NPHP19
MCID: NPH077
MIFTS: 40

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 57 12 72 29 6 15 70
Nphp19 57 12 72
Nephronophthisis, Type 19 39

Characteristics:

OMIM®:

57 (Updated 20-May-2021)
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® 57 616217
OMIM Phenotypic Series 57 PS256100
MeSH 44 D052177
UMLS 70 C4015542

Summaries for Nephronophthisis 19

UniProtKB/Swiss-Prot : 72 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 dyslexia 2 and sclerosing cholangitis, neonatal. 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 liver, kidney and eye, 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 113)
# Related Disease Score Top Affiliating Genes
1 dyslexia 2 10.3 KAAG1 DCDC2
2 sclerosing cholangitis, neonatal 10.3 KAAG1 DCDC2
3 deafness, autosomal recessive 66 10.3 KAAG1 DCDC2
4 late-onset nephronophthisis 10.3 XPNPEP3 NPHP3
5 nephronophthisis-like nephropathy 1 10.2 XPNPEP3 NPHP1
6 senior-boichis syndrome 10.2 TMEM67 KAAG1 DCDC2
7 renal dysplasia, cystic 10.2 NPHP3 CEP290
8 nephronophthisis 4 10.2 NPHP4 NPHP1
9 caroli disease 10.2 NPHP3 NPHP1 INVS
10 infantile nephronophthisis 10.2 NPHP4 NPHP3 INVS
11 leber congenital amaurosis 13 10.1 IQCB1 CEP290
12 joubert syndrome 14 10.1 TMEM216 NPHP4
13 ciliary dyskinesia, primary, 9 10.1 NPHP3 IFT88
14 retinitis pigmentosa 34 10.1 RPGR IQCB1
15 simpson-golabi-behmel syndrome, type 2 10.1 IFT88 CEP290
16 leber congenital amaurosis 3 10.1 NPHP4 IQCB1 CEP290
17 leber congenital amaurosis 4 10.0 IQCB1 CEP290
18 orofaciodigital syndrome i 10.0 IFT88 CEP290
19 retinal aplasia 10.0 NPHP4 NPHP1 IQCB1 CEP290
20 tubulointerstitial kidney disease, autosomal dominant, 1 9.9 NPHP4 NPHP1
21 retinal ciliopathy 9.9 RPGR IQCB1 CEP290
22 leber congenital amaurosis 10 9.9 RPGR IQCB1 CEP290
23 usher syndrome type 2 9.9 RPGR NPHP1 CEP290
24 acrocallosal syndrome 9.9 TMEM216 RPGRIP1L NPHP1 AHI1
25 nephronophthisis 13 9.9 NPHP4 NPHP3 NPHP1 IQCB1 INVS
26 nephronophthisis 18 9.9 NPHP4 NPHP3 NPHP1 IQCB1 INVS
27 cone-rod dystrophy 13 9.9 RPGRIP1L RPGR NPHP4 IQCB1
28 choroid disease 9.9 RPGR CEP290
29 joubert syndrome 15 9.9 RPGRIP1L NPHP4 NPHP1 CC2D2A
30 eye degenerative disease 9.9 RPGR IQCB1 CEP290
31 achromatopsia 9.9 RPGR IQCB1 CEP290
32 congenital hepatic fibrosis 9.8 TMEM67 RPGRIP1L CC2D2A AHI1
33 leber congenital amaurosis 6 9.8 MKS1 CEP290
34 leber congenital amaurosis 2 9.8 RPGR CEP290
35 bardet-biedl syndrome 13 9.8 MKS1 CEP290
36 bardet-biedl syndrome 11 9.8 RPGRIP1L MKS1 CEP290
37 joubert syndrome 24 9.8 RPGRIP1L NPHP1 IFT88 CEP290 AHI1
38 orofaciodigital syndrome 9.7 TMEM67 TMEM216 IFT88 CEP290
39 renal-hepatic-pancreatic dysplasia 9.7 NPHP4 NPHP3 NPHP1 IQCB1 INVS CEP290
40 nephronophthisis 15 9.7 NPHP4 NPHP3 NPHP1 IQCB1 INVS GLIS2
41 bardet-biedl syndrome 8 9.7 MKS1 IFT88 CEP290
42 bardet-biedl syndrome 3 9.7 MKS1 IFT88 CEP290
43 ciliopathy 9.6 TMEM67 RPGRIP1L NPHP4 CEP290 CC2D2A
44 apraxia 9.6 TMEM67 NPHP1 CEP290 CC2D2A AHI1
45 johanson-blizzard syndrome 9.6 TMEM216 RPGRIP1L CEP290 CC2D2A
46 arima syndrome 9.6 TMEM216 NPHP4 CEP290 CC2D2A
47 nephronophthisis 12 9.6 RPGRIP1L NPHP4 NPHP3 NPHP1 IQCB1 INVS
48 ellis-van creveld syndrome 9.6 TMEM216 RPGRIP1L INVS IFT88 CEP290
49 cogan syndrome 9.6 RPGRIP1L NPHP4 NPHP1 CEP290 CC2D2A AHI1
50 alstrom syndrome 9.5 RPGRIP1L RPGR NPHP3 IQCB1 INVS CEP290

