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XRN
MCID: XLN243
MIFTS: 26

X-Linked Nephrolithiasis Type I (XRN)

Categories: Genetic diseases, Nephrological diseases
Genes Tissues Related diseases Publications Pathways
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Aliases & Classifications for X-Linked Nephrolithiasis Type I

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MalaCards integrated aliases for X-Linked Nephrolithiasis Type I:

Name: X-Linked Nephrolithiasis Type I 12 15
X-Linked Nephrolithiasis with Renal Failure 12
Nephrolithiasis X-Linked Recessive Type 1 12
X-Linked Recessive Urolithiasis Type 1 12
Nephrolithiasis 1 12
Nphl1 12
Xrn 12

Classifications:

MalaCards categories:
Global: Genetic diseases
Anatomical: Nephrological diseases
See all MalaCards categories (disease lists)


External Ids:

Disease Ontology 12 DOID:0111798
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Summaries for X-Linked Nephrolithiasis Type I

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Disease Ontology : 12 A renal tubular transport disease characterized by proximal renal tubular reabsorptive failure, hypercalciuria, nephrolithiasis, and renal insufficiency with absence of rickets that has material basis in hemizygous or homozygous mutation in CLCN5 on chromosome Xp11.23.

MalaCards based summary : X-Linked Nephrolithiasis Type I, also known as x-linked nephrolithiasis with renal failure, is related to nephrolithiasis, x-linked recessive, with renal failure and hepatitis c virus. An important gene associated with X-Linked Nephrolithiasis Type I is XRN2 (5'-3' Exoribonuclease 2), and among its related pathways/superpathways are Gene Expression and Metabolism of proteins. Affiliated tissues include kidney, and related phenotypes are Decreased viability and Decreased viability

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Related Diseases for X-Linked Nephrolithiasis Type I

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Diseases related to X-Linked Nephrolithiasis Type I via text searches within MalaCards or GeneCards Suite gene sharing:

(show all 16)
# Related Disease Score Top Affiliating Genes
1 nephrolithiasis, x-linked recessive, with renal failure 11.4
2 hepatitis c virus 9.9
3 hepatitis c 9.9
4 hepatitis 9.9
5 nephrolithiasis 9.8
6 aortic valve prolapse 9.8 EXOSC9 EXOSC8
7 pontocerebellar hypoplasia type 1 9.8 EXOSC9 EXOSC8
8 amyotrophic lateral sclerosis 4, juvenile 9.8 XRN2 EXOSC9
9 gm1-gangliosidosis, type i 9.7 EXOSC9 EXOSC8
10 spherocytosis, type 2 9.7 EXOSC9 EXOSC1
11 pontocerebellar hypoplasia 9.7 EXOSC9 EXOSC8 EXOSC1
12 spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2 9.6 XRN2 EXOSC9
13 hyperoxaluria, primary, type ii 9.6 EXOSC9 EXOSC8 EXOSC1
14 hyperoxaluria, primary, type iii 9.6 EXOSC9 EXOSC8 EXOSC1
15 pontocerebellar hypoplasia, type 1b 9.6 EXOSC9 EXOSC8 EXOSC1 DIS3
16 perlman syndrome 9.6 LSM1 ERI1 DIS3L2 DIS3

Graphical network of the top 20 diseases related to X-Linked Nephrolithiasis Type I:



Diseases related to X-Linked Nephrolithiasis Type I
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Symptoms & Phenotypes for X-Linked Nephrolithiasis Type I

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GenomeRNAi Phenotypes related to X-Linked Nephrolithiasis Type I according to GeneCards Suite gene sharing:

26
# Description GenomeRNAi Source Accession Score Top Affiliating Genes
1 Decreased viability GR00106-A-0 10.03 MTREX
2 Decreased viability GR00221-A-1 10.03 EXOSC10
3 Decreased viability GR00221-A-2 10.03 EXOSC10
4 Decreased viability GR00240-S-1 10.03 WDR61
5 Decreased viability GR00249-S 10.03 ERI1 EXOSC10 EXOSC9 WDR61
6 Decreased viability GR00342-S-1 10.03 EXOSC10
7 Decreased viability GR00381-A-1 10.03 EXOSC1 WDR61
8 Decreased viability GR00386-A-1 10.03 DXO EXOSC1 EXOSC7 MTREX SKIV2L
9 Decreased viability GR00402-S-2 10.03 DIS3 EXOSC1 EXOSC10 EXOSC6 EXOSC8 EXOSC9
10 shRNA abundance <= 50% GR00343-S 8.92 DIS3 LSM1 XRN1 XRN2
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Drugs & Therapeutics for X-Linked Nephrolithiasis Type I

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Search Clinical Trials , NIH Clinical Center for X-Linked Nephrolithiasis Type I

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Genetic Tests for X-Linked Nephrolithiasis Type I

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Anatomical Context for X-Linked Nephrolithiasis Type I

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MalaCards organs/tissues related to X-Linked Nephrolithiasis Type I:

40
Kidney
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Publications for X-Linked Nephrolithiasis Type I

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Articles related to X-Linked Nephrolithiasis Type I:

# Title Authors PMID Year
1
Nephrogenic adenoma of the urinary tract: A 6-year single center experience. 61
28554748 2017
2
Infrared vibrational spectroscopy: a rapid and novel diagnostic and monitoring tool for cystinuria. 61
27721432 2016
3
Twenty-year experience with laparoscopic and retroperitoneoscopic nephrectomy in children: considerations and details of technique. 61
26281905 2016
4
Dietary and pharmacologic management to prevent recurrent nephrolithiasis in adults: a clinical practice guideline from the American College of Physicians. 61
25364887 2014
5
Surgical management of adrenal myelolipoma: a series of 10 patients and review of the literature. 61
16858306 2006
6
Familial hyperparathyroidism without multiple endocrine neoplasia. 61
8943173 1997
7
Use of extracorporeal shock wave lithotripsy for treatment of nephrolithiasis and ureterolithiasis in five dogs. 61
8603902 1996
8
[Preventive or therapeutic parathyroidectomy in primary hyperparathyroidism]. 61
1405951 1992
9
Idiopathic calcium nephrolithiasis. 1. Differences in urine crystalloids, urine saturation with brushite and urine inhibitors of calcification between persons with and persons without recurrent kidney stone formation. 61
436047 1979
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Variations for X-Linked Nephrolithiasis Type I

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Expression for X-Linked Nephrolithiasis Type I

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Search GEO for disease gene expression data for X-Linked Nephrolithiasis Type I.
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Pathways for X-Linked Nephrolithiasis Type I

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Pathways related to X-Linked Nephrolithiasis Type I according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1
Gene Expression 65
Show member pathways
 13.62 XRN2 XRN1 WDR61 SKIV2L PARN MTREX
2
Metabolism of proteins 65
Show member pathways
 13.61 XRN2 WDR61 SKIV2L PARN EXOSC9 EXOSC8
3
rRNA processing in the nucleus and cytosol 65
Show member pathways
 12.87 XRN2 MTREX EXOSC9 EXOSC8 EXOSC7 EXOSC6
4
Unfolded Protein Response (UPR) 65
Show member pathways
 12.34 PARN EXOSC9 EXOSC8 EXOSC7 EXOSC6 EXOSC5
5
Deadenylation-dependent mRNA decay 65
Show member pathways
 11.81 XRN2 XRN1 WDR61 SKIV2L PARN MTREX
6
ATP/ITP metabolism 23
11.69 EXOSC9 EXOSC8 EXOSC7 EXOSC6 EXOSC5 EXOSC10
7
PERK regulates gene expression 65
Show member pathways
 11.36 PARN EXOSC9 EXOSC8 EXOSC7 EXOSC6 EXOSC5
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GO Terms for X-Linked Nephrolithiasis Type I

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Cellular components related to X-Linked Nephrolithiasis Type I according to GeneCards Suite gene sharing:

(show all 11)
# Name GO ID Score Top Affiliating Genes
1 cytoplasm GO:0005737 10.34 XRN1 WDR61 SKIV2L PARN LSM1 EXOSC9
2 cytosol GO:0005829 10.28 XRN1 WDR61 SKIV2L PARN LSM1 EXOSC9
3 nucleus GO:0005634 10.28 XRN2 XRN1 WDR61 SKIV2L PARN MTREX
4 nucleoplasm GO:0005654 10.21 XRN2 WDR61 MTREX EXOSC9 EXOSC8 EXOSC7
5 nucleolus GO:0005730 10.03 XRN2 PARN MTREX EXOSC9 EXOSC8 EXOSC7
6 P-body GO:0000932 9.76 XRN1 LSM1 DIS3L2 DCP2
7 transcriptionally active chromatin GO:0035327 9.65 WDR61 EXOSC5 EXOSC10
8 cytoplasmic exosome (RNase complex) GO:0000177 9.63 EXOSC9 EXOSC8 EXOSC7 EXOSC6 EXOSC5 DIS3
9 nuclear exosome (RNase complex) GO:0000176 9.61 MTREX EXOSC9 EXOSC8 EXOSC7 EXOSC6 EXOSC5
10 Ski complex GO:0055087 9.49 WDR61 SKIV2L
11 exosome (RNase complex) GO:0000178 9.32 MTREX EXOSC9 EXOSC8 EXOSC7 EXOSC6 EXOSC5

Biological processes related to X-Linked Nephrolithiasis Type I according to GeneCards Suite gene sharing:

(show all 30)
# Name GO ID Score Top Affiliating Genes
1 RNA processing GO:0006396 10.04 XRN2 EXOSC9 EXOSC8 EXOSC10 EXOSC1
2 nucleic acid phosphodiester bond hydrolysis GO:0090305 10.03 XRN1 PARN ERI1 DXO DIS3L2 DIS3
3 RNA catabolic process GO:0006401 9.93 XRN2 SKIV2L MTREX EXOSC8 EXOSC7 EXOSC5
4 nuclear mRNA surveillance GO:0071028 9.92 XRN1 EXOSC9 EXOSC8 EXOSC7 EXOSC6 EXOSC5
5 histone mRNA catabolic process GO:0071044 9.91 XRN1 LSM1 EXOSC10 ERI1 DCP2
6 nuclear-transcribed mRNA catabolic process GO:0000956 9.91 XRN2 XRN1 LSM1 EXOSC9 EXOSC10 DXO
7 rRNA catabolic process GO:0016075 9.91 XRN1 EXOSC9 EXOSC8 EXOSC7 EXOSC6 EXOSC5
8 RNA phosphodiester bond hydrolysis, exonucleolytic GO:0090503 9.91 XRN2 XRN1 PARN EXOSC6 EXOSC5 EXOSC1
9 mRNA catabolic process GO:0006402 9.9 PARN DXO DIS3L2 DCP2
10 exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) GO:0000467 9.89 EXOSC9 EXOSC8 EXOSC7 EXOSC10 ERI1
11 U4 snRNA 3'-end processing GO:0034475 9.88 EXOSC9 EXOSC8 EXOSC7 EXOSC6 EXOSC5
12 nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' GO:0034427 9.88 EXOSC9 EXOSC8 EXOSC7 EXOSC6 EXOSC5 DIS3L2
13 polyadenylation-dependent snoRNA 3'-end processing GO:0071051 9.85 PARN EXOSC6 EXOSC5 EXOSC10
14 regulation of mRNA stability GO:0043488 9.85 XRN1 PARN EXOSC9 EXOSC8 EXOSC7 EXOSC6
15 nuclear polyadenylation-dependent tRNA catabolic process GO:0071038 9.84 EXOSC9 EXOSC8 EXOSC7 EXOSC10
16 nuclear polyadenylation-dependent rRNA catabolic process GO:0071035 9.83 EXOSC9 EXOSC8 EXOSC7 EXOSC10
17 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay GO:0000184 9.82 PARN EXOSC10 DCP2
18 negative regulation of telomere maintenance via telomerase GO:0032211 9.78 XRN1 EXOSC10 DCP2
19 regulation of telomerase RNA localization to Cajal body GO:1904872 9.77 PARN EXOSC10 DCP2
20 nuclear polyadenylation-dependent mRNA catabolic process GO:0071042 9.76 EXOSC9 EXOSC8 EXOSC7
21 U5 snRNA 3'-end processing GO:0034476 9.75 EXOSC9 EXOSC8 EXOSC7
22 U1 snRNA 3'-end processing GO:0034473 9.74 EXOSC9 EXOSC8 EXOSC7
23 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay GO:0043928 9.7 WDR61 SKIV2L LSM1 EXOSC9 EXOSC8 EXOSC7
24 maturation of 5.8S rRNA GO:0000460 9.64 MTREX EXOSC10
25 deadenylation-dependent decapping of nuclear-transcribed mRNA GO:0000290 9.63 LSM1 DCP2
26 DNA catabolic process, exonucleolytic GO:0000738 9.63 XRN2 ERI1
27 miRNA catabolic process GO:0010587 9.62 PARN DIS3L2
28 CUT catabolic process GO:0071034 9.62 EXOSC10 DIS3
29 DNA deamination GO:0045006 9.61 EXOSC6 EXOSC5
30 rRNA processing GO:0006364 9.36 XRN2 MTREX EXOSC9 EXOSC8 EXOSC7 EXOSC6

Molecular functions related to X-Linked Nephrolithiasis Type I according to GeneCards Suite gene sharing:

(show all 13)
# Name GO ID Score Top Affiliating Genes
1 hydrolase activity GO:0016787 10.17 XRN2 XRN1 SKIV2L PARN MTREX EXOSC10
2 nucleic acid binding GO:0003676 10.04 XRN2 XRN1 SKIV2L PARN MTREX EXOSC10
3 nuclease activity GO:0004518 9.92 XRN2 XRN1 PARN EXOSC10 ERI1 DXO
4 exoribonuclease activity GO:0004532 9.8 EXOSC9 EXOSC8 EXOSC7 EXOSC6 EXOSC5 EXOSC10
5 exonuclease activity GO:0004527 9.76 XRN2 XRN1 PARN EXOSC10 ERI1 DXO
6 telomerase RNA binding GO:0070034 9.71 XRN1 PARN EXOSC10 DCP2
7 mRNA 3'-UTR AU-rich region binding GO:0035925 9.65 EXOSC9 EXOSC8 EXOSC7
8 5'-3' exonuclease activity GO:0008409 9.63 XRN2 XRN1 DXO
9 3'-5'-exoribonuclease activity GO:0000175 9.61 XRN2 PARN EXOSC9 EXOSC7 EXOSC5 EXOSC10
10 RNA binding GO:0003723 9.58 XRN2 XRN1 SKIV2L PARN MTREX LSM1
11 5'-3' exoribonuclease activity GO:0004534 9.54 XRN2 XRN1 DCP2
12 ribonuclease activity GO:0004540 9.52 DIS3L2 DIS3
13 3'-5' exonuclease activity GO:0008408 9.51 EXOSC10 ERI1
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Sources for X-Linked Nephrolithiasis Type I

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3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
19 FMA
20 GARD
28 GO
29 GTR
30 HMDB
31 HPO
32 ICD10
33 ICD10 via Orphanet
34 ICD9CM
35 IUPHAR
36 KEGG
37 LifeMap
39 LOVD
41 MedGen
44 MeSH
45 MESH via Orphanet
46 MGI
49 NCI
50 NCIt
51 NDF-RT
53 NINDS
54 Novoseek
56 OMIM via Orphanet
57 OMIM® (Updated 05-Mar-2021)
61 PubMed
63 QIAGEN
68 SNOMED-CT via HPO
69 TGDB
70 Tocris
71 UMLS
72 UMLS via Orphanet
The MalaCards human disease database index: 1-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
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