NPHP13
MCID: NPH065
MIFTS: 40

Nephronophthisis 13 (NPHP13)

Categories: Genetic diseases, Liver diseases, Nephrological diseases, Neuronal diseases, Rare diseases

Aliases & Classifications for Nephronophthisis 13

MalaCards integrated aliases for Nephronophthisis 13:

Name: Nephronophthisis 13 57 12 72 29 13 6 15 70
Nphp13 57 12 72
Nephronophthisis, Type 13 39

Characteristics:

OMIM®:

57 (Updated 20-May-2021)
Inheritance:
autosomal recessive


HPO:

31
nephronophthisis 13:
Inheritance autosomal recessive inheritance


Classifications:



External Ids:

Disease Ontology 12 DOID:0111121
OMIM® 57 614377
OMIM Phenotypic Series 57 PS256100
MeSH 44 D052177
MedGen 41 C3280612
UMLS 70 C3280612

Summaries for Nephronophthisis 13

UniProtKB/Swiss-Prot : 72 Nephronophthisis 13: An autosomal recessive disorder resulting in end-stage renal disease. It is a progressive tubulo-interstitial kidney disorder histologically characterized by modifications of the tubules with thickening of the basement membrane, interstitial fibrosis and, in the advanced stages, medullary cysts.

MalaCards based summary : Nephronophthisis 13, also known as nphp13, is related to ciliopathy and short-rib thoracic dysplasia 1 with or without polydactyly. An important gene associated with Nephronophthisis 13 is WDR19 (WD Repeat Domain 19), and among its related pathways/superpathways are Regulation of PLK1 Activity at G2/M Transition and Organelle biogenesis and maintenance. Affiliated tissues include liver, kidney and eye, and related phenotypes are pancreatic cysts and retinal dystrophy

Disease Ontology : 12 A nephronophthisis that has material basis in homozygous or compound heterozygous mutation in the WDR19 gene on chromosome 4p14.

More information from OMIM: 614377 PS256100

Related Diseases for Nephronophthisis 13

Diseases in the Nephronophthisis family:

Nephronophthisis 1 Nephronophthisis 2
Nephronophthisis 3 Nephronophthisis 4
Nephronophthisis 7 Nephronophthisis 11
Nephronophthisis 12 Nephronophthisis 9
Nephronophthisis 13 Nephronophthisis 14
Nephronophthisis 15 Nephronophthisis 16
Nephronophthisis 18 Nephronophthisis 19
Nephronophthisis 20 Infantile Nephronophthisis
Juvenile Nephronophthisis Late-Onset Nephronophthisis

Diseases related to Nephronophthisis 13 via text searches within MalaCards or GeneCards Suite gene sharing:

(show top 50) (show all 77)
# Related Disease Score Top Affiliating Genes
1 ciliopathy 29.9 TTC21B SDCCAG8 NPHP4
2 short-rib thoracic dysplasia 1 with or without polydactyly 29.5 WDR19 TTC21B NPHP1 INVS
3 caroli disease 29.1 WDR19 NPHP3 NPHP1 INVS
4 nephronophthisis 26.7 WDR19 TTC21B SDCCAG8 NPHP4 NPHP3 NPHP1
5 senior-loken syndrome 1 26.7 WDR19 TTC21B SDCCAG8 NPHP4 NPHP3 NPHP1
6 short-rib thoracic dysplasia 7 with or without polydactyly 10.2 WDR19 TTC21B
7 short-rib thoracic dysplasia 4 with or without polydactyly 10.2 WDR19 TTC21B
8 short-rib thoracic dysplasia 2 with or without polydactyly 10.2 WDR19 TTC21B
9 cone-rod dystrophy 13 10.2 NPHP4 IQCB1
10 joubert syndrome 13 10.2 TTC21B NPHP1
11 cogan syndrome 10.1 NPHP4 NPHP1
12 leber congenital amaurosis 3 10.1 NPHP4 IQCB1
13 short-rib thoracic dysplasia 12 10.1 WDR19 TTC21B
14 joubert syndrome 15 10.1 NPHP4 NPHP1
15 meckel syndrome, type 2 10.1 NPHP4 NPHP1
16 nephronophthisis 4 10.1 NPHP4 NPHP1
17 bardet-biedl syndrome 14 10.1 SDCCAG8 IQCB1
18 joubert syndrome 5 10.1 NPHP1 IQCB1
19 meckel syndrome, type 5 10.1 NPHP4 NPHP1
20 polydactyly 10.1 WDR19 TTC21B SDCCAG8
21 short-rib thoracic dysplasia 9 with or without polydactyly 10.1 WDR19 TTC21B
22 tubulointerstitial kidney disease, autosomal dominant, 1 10.1 NPHP4 NPHP1
23 joubert syndrome 24 10.1 NPHP1 CEP164
24 polycystic liver disease 1 with or without kidney cysts 10.0 NPHP4 NPHP1
25 bardet-biedl syndrome 6 10.0 SDCCAG8 INVS
26 weyers acrofacial dysostosis 10.0 WDR19 TTC21B
27 ellis-van creveld syndrome 10.0 WDR19 TTC21B INVS
28 bardet-biedl syndrome 1 10.0 SDCCAG8 NPHP4 NPHP1
29 caroli disease, isolated 9.9
30 short-rib thoracic dysplasia 5 with or without polydactyly 9.9
31 senior-loken syndrome 8 9.9
32 joubert syndrome 8 9.9 NPHP3 NPHP1
33 right atrial isomerism 9.8 NEK8 INVS
34 joubert syndrome 4 9.8 TTC21B NPHP4 NPHP1 IQCB1
35 end stage renal disease 9.7 NPHP4 NEK8 INVS
36 retinal aplasia 9.7 TTC21B SDCCAG8 NPHP4 NPHP1 IQCB1
37 eye disease 9.6 WDR19 SDCCAG8 NPHP4 NPHP1 IQCB1
38 nephronophthisis 3 9.6 NPHP3 NPHP1
39 interstitial nephritis 9.6 INVS CEP164
40 polycystic kidney disease 2 with or without polycystic liver disease 9.5 NPHP4 NEK9 NEK8 INVS
41 nephronophthisis 1 9.5 NPHP4 NPHP3 NPHP1 INVS
42 meckel syndrome, type 3 9.4 NPHP4 NPHP3 NPHP1 INVS
43 alstrom syndrome 9.4 NPHP3 NEK9 IQCB1 INVS
44 cranioectodermal dysplasia 9.4 WDR19 TTC21B NPHP4 NPHP1 IQCB1 INVS
45 coloboma of macula 9.4 TTC21B NPHP4 NPHP3 NPHP1 IQCB1
46 nephronophthisis 19 9.3 NPHP4 NPHP3 NPHP1 IQCB1 INVS
47 meckel syndrome, type 4 9.3 NPHP4 NPHP3 NPHP1 IQCB1 CEP164
48 retinal degeneration 9.2 TTC21B NPHP4 NPHP3 NPHP1 CEP164
49 kidney disease 9.2 TTC21B NPHP4 NPHP3 NPHP1 NEK8
50 coach syndrome 1 9.2 TTC21B SDCCAG8 NPHP4 NPHP3 NPHP1 IQCB1

Graphical network of the top 20 diseases related to Nephronophthisis 13:



Diseases related to Nephronophthisis 13

Symptoms & Phenotypes for Nephronophthisis 13

Human phenotypes related to Nephronophthisis 13:

31 (show all 8)
# Description HPO Frequency HPO Source Accession
1 pancreatic cysts 31 occasional (7.5%) HP:0001737
2 retinal dystrophy 31 occasional (7.5%) HP:0000556
3 polydactyly 31 occasional (7.5%) HP:0010442
4 hepatic cysts 31 occasional (7.5%) HP:0001407
5 mild proteinuria 31 occasional (7.5%) HP:0012595
6 renal hypoplasia 31 HP:0000089
7 nephronophthisis 31 HP:0000090
8 stage 5 chronic kidney disease 31 HP:0003774

Symptoms via clinical synopsis from OMIM®:

57 (Updated 20-May-2021)
Genitourinary Kidneys:
small kidneys
interstitial fibrosis
renal failure, endstage
mild proteinuria (in some patients)
sclerotic glomeruli, 50% to 75%

Head And Neck Eyes:
retinal dystrophy (in some patients)

Abdomen Pancreas:
pancreatic cysts (in some patients)

Skeletal Hands:
polydactyly (in some patients)

Abdomen Liver:
hepatic cysts (in some patients)
dilatation of the intrahepatic bile ducts (in some patients)

Clinical features from OMIM®:

614377 (Updated 20-May-2021)

MGI Mouse Phenotypes related to Nephronophthisis 13:

46
# Description MGI Source Accession Score Top Affiliating Genes
1 mortality/aging MP:0010768 9.61 CEP164 INVS IQCB1 NEK8 NEK9 NPHP3
2 renal/urinary system MP:0005367 9.17 INVS NEK8 NPHP1 NPHP3 NPHP4 SDCCAG8

Drugs & Therapeutics for Nephronophthisis 13

Search Clinical Trials , NIH Clinical Center for Nephronophthisis 13

Genetic Tests for Nephronophthisis 13

Genetic tests related to Nephronophthisis 13:

# Genetic test Affiliating Genes
1 Nephronophthisis 13 29 WDR19

Anatomical Context for Nephronophthisis 13

MalaCards organs/tissues related to Nephronophthisis 13:

40
Liver, Kidney, Eye

Publications for Nephronophthisis 13

Articles related to Nephronophthisis 13:

# Title Authors PMID Year
1
Identification of 99 novel mutations in a worldwide cohort of 1,056 patients with a nephronophthisis-related ciliopathy. 61 57 6
23559409 2013
2
Ciliopathies with skeletal anomalies and renal insufficiency due to mutations in the IFT-A gene WDR19. 6 57
22019273 2011
3
Nephronophthisis 13: implications of its association with Caroli disease and altered intracellular localization of WDR19 in the kidney. 61 6
25726036 2015
4
Clinical utility of genetic testing in early-onset kidney disease: seven genes are the main players. 6
33532864 2021
5
Next-generation sequencing-based molecular diagnosis of 35 Hispanic retinitis pigmentosa probands. 6
27596865 2016
6
WDR19: an ancient, retrograde, intraflagellar ciliary protein is mutated in autosomal recessive retinitis pigmentosa and in Senior-Loken syndrome. 6
23683095 2013
7
Hepatorenal fibrocystic diseases in children. 61
26260382 2016

Variations for Nephronophthisis 13

ClinVar genetic disease variations for Nephronophthisis 13:

6 (show all 14)
# Gene Name Type Significance ClinVarId dbSNP ID Position
1 WDR19 NM_025132.4(WDR19):c.1034T>G (p.Val345Gly) SNV Pathogenic 30706 rs387906983 GRCh37: 4:39217533-39217533
GRCh38: 4:39215913-39215913
2 WDR19 NM_025132.4(WDR19):c.3068dup (p.Tyr1023Ter) Duplication Pathogenic 30707 rs786205114 GRCh37: 4:39257533-39257534
GRCh38: 4:39255913-39255914
3 WDR19 NM_025132.4(WDR19):c.682C>T (p.Gln228Ter) SNV Pathogenic 127156 rs587777350 GRCh37: 4:39206852-39206852
GRCh38: 4:39205232-39205232
4 WDR19 NM_025132.4(WDR19):c.3703G>A (p.Glu1235Lys) SNV Pathogenic 127157 rs587777351 GRCh37: 4:39276565-39276565
GRCh38: 4:39274945-39274945
5 WDR19 GRCh37/hg19 4p14(chr4:39215680-39219295) copy number loss Pathogenic 625691 GRCh37: 4:39215680-39219295
GRCh38:
6 WDR19 NM_025132.4(WDR19):c.781dup (p.Thr261fs) Duplication Pathogenic 446634 rs748656635 GRCh37: 4:39207246-39207247
GRCh38: 4:39205626-39205627
7 WDR19 NM_025132.4(WDR19):c.3533G>A (p.Arg1178Gln) SNV Pathogenic 127158 rs79436363 GRCh37: 4:39274649-39274649
GRCh38: 4:39273029-39273029
8 WDR19 NM_025132.4(WDR19):c.2333C>G (p.Ser778Ter) SNV Pathogenic 974370 GRCh37: 4:39236465-39236465
GRCh38: 4:39234845-39234845
9 WDR19 NM_025132.4(WDR19):c.3565+1G>A SNV Pathogenic 127159 rs587777352 GRCh37: 4:39274682-39274682
GRCh38: 4:39273062-39273062
10 WDR19 NM_025132.4(WDR19):c.3112C>T (p.Arg1038Ter) SNV Pathogenic 632440 rs748174246 GRCh37: 4:39257578-39257578
GRCh38: 4:39255958-39255958
11 WDR19 NM_025132.4(WDR19):c.3184-2A>C SNV Pathogenic 1034087 GRCh37: 4:39267681-39267681
GRCh38: 4:39266061-39266061
12 WDR19 NM_025132.4(WDR19):c.1559T>C (p.Ile520Thr) SNV Likely pathogenic 917968 GRCh37: 4:39226583-39226583
GRCh38: 4:39224963-39224963
13 WDR19 NM_025132.4(WDR19):c.1442A>G (p.His481Arg) SNV Likely pathogenic 974369 GRCh37: 4:39219688-39219688
GRCh38: 4:39218068-39218068
14 WDR19 NM_025132.4(WDR19):c.1477G>C (p.Asp493His) SNV Likely pathogenic 127155 rs587777349 GRCh37: 4:39219723-39219723
GRCh38: 4:39218103-39218103

UniProtKB/Swiss-Prot genetic disease variations for Nephronophthisis 13:

72
# Symbol AA change Variation ID SNP ID
1 WDR19 p.Val345Gly VAR_067313 rs387906983

Expression for Nephronophthisis 13

Search GEO for disease gene expression data for Nephronophthisis 13.

Pathways for Nephronophthisis 13

GO Terms for Nephronophthisis 13

Cellular components related to Nephronophthisis 13 according to GeneCards Suite gene sharing:

(show all 14)
# Name GO ID Score Top Affiliating Genes
1 cytoplasm GO:0005737 10.13 WDR19 TTC21B SDCCAG8 NPHP4 NPHP1 NEK9
2 centrosome GO:0005813 9.8 SDCCAG8 NPHP4 NEK9 NEK8 IQCB1 CEP164
3 microtubule organizing center GO:0005815 9.76 SDCCAG8 NPHP4 NEK8 IQCB1
4 cell projection GO:0042995 9.76 WDR19 TTC21B SDCCAG8 NPHP4 NPHP3 NPHP1
5 cell-cell junction GO:0005911 9.67 SDCCAG8 NPHP4 NPHP1
6 centriole GO:0005814 9.65 SDCCAG8 IQCB1 CEP164
7 cytoskeleton GO:0005856 9.61 WDR19 TTC21B SDCCAG8 NPHP4 NPHP1 NEK8
8 photoreceptor connecting cilium GO:0032391 9.56 WDR19 NPHP4 NPHP1 IQCB1
9 ciliary tip GO:0097542 9.54 WDR19 TTC21B
10 ciliary base GO:0097546 9.52 NPHP4 NEK8
11 non-motile cilium GO:0097730 9.51 WDR19 NPHP4
12 intraciliary transport particle A GO:0030991 9.4 WDR19 TTC21B
13 ciliary inversin compartment GO:0097543 9.37 NEK8 INVS
14 cilium GO:0005929 9.23 WDR19 TTC21B NPHP4 NPHP3 NPHP1 NEK8

Biological processes related to Nephronophthisis 13 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 negative regulation of canonical Wnt signaling pathway GO:0090090 9.63 NPHP4 NPHP3 INVS
2 cilium assembly GO:0060271 9.56 WDR19 NPHP3 IQCB1 CEP164
3 intraciliary transport involved in cilium assembly GO:0035735 9.48 WDR19 TTC21B
4 intraciliary retrograde transport GO:0035721 9.43 WDR19 TTC21B
5 positive regulation of bicellular tight junction assembly GO:1903348 9.4 NPHP4 NPHP1
6 maintenance of animal organ identity GO:0048496 9.37 NPHP3 IQCB1
7 cell projection organization GO:0030030 9.35 WDR19 SDCCAG8 NPHP1 IQCB1 CEP164
8 photoreceptor cell maintenance GO:0045494 9.33 NPHP4 NPHP3 IQCB1
9 visual behavior GO:0007632 9.32 NPHP4 NPHP1
10 ciliary basal body-plasma membrane docking GO:0097711 9.02 SDCCAG8 NPHP4 NPHP1 IQCB1 CEP164

Sources for Nephronophthisis 13

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 20-May-2021)
61 PubMed
63 QIAGEN
68 SNOMED-CT via HPO
69 Tocris
70 UMLS
71 UMLS via Orphanet
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