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®:

57 (Updated 20-May-2021)
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 (Updated 20-May-2021)

MGI Mouse Phenotypes related to Nephronophthisis 19:

46
# Description MGI Source Accession Score Top Affiliating Genes
1 cellular MP:0005384 10.1 AHI1 CC2D2A CEP290 GLIS2 IFT88 INVS
2 cardiovascular system MP:0005385 10.07 CC2D2A CEP290 IFT88 INVS MKS1 NPHP3
3 nervous system MP:0003631 9.93 AHI1 CC2D2A CEP290 DCDC2 IFT88 MKS1
4 craniofacial MP:0005382 9.8 CC2D2A CEP290 IFT88 MKS1 NPHP3 RPGRIP1L
5 renal/urinary system MP:0005367 9.73 AHI1 CC2D2A CEP290 GLIS2 IFT88 INVS
6 vision/eye MP:0005391 9.28 AHI1 CC2D2A CEP290 IFT88 MKS1 NPHP1

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
Liver, Kidney, Eye

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 57
25557784 2015
2
Mutations in DCDC2 (doublecortin domain containing protein 2) in neonatal sclerosing cholangitis. 6
27469900 2016
3
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 Position
1 DCDC2 NM_016356.5(DCDC2):c.649A>T (p.Lys217Ter) SNV Pathogenic 180687 rs730880299 GRCh37: 6:24291215-24291215
GRCh38: 6:24290987-24290987
2 DCDC2 , KAAG1 NM_016356.5(DCDC2):c.121_122GT[1] (p.Ser42fs) Microsatellite Pathogenic 180688 rs757704417 GRCh37: 6:24357855-24357856
GRCh38: 6:24357627-24357628
3 DCDC2 NM_016356.5(DCDC2):c.349-2A>G SNV Pathogenic 180689 rs760040426 GRCh37: 6:24302274-24302274
GRCh38: 6:24302046-24302046
4 DCDC2 NM_016356.5(DCDC2):c.549dup (p.Val184fs) Duplication Likely pathogenic 804454 rs1581640646 GRCh37: 6:24301950-24301951
GRCh38: 6:24301722-24301723
5 DCDC2 , KAAG1 NM_016356.5(DCDC2):c.223_293del (p.Arg75fs) Deletion Likely pathogenic 917935 GRCh37: 6:24357686-24357756
GRCh38: 6:24357458-24357528
6 DCDC2 NM_016356.5(DCDC2):c.769C>T (p.Arg257Cys) SNV Uncertain significance 523063 rs909339162 GRCh37: 6:24278430-24278430
GRCh38: 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 16)
# Name GO ID Score Top Affiliating Genes
1 cytoplasm GO:0005737 10.41 XPNPEP3 TMEM67 TMEM216 RPGRIP1L RPGR NPHP4
2 cytosol GO:0005829 10.31 XPNPEP3 TMEM216 RPGRIP1L NPHP4 NPHP3 NPHP1
3 cytoskeleton GO:0005856 10.17 TMEM67 TMEM216 RPGRIP1L RPGR NPHP4 NPHP1
4 microtubule organizing center GO:0005815 10.06 RPGRIP1L RPGR NPHP4 MKS1 IQCB1 IFT88
5 centrosome GO:0005813 10.06 TMEM67 RPGRIP1L RPGR NPHP4 MKS1 IQCB1
6 ciliary basal body GO:0036064 9.91 RPGRIP1L RPGR NPHP4 MKS1 IFT88 CEP290
7 centriole GO:0005814 9.89 MKS1 IQCB1 IFT88 CEP290 AHI1
8 cell-cell junction GO:0005911 9.83 RPGRIP1L NPHP4 NPHP1 AHI1
9 photoreceptor connecting cilium GO:0032391 9.83 RPGRIP1L NPHP4 NPHP1 IQCB1 CEP290
10 cell projection GO:0042995 9.8 TMEM67 TMEM216 RPGRIP1L RPGR NPHP4 NPHP3
11 non-motile cilium GO:0097730 9.78 NPHP4 IFT88 GLIS2 AHI1
12 motile cilium GO:0031514 9.73 RPGR NPHP1 IFT88
13 MKS complex GO:0036038 9.73 TMEM67 TMEM216 MKS1 CEP290 CC2D2A AHI1
14 bicellular tight junction GO:0005923 9.72 RPGRIP1L NPHP4 NPHP1
15 ciliary transition zone GO:0035869 9.7 TMEM67 TMEM216 RPGRIP1L NPHP4 MKS1 CEP290
16 cilium GO:0005929 9.5 TMEM67 TMEM216 RPGRIP1L RPGR NPHP4 NPHP3

