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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 and serine--pyruvate aminotransferase ISO ClinVar Annotator: match by term: Nephrocalcinosis ClinVar PMID:8101040 PMID:9136629 PMID:9192270 PMID:10541294 PMID:10960483 PMID:12777626 PMID:15327387 PMID:15802217 PMID:16912707 PMID:17460142 PMID:17495019 PMID:19155213 PMID:20133649 PMID:23229545 PMID:24012869 PMID:24055001 PMID:24718375 PMID:24988064 PMID:25629080 PMID:28492532 PMID:28893421 NCBI chr 9:100,281,339...100,291,292
Ensembl chr 9:100,281,339...100,291,291
JBrowse link
G Atp6v1b1 ATPase H+ transporting V1 subunit B1 ISO ClinVar Annotator: match by term: Nephrocalcinosis ClinVar PMID:9916796 PMID:22509993 PMID:28893421 NCBI chr 4:115,417,100...115,435,754
Ensembl chr 4:115,416,580...115,437,206
JBrowse link
G Cldn16 claudin 16 ISO ClinVar Annotator: match by term: Nephrocalcinosis ClinVar PMID:10390358 PMID:28893421 NCBI chr11:77,683,942...77,703,232
Ensembl chr11:77,681,794...77,703,255
JBrowse link
G Cldn19 claudin 19 ISO ClinVar Annotator: match by term: Nephrocalcinosis ClinVar PMID:28893421 NCBI chr 5:138,300,692...138,307,982
Ensembl chr 5:138,300,107...138,305,683
JBrowse link
G Grhpr glyoxylate and hydroxypyruvate reductase ISO ClinVar Annotator: match by term: Nephrocalcinosis ClinVar PMID:10484776 PMID:11030416 PMID:12185464 PMID:14635115 PMID:15327387 PMID:18560364 PMID:24033266 PMID:24116921 PMID:25644115 PMID:25741868 PMID:28492532 PMID:28893421 NCBI chr 5:60,528,981...60,538,410
Ensembl chr 5:60,528,997...60,538,375
JBrowse link
G Phex phosphate regulating endopeptidase homolog, X-linked ISO CTD Direct Evidence: marker/mechanism CTD PMID:9430241 NCBI chr  X:40,460,047...40,717,982
Ensembl chr  X:40,460,047...40,717,982
JBrowse link
G Pomc proopiomelanocortin ISO CTD Direct Evidence: marker/mechanism CTD PMID:3017235 NCBI chr 6:28,382,937...28,388,771
Ensembl chr 6:28,382,962...28,388,967
JBrowse link
G Pth parathyroid hormone IDA RGD PMID:23344571 RGD:7242573 NCBI chr 1:178,215,829...178,218,761
Ensembl chr 1:178,215,829...178,218,761
JBrowse link
G Slc12a1 solute carrier family 12 member 1 ISO ClinVar Annotator: match by term: Nephrocalcinosis ClinVar PMID:28893421 NCBI chr 3:117,421,531...117,498,372
Ensembl chr 3:117,421,604...117,498,367
JBrowse link
G Slc26a1 solute carrier family 26 member 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:20160351 NCBI chr14:2,050,805...2,056,091
Ensembl chr14:2,050,483...2,056,089
JBrowse link
G Slc34a1 solute carrier family 34 member 1 ISO associated with Hypercalciuria
ClinVar Annotator: match by term: Nephrocalcinosis
ClinVar PMID:16688119 PMID:26047794 PMID:28492532 PMID:28893421, PMID:12674325 RGD:7242938 NCBI chr17:9,747,766...9,762,739
Ensembl chr17:9,747,752...9,762,813
JBrowse link
G Slc3a1 solute carrier family 3 member 1 ISO ClinVar Annotator: match by term: Nephrocalcinosis ClinVar PMID:25741868 PMID:28893421 NCBI chr 6:8,284,937...8,318,649
Ensembl chr 6:8,284,878...8,318,674
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: Enamel-renal syndrome
ClinVar Annotator: match by term: Amelogenesis imperfecta and gingival fibromatosis syndrome
OMIM
ClinVar
PMID:18597613 PMID:21549343 PMID:21990045 PMID:23434854 PMID:23468644 PMID:24196488 PMID:25741868 NCBI chr10:97,962,467...98,017,171
Ensembl chr10:97,962,693...98,018,014
JBrowse link
G Prkar1a protein kinase cAMP-dependent type I regulatory subunit alpha ISO ClinVar Annotator: match by term: Enamel-renal syndrome
ClinVar Annotator: match by term: Amelogenesis imperfecta and gingival fibromatosis syndrome
ClinVar PMID:21990045 PMID:23434854 PMID:23468644 PMID:24196488 PMID:25741868 NCBI chr10:97,940,705...97,959,199
Ensembl chr10:97,940,705...97,957,336
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
ClinVar Annotator: match by OMIM:308990
OMIM
ClinVar
PMID:8559248 PMID:9062355 PMID:25741868 NCBI chr  X:16,170,585...16,196,691
Ensembl chr  X:16,050,780...16,196,789
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: Midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis ClinVar
OMIM
PMID:21681106 PMID:25741868 PMID:27811305 PMID:28089922 PMID:29174631 NCBI chr  X:114,129,829...114,233,013
Ensembl chr  X:114,131,898...114,232,939
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:114,367,028...114,379,646
Ensembl chr  X:114,373,907...114,378,622
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:113,947,355...114,110,064
Ensembl chr  X:113,948,654...114,110,062
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 ClinVar Annotator: match by term: SHORT syndrome
ClinVar Annotator: match by OMIM:269880
OMIM
ClinVar
PMID:6407320 PMID:7705412 PMID:8574420 PMID:11135494 PMID:12514365 PMID:18384141 PMID:18414213 PMID:22351933 PMID:23810378 PMID:23810379 PMID:23810382 PMID:23980586 PMID:24033266 PMID:24088041 PMID:24886349 PMID:25133428 PMID:25157968 PMID:25326637 PMID:25488983 PMID:25741868 PMID:25939554 PMID:26529633 PMID:26633545 PMID:26974159 PMID:27076228 PMID:27116393 PMID:27693481 PMID:27766312 PMID:28302518 PMID:28492532 PMID:28632845 PMID:29740032 NCBI chr 2:31,742,326...31,826,882
Ensembl chr 2:31,745,088...31,826,867
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 16122
    disease of anatomical entity 15369
      Urogenital Diseases 4159
        urinary system disease 2075
          kidney disease 1859
            nephrocalcinosis 19
              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 3
Path 2
Term Annotations click to browse term
  disease 16122
    Nutritional and Metabolic Diseases 4714
      disease of metabolism 4714
        acquired metabolic disease 2762
          mineral metabolism disease 432
            calcium metabolism disease 271
              calcinosis 241
                nephrocalcinosis 19
                  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 3
paths to the root