NPHP3
MCID: NPH031
MIFTS: 40

Nephronophthisis 3 (NPHP3)

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

Aliases & Classifications for Nephronophthisis 3

MalaCards integrated aliases for Nephronophthisis 3:

Name: Nephronophthisis 3 58 12 76 13 15 74
Adolescent Nephronophthisis 76 30 6
Nphp3 58 12 76
Nph3 58 12
Nephronophthisis, Type 3 41

Characteristics:

OMIM:

58
Inheritance:
autosomal recessive


HPO:

33
nephronophthisis 3:
Inheritance autosomal recessive inheritance


Classifications:



Summaries for Nephronophthisis 3

UniProtKB/Swiss-Prot : 76 Nephronophthisis 3: An autosomal recessive disorder resulting in end-stage renal disease. It is characterized by polyuria, polydipsia, anemia. Onset of terminal renal failure occurr significantly later (median age, 19 years) than in juvenile nephronophthisis. Renal pathology is characterized by alterations of tubular basement membranes, tubular atrophy and dilation, sclerosing tubulointerstitial nephropathy, and renal cyst development predominantly at the corticomedullary junction.

MalaCards based summary : Nephronophthisis 3, also known as adolescent nephronophthisis, is related to nephronophthisis and nephronophthisis 2, and has symptoms including polydipsia, polyuria and secondary enuresis. An important gene associated with Nephronophthisis 3 is NPHP3 (Nephrocystin 3), and among its related pathways/superpathways are Diurnally Regulated Genes with Circadian Orthologs and Circadian rhythm. Affiliated tissues include kidney, and related phenotypes are renal insufficiency and polydipsia

Disease Ontology : 12 A nephronophthisis that has material basis in homozygous or compound heterozygous mutation in the NPHP3 gene on chromosome 3q22.

Description from OMIM: 604387

Related Diseases for Nephronophthisis 3

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

(show all 33)
# Related Disease Score Top Affiliating Genes
1 nephronophthisis 32.8 DNAJC13 NPHP1 NPHP3
2 nephronophthisis 2 32.3 NPHP1 NPHP3
3 nephronophthisis 1 31.8 NPHP1 NPHP3
4 juvenile nephronophthisis 31.7 NPHP1 NPHP3
5 nephronophthisis 18 31.6 NPHP1 NPHP3
6 nephronophthisis 11 31.6 NPHP1 NPHP3
7 senior-loken syndrome 1 31.6 NPHP1 NPHP3
8 cogan syndrome 31.6 NPHP1 NPHP3
9 nephronophthisis 9 31.5 NPHP1 NPHP3
10 visceral heterotaxy 31.2 NPHP1 NPHP3
11 leber congenital amaurosis 31.2 NPHP1 NPHP3 NRL
12 retinitis pigmentosa 30.7 CUL3 NPHP1 NPHP3 NRL
13 meckel syndrome, type 7 11.9
14 renal-hepatic-pancreatic dysplasia 11.7
15 cystic kidney disease 11.6
16 infantile nephronophthisis 11.5
17 renal-hepatic-pancreatic dysplasia 1 11.3
18 polycystic kidney disease 1 with or without polycystic liver disease 11.2
19 right atrial isomerism 11.1
20 bardet-biedl syndrome 13 11.1
21 bardet-biedl syndrome 14 11.1
22 bardet-biedl syndrome 15 11.1
23 joubert syndrome 1 10.9
24 late-onset nephronophthisis 10.9
25 caroli disease, isolated 10.0
26 polydactyly 10.0
27 caroli disease 10.0
28 kidney disease 10.0
29 situs inversus 10.0
30 retinal degeneration 10.0
31 renal dysplasia diffuse cystic 10.0
32 renal dysplasia 10.0
33 polycystic kidney disease 9.9

Graphical network of the top 20 diseases related to Nephronophthisis 3:



Diseases related to Nephronophthisis 3

Symptoms & Phenotypes for Nephronophthisis 3

Human phenotypes related to Nephronophthisis 3:

33 (show all 9)
# Description HPO Frequency HPO Source Accession
1 renal insufficiency 33 HP:0000083
2 polydipsia 33 HP:0001959
3 hepatic fibrosis 33 HP:0001395
4 nephronophthisis 33 HP:0000090
5 tubular atrophy 33 HP:0000092
6 tubulointerstitial fibrosis 33 HP:0005576
7 enuresis 33 HP:0000805
8 polyuria 33 HP:0000103
9 renal corticomedullary cysts 33 HP:0000108

Symptoms via clinical synopsis from OMIM:

58
Metabolic Features:
polydipsia
polyuria

Genitourinary Kidneys:
tubular atrophy
interstitial fibrosis
corticomedullary cysts
median onset of renal failure 19 years
altered basement membrane

Laboratory Abnormalities:
no proteinuria
no hematuria

Abdomen Liver:
hepatic fibrosis

Genitourinary:
secondary enuresis

Clinical features from OMIM:

604387

UMLS symptoms related to Nephronophthisis 3:


polydipsia, polyuria, secondary enuresis

Drugs & Therapeutics for Nephronophthisis 3

Interventional clinical trials:


# Name Status NCT ID Phase Drugs
1 Nephronophthisis : Clinical and Genetic Study Completed NCT01022957 Not Applicable

Search NIH Clinical Center for Nephronophthisis 3

Genetic Tests for Nephronophthisis 3

Genetic tests related to Nephronophthisis 3:

# Genetic test Affiliating Genes
1 Adolescent Nephronophthisis 30 NPHP3

Anatomical Context for Nephronophthisis 3

MalaCards organs/tissues related to Nephronophthisis 3:

42
Kidney

Publications for Nephronophthisis 3

Articles related to Nephronophthisis 3:

# Title Authors Year
1
Renal Cyclooxygenase Products are Higher and Lipoxygenase Products are Lower in Early Disease in the pcy Mouse Model of Adolescent Nephronophthisis. ( 24178445 )
2014
2
Analysis of the NPHP genes in two Japanese patients with suspected sporadic juvenile or adolescent nephronophthisis. ( 16724659 )
2006
3
Mutations in a novel gene, NPHP3, cause adolescent nephronophthisis, tapeto-retinal degeneration and hepatic fibrosis. ( 12872122 )
2003
4
Candidate gene analysis of KIAA0678 encoding a DnaJ-like protein for adolescent nephronophthisis and Senior-LA,ken syndrome type 3. ( 12438707 )
2002
5
Human adolescent nephronophthisis: gene locus synteny with polycystic kidney disease in pcy mice. ( 11134256 )
2001
6
Identification of a new gene locus for adolescent nephronophthisis, on chromosome 3q22 in a large Venezuelan pedigree. ( 10631142 )
2000

Variations for Nephronophthisis 3

UniProtKB/Swiss-Prot genetic disease variations for Nephronophