NPHP19
MCID: NPH077
MIFTS: 38

Nephronophthisis 19 (NPHP19)

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

Aliases & Classifications for Nephronophthisis 19

MalaCards integrated aliases for Nephronophthisis 19:

Name: Nephronophthisis 19 56 12 73 29 6 15 71
Nphp19 56 12 73
Nephronophthisis, Type 19 39

Characteristics:

OMIM:

56
Inheritance:
autosomal recessive

Miscellaneous:
two unrelated patients have been reported (last curated february 2015)
onset of liver involvement in infancy


HPO:

31
nephronophthisis 19:
Inheritance autosomal recessive inheritance


Classifications:



External Ids:

Disease Ontology 12 DOID:0111126
OMIM 56 616217
OMIM Phenotypic Series 56 PS256100
MeSH 43 D052177
UMLS 71 C4015542

Summaries for Nephronophthisis 19

UniProtKB/Swiss-Prot : 73 Nephronophthisis 19: A form of nephronophthisis, an autosomal recessive disorder characterized by chronic tubulointerstitial nephritis resulting in end-stage renal disease. NPHP19 patients also manifest hepatosplenomegaly, hepatic fibrosis, destruction of the bile ducts, focal bile ductal proliferation, ductal plate malformation, and cholestasis.

MalaCards based summary : Nephronophthisis 19, also known as nphp19, is related to sclerosing cholangitis, neonatal and deafness, autosomal recessive 66. An important gene associated with Nephronophthisis 19 is DCDC2 (Doublecortin Domain Containing 2), and among its related pathways/superpathways are Regulation of PLK1 Activity at G2/M Transition and Organelle biogenesis and maintenance. Affiliated tissues include kidney and liver, and related phenotypes are splenomegaly and hepatomegaly

Disease Ontology : 12 A nephronophthisis that has material basis in homozygous or compound heterozygous mutation in the DCDC2 gene on chromosome 6p22.

More information from OMIM: 616217 PS256100

Related Diseases for Nephronophthisis 19

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 19 via text searches within MalaCards or GeneCards Suite gene sharing:

(show top 50) (show all 90)
# Related Disease Score Top Affiliating Genes
1 sclerosing cholangitis, neonatal 10.3 KAAG1 DCDC2
2 deafness, autosomal recessive 66 10.3 KAAG1 DCDC2
3 senior-boichis syndrome 10.3 TMEM67 DCDC2
4 late-onset nephronophthisis 10.2 XPNPEP3 NPHP3
5 nephronophthisis-like nephropathy 1 10.2 XPNPEP3 NPHP1
6 cone-rod dystrophy 1 10.1 RPGR NPHP4
7 nephronophthisis 4 10.1 NPHP4 NPHP1
8 hyperuricemic nephropathy, familial juvenile, 1 10.1 NPHP4 NPHP1
9 renal dysplasia, cystic 10.1 NPHP3 CEP290
10 encephalocele 10.1 TMEM67 CEP290
11 leber congenital amaurosis 3 10.0 NPHP4 CEP290
12 caroli disease 10.0 NPHP3 INVS
13 joubert syndrome 15 10.0 RPGRIP1L NPHP4 NPHP1
14 oculomotor apraxia 10.0 NPHP1 AHI1
15 meckel syndrome, type 8 10.0 TMEM67 RPGRIP1L NPHP3
16 retinal ciliopathy 9.9 RPGR CEP290
17 congenital hepatic fibrosis 9.9 TMEM67 RPGRIP1L AHI1
18 retinal aplasia 9.9 NPHP4 NPHP1 CEP290
19 ciliopathy 9.9 TMEM67 RPGRIP1L NPHP4
20 orofaciodigital syndrome 9.9 TMEM67 NPHP1 CEP290
21 leber congenital amaurosis 10 9.9 RPGR CEP290
22 polycystic kidney disease 9.9 TMEM67 NPHP3 INVS
23 yemenite deaf-blind hypopigmentation syndrome 9.9 RPGR CEP290
24 retinitis pigmentosa 2 9.9 RPGR CEP290
25 infantile nephronophthisis 9.9 NPHP4 NPHP3 INVS
26 retinitis pigmentosa 28 9.8 RPGR CEP290
27 cone-rod dystrophy 13 9.8 RPGRIP1L RPGR NPHP4
28 asphyxiating thoracic dystrophy 9.8 RPGRIP1L NPHP4 CEP290
29 end stage renal disease 9.8 NPHP4 NPHP3 INVS
30 polycystic liver disease 1 with or without kidney cysts 9.8 NPHP4 NPHP1
31 choroid disease 9.8 RPGR CEP290
32 polycystic kidney disease 2 with or without polycystic liver disease 9.8 TMEM67 NPHP4 INVS
33 leber congenital amaurosis 2 9.7 RPGR CEP290
34 joubert syndrome 10 9.7 TMEM67 RPGRIP1L NPHP1 AHI1
35 johanson-blizzard syndrome 9.7 RPGRIP1L CEP290
36 cogan syndrome 9.7 NPHP4 NPHP1 CEP290 AHI1
37 nephronophthisis 18 9.7 NPHP4 NPHP3 NPHP1 INVS
38 joubert syndrome 24 9.6 RPGRIP1L NPHP1 CEP290 AHI1
39 bardet-biedl syndrome 14 9.6 TMEM67 RPGRIP1L NPHP3 CEP290
40 bardet-biedl syndrome 6 9.6 RPGRIP1L INVS CEP290
41 nephronophthisis 1 9.5 NPHP4 NPHP3 NPHP1 INVS AHI1
42 kidney disease 9.4 TMEM67 NPHP4 NPHP1 CEP290 AHI1
43 pathologic nystagmus 9.4 TMEM67 RPGR CEP290 AHI1
44 eye disease 9.4 RPGR NPHP4 NPHP1 CEP290
45 meckel syndrome, type 4 9.4 TMEM67 RPGRIP1L NPHP3 NPHP1 CEP290
46 meckel syndrome, type 2 9.4 TMEM67 RPGRIP1L NPHP4 NPHP1 CEP290
47 joubert syndrome 6 9.4 TMEM67 RPGRIP1L NPHP1 CEP290 AHI1
48 meckel syndrome, type 5 9.4 TMEM67 RPGRIP1L NPHP4 NPHP1 CEP290
49 joubert syndrome 9 9.4 TMEM67 RPGRIP1L NPHP1 CEP290 AHI1
50 joubert syndrome 7 9.4 TMEM67 RPGRIP1L NPHP1 CEP290 AHI1

Graphical network of the top 20 diseases related to Nephronophthisis 19:



Diseases related to Nephronophthisis 19

Symptoms & Phenotypes for Nephronophthisis 19

Human phenotypes related to Nephronophthisis 19:

31 (show all 7)
# Description HPO Frequency HPO Source Accession
1 splenomegaly 31 HP:0001744
2 hepatomegaly 31 HP:0002240
3 hepatic fibrosis 31 HP:0001395
4 cholestasis 31 HP:0001396
5 nephronophthisis 31 HP:0000090
6 stage 5 chronic kidney disease 31 HP:0003774
7 bile duct proliferation 31 HP:0001408

Symptoms via clinical synopsis from OMIM:

56
Abdomen Spleen:
splenomegaly

Genitourinary Kidneys:
nephronophthisis (1 of 2 patients)
increased echogenicity (1 of 2 patients)
tubular dilation (1 of 2 patients)
prominent epithelial luminal budding (1 of 2 patients)
end-stage renal disease (1 of 2 patients)

Abdomen Liver:
hepatomegaly
hepatic fibrosis
cholestasis
bile duct proliferation
destruction of bile ducts

Clinical features from OMIM:

616217

MGI Mouse Phenotypes related to Nephronophthisis 19:

45
# Description MGI Source Accession Score Top Affiliating Genes
1 cellular MP:0005384 9.81 AHI1 CEP290 GLIS2 INVS NPHP1 NPHP3
2 nervous system MP:0003631 9.61 AHI1 CEP290 DCDC2 NPHP1 NPHP3 NPHP4
3 renal/urinary system MP:0005367 9.28 AHI1 CEP290 GLIS2 INVS NPHP1 NPHP3

Drugs & Therapeutics for Nephronophthisis 19

Search Clinical Trials , NIH Clinical Center for Nephronophthisis 19

Genetic Tests for Nephronophthisis 19

Genetic tests related to Nephronophthisis 19:

# Genetic test Affiliating Genes
1 Nephronophthisis 19 29 DCDC2

Anatomical Context for Nephronophthisis 19

MalaCards organs/tissues related to Nephronophthisis 19:

40
Kidney, Liver

Publications for Nephronophthisis 19

Articles related to Nephronophthisis 19:

# Title Authors PMID Year
1
DCDC2 mutations cause a renal-hepatic ciliopathy by disrupting Wnt signaling. 6 56
25557784 2015
2
Mutations in DCDC2 (doublecortin domain containing protein 2) in neonatal sclerosing cholangitis. 6
27469900 2016
3
Nephronophthisis 6
27336129 2016
4
Nephronophthisis due to a novel DCDC2 variant in a patient from African-Caribbean descent: A case report. 61
31821705 2020

Variations for Nephronophthisis 19

ClinVar genetic disease variations for Nephronophthisis 19:

6 ‎‎ ‎‎ ‎‎ ‎‎ ‎‎
# Gene Name Type Significance ClinVarId dbSNP ID GRCh37 Pos GRCh38 Pos
1 DCDC2 NM_016356.5(DCDC2):c.649A>T (p.Lys217Ter)SNV Pathogenic 180687 rs730880299 6:24291215-24291215 6:24290987-24290987
2 DCDC2 NM_016356.5(DCDC2):c.121_122GT[1] (p.Ser42fs)short repeat Pathogenic 180688 rs757704417 6:24357855-24357856 6:24357627-24357628
3 DCDC2 NM_016356.5(DCDC2):c.349-2A>GSNV Pathogenic 180689 rs760040426 6:24302274-24302274 6:24302046-24302046
4 DCDC2 NM_016356.5(DCDC2):c.549dup (p.Val184fs)duplication Likely pathogenic 804454 6:24301950-24301951 6:24301722-24301723
5 DCDC2 NM_016356.5(DCDC2):c.769C>T (p.Arg257Cys)SNV Uncertain significance 523063 rs909339162 6:24278430-24278430 6:24278202-24278202

Expression for Nephronophthisis 19

Search GEO for disease gene expression data for Nephronophthisis 19.

Pathways for Nephronophthisis 19

GO Terms for Nephronophthisis 19

Cellular components related to Nephronophthisis 19 according to GeneCards Suite gene sharing:

(show all 13)
# Name GO ID Score Top Affiliating Genes
1 cytoplasm GO:0005737 10.25 XPNPEP3 TMEM67 RPGRIP1L RPGR NPHP4 NPHP1
2 centrosome GO:0005813 9.91 TMEM67 RPGRIP1L RPGR NPHP4 CEP290 AHI1
3 microtubule organizing center GO:0005815 9.88 RPGRIP1L RPGR NPHP4 DCDC2 CEP290
4 cytoskeleton GO:0005856 9.81 TMEM67 RPGRIP1L RPGR NPHP4 NPHP1 INVS
5 cell-cell junction GO:0005911 9.8 RPGRIP1L NPHP4 NPHP1 AHI1
6 ciliary basal body GO:0036064 9.77 RPGRIP1L RPGR NPHP4 CEP290 AHI1
7 bicellular tight junction GO:0005923 9.7 RPGRIP1L NPHP4 NPHP1
8 cell projection GO:0042995 9.65 TMEM67 RPGRIP1L RPGR NPHP4 NPHP3 NPHP1
9 non-motile cilium GO:0097730 9.63 NPHP4 GLIS2 AHI1
10 photoreceptor connecting cilium GO:0032391 9.62 RPGRIP1L NPHP4 NPHP1 CEP290
11 MKS complex GO:0036038 9.58 TMEM67 CEP290 AHI1
12 ciliary transition zone GO:0035869 9.56 TMEM67 RPGRIP1L NPHP4 CEP290
13 cilium GO:0005929 9.32 TMEM67 RPGRIP1L RPGR NPHP4 NPHP3 NPHP1

Biological processes related to Nephronophthisis 19 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 cell projection organization GO:0030030 9.63 TMEM67 RPGR NPHP1 DCDC2 CEP290 AHI1
3 kidney development GO:0001822 9.58 RPGRIP1L NPHP3 GLIS2
4 photoreceptor cell maintenance GO:0045494 9.48 NPHP4 NPHP3
5 hindbrain development GO:0030902 9.43 CEP290 AHI1
6 ciliary basal body-plasma membrane docking GO:0097711 9.43 TMEM67 RPGRIP1L NPHP4 NPHP1 CEP290 AHI1
7 photoreceptor cell outer segment organization GO:0035845 9.37 NPHP4 AHI1
8 positive regulation of bicellular tight junction assembly GO:1903348 9.32 NPHP4 NPHP1
9 visual behavior GO:0007632 9.26 NPHP4 NPHP1
10 cilium assembly GO:0060271 9.17 TMEM67 RPGRIP1L RPGR NPHP3 DCDC2 CEP290

Sources for Nephronophthisis 19

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
19 FMA
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
43 MeSH
44 MESH via Orphanet
45 MGI
48 NCI
49 NCIt
50 NDF-RT
53 NINDS
54 Novoseek
56 OMIM
57 OMIM via Orphanet
61 PubMed
63 QIAGEN
68 SNOMED-CT via HPO
69 TGDB
70 Tocris
71 UMLS
72 UMLS via Orphanet
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