ACIDOSIS with calcium deposition in the DISTAL KIDNEY TUBULES and the surrounding interstitium. Nephrocalcinosis causes RENAL INSUFFICIENCY.
Synonyms:exact_synonym: Nephrocalcinoses;   kidney disorder involving deposition of calcium and oxalate or phosphate in the renal tubules
 primary_id: MESH:D009397
 alt_id: MESH:C531755;   RDO:0000168;   RDO:0000169
 xref: GARD:7177;   NCI:C84918
For additional species annotation, visit the Alliance of Genome Resources.


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nephrocalcinosis term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Agxt alanine--glyoxylate aminotransferase ISO ClinVar Annotator: match by term: Nephrocalcinosis ClinVar PMID:8101040 PMID:9136629 PMID:9192270 PMID:10541294 PMID:10960483 More... NCBI chr 9:93,675,384...93,685,337
Ensembl chr 9:93,675,384...93,685,336 		JBrowse link
G Atp6v1b1 ATPase H+ transporting V1 subunit B1 ISO ClinVar Annotator: match by term: Nephrocalcinosis ClinVar PMID:9916796 PMID:12414817 PMID:16199547 PMID:16611712 PMID:16769747 More... NCBI chr 4:116,223,799...116,242,475
Ensembl chr 4:116,223,799...116,242,475 		JBrowse link
G Brd4 bromodomain containing 4 ISS MouseDO NCBI chr 7:11,216,446...11,296,029
Ensembl chr 7:11,216,446...11,295,539 		JBrowse link
G Cldn16 claudin 16 ISO ClinVar Annotator: match by term: Nephrocalcinosis ClinVar PMID:10390358 PMID:25741868 PMID:28893421 NCBI chr11:74,290,298...74,309,588
Ensembl chr11:74,290,298...74,309,588 		JBrowse link
G Cldn19 claudin 19 ISO ClinVar Annotator: match by term: Nephrocalcinosis ClinVar PMID:25741868 PMID:28492532 PMID:28893421 PMID:33025205 PMID:34805638 NCBI chr 5:132,862,939...132,870,364
Ensembl chr 5:132,863,267...132,868,227 		JBrowse link
G Grhpr glyoxylate and hydroxypyruvate reductase ISO ClinVar Annotator: match by term: Nephrocalcinosis ClinVar PMID:9536098 PMID:10484776 PMID:11030416 PMID:12185464 PMID:14635115 More... NCBI chr 5:59,234,179...59,243,614
Ensembl chr 5:59,234,192...59,243,603 		JBrowse link
G Phex phosphate regulating endopeptidase X-linked ISO CTD Direct Evidence: marker/mechanism CTD PMID:9430241 NCBI chr  X:37,607,553...37,856,183
Ensembl chr  X:37,610,760...37,854,469 		JBrowse link
G Polg2 DNA polymerase gamma 2, accessory subunit ISS MouseDO NCBI chr10:91,712,586...91,723,008
Ensembl chr10:91,712,586...91,723,008 		JBrowse link
G Pomc proopiomelanocortin ISO CTD Direct Evidence: marker/mechanism CTD PMID:3017235 NCBI chr 6:26,939,844...26,945,666
Ensembl chr 6:26,939,837...26,945,664 		JBrowse link
G Pth parathyroid hormone IDA RGD PMID:23344571 RGD:7242573 NCBI chr 1:167,508,121...167,511,530
Ensembl chr 1:167,508,598...167,511,530 		JBrowse link
G Slc12a1 solute carrier family 12 member 1 ISO ClinVar Annotator: match by term: Nephrocalcinosis ClinVar PMID:8640224 PMID:9585600 PMID:17998760 PMID:18391953 PMID:19096086 More... NCBI chr 3:112,406,140...112,482,913
Ensembl chr 3:112,406,140...112,482,899 		JBrowse link
G Slc26a1 solute carrier family 26 member 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:20160351 NCBI chr14:1,040,565...1,045,851
Ensembl chr14:1,040,243...1,045,849 		JBrowse link
G Slc34a1 solute carrier family 34 member 1 ISO associated with Hypercalciuria
ClinVar Annotator: match by term: Nephrocalcinosis		 ClinVar
RGD		 PMID:16199547 PMID:16688119 PMID:25741868 PMID:26047794 PMID:28492532 More... RGD:7242938 NCBI chr17:9,218,876...9,233,852
Ensembl chr17:9,218,876...9,233,852 		JBrowse link
G Slc3a1 solute carrier family 3 member 1 ISO ClinVar Annotator: match by term: Nephrocalcinosis ClinVar PMID:18947684 PMID:24610330 PMID:25109415 PMID:25741868 PMID:25964309 More... NCBI chr 6:9,608,169...9,641,881
Ensembl chr 6:9,608,178...9,641,907 		JBrowse link
amelogenesis imperfecta type 1G term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Fam20a FAM20A, golgi associated secretory pathway pseudokinase ISO ClinVar Annotator: match by term: Amelogenesis imperfecta type 1G | ClinVar Annotator: match by term: Generalized enamel hypoplasia and renal dysfunction OMIM
