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
Accession: DOID:12679
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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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
Term paths to the root one shortest all shortest one longest all longest one shortest and longest all
Path 1
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
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