Biological processes related to Nephronophthisis 19 according to GeneCards Suite gene sharing:

(show all 19)
# Name GO ID Score Top Affiliating Genes
1 ciliary basal body-plasma membrane docking GO:0097711 9.85 TMEM67 TMEM216 RPGRIP1L NPHP4 NPHP1 MKS1
2 kidney development GO:0001822 9.72 RPGRIP1L NPHP3 IFT88 GLIS2 CC2D2A
3 cell projection organization GO:0030030 9.7 TMEM67 TMEM216 RPGR NPHP1 MKS1 IQCB1
4 determination of left/right symmetry GO:0007368 9.67 RPGRIP1L NPHP3 MKS1 CC2D2A
5 non-motile cilium assembly GO:1905515 9.65 TMEM216 RPGRIP1L MKS1 IFT88 CC2D2A
6 photoreceptor cell maintenance GO:0045494 9.61 NPHP4 NPHP3 IQCB1
7 motile cilium assembly GO:0044458 9.58 MKS1 CC2D2A
8 inner ear receptor cell stereocilium organization GO:0060122 9.58 MKS1 IFT88
9 regulation of smoothened signaling pathway GO:0008589 9.57 RPGRIP1L MKS1
10 hindbrain development GO:0030902 9.56 CEP290 AHI1
11 head development GO:0060322 9.55 RPGRIP1L MKS1
12 embryonic brain development GO:1990403 9.54 MKS1 CC2D2A
13 photoreceptor cell outer segment organization GO:0035845 9.52 NPHP4 AHI1
14 protein localization to ciliary transition zone GO:1904491 9.51 NPHP4 CC2D2A
15 positive regulation of bicellular tight junction assembly GO:1903348 9.49 NPHP4 NPHP1
16 regulation of Wnt signaling pathway, planar cell polarity pathway GO:2000095 9.48 NPHP3 MKS1
17 maintenance of animal organ identity GO:0048496 9.46 NPHP3 IQCB1
18 visual behavior GO:0007632 9.4 NPHP4 NPHP1
19 cilium assembly GO:0060271 9.4 TMEM67 TMEM216 RPGRIP1L RPGR NPHP3 MKS1

Sources for Nephronophthisis 19

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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