ClinVar		 PMID:18597613 PMID:21549343 PMID:21990045 PMID:23434854 PMID:23468644 More... NCBI chr10:94,638,836...94,697,814
Ensembl chr10:94,642,850...94,697,672 		JBrowse link
G Prkar1a protein kinase cAMP-dependent type I regulatory subunit alpha ISO ClinVar Annotator: match by term: Amelogenesis imperfecta type 1G | ClinVar Annotator: match by term: Generalized enamel hypoplasia and renal dysfunction ClinVar PMID:21990045 PMID:23434854 PMID:23468644 PMID:24196488 PMID:25741868 More... NCBI chr10:94,621,042...94,639,534
Ensembl chr10:94,620,039...94,639,041 		JBrowse link
low molecular weight proteinuria with hypercalciuric nephrocalcinosis term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Clcn5 chloride voltage-gated channel 5 ISO ClinVar Annotator: match by term: Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis
CTD Direct Evidence: marker/mechanism		 OMIM
ClinVar
CTD		 PMID:7915957 PMID:8559248 PMID:9062355 PMID:9187673 PMID:9734595 More... NCBI chr  X:15,185,380...15,339,977
Ensembl chr  X:15,185,451...15,334,264 		JBrowse link
midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ammecr1 AMMECR nuclear protein 1 ISO ClinVar Annotator: match by term: AMMECR1-related condition | ClinVar Annotator: match by term: Midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis OMIM
ClinVar		 PMID:21681106 PMID:25741868 PMID:27811305 PMID:28089922 PMID:28492532 More... NCBI chr  X:106,465,982...106,571,382
Ensembl chr  X:106,466,699...106,571,487 		JBrowse link
G Gng5-ps4 G protein subunit gamma 5, pseudogene 4 ISO ClinVar Annotator: match by term: Midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis ClinVar NCBI chr11:44,627,213...44,627,733
Ensembl chr11:44,627,300...44,627,503 		JBrowse link
G Rtl9 retrotransposon Gag like 9 ISO ClinVar Annotator: match by term: Midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis ClinVar NCBI chr  X:106,708,454...106,720,607
Ensembl chr  X:106,714,868...106,719,794 		JBrowse link
G Tmem164 transmembrane protein 164 ISO ClinVar Annotator: match by term: Midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis ClinVar PMID:21681106 PMID:27811305 PMID:28089922 NCBI chr  X:106,288,019...106,448,642
Ensembl chr  X:106,289,371...106,448,640 		JBrowse link
SHORT syndrome term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Pik3r1 phosphoinositide-3-kinase regulatory subunit 1 ISO
ISS		 ClinVar Annotator: match by term: SHORT syndrome
OMIM:269880
CTD Direct Evidence: marker/mechanism		 OMIM
ClinVar
MouseDO
CTD		 PMID:269880 PMID:6407320 PMID:7705412 PMID:8574420 PMID:9536098 More... NCBI chr 2:32,878,942...32,963,668
Ensembl chr 2:32,882,032...32,963,631 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 19137
    disease of anatomical entity 18450
      Urogenital Diseases 5390
        urinary system disease 2833
          kidney disease 2581
            nephrocalcinosis 22
              Distal Renal Tubular Acidosis, with Nephrocalcinosis, Short Stature, Mental Retardation, and Distinctive Facies 0
              Manz Syndrome 0
              SHORT syndrome 1
              amelogenesis imperfecta type 1G 2
              low molecular weight proteinuria with hypercalciuric nephrocalcinosis 1
              midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis 4
Path 2
Term Annotations click to browse term
  disease 19137
    Nutritional and Metabolic Diseases 8542
      disease of metabolism 8542
        acquired metabolic disease 2538
          mineral metabolism disease 959
            calcium metabolism disease 630
              calcinosis 553
                nephrocalcinosis 22
                  Distal Renal Tubular Acidosis, with Nephrocalcinosis, Short Stature, Mental Retardation, and Distinctive Facies 0
                  Manz Syndrome 0
                  SHORT syndrome 1
                  amelogenesis imperfecta type 1G 2
                  low molecular weight proteinuria with hypercalciuric nephrocalcinosis 1
                  midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis 4
paths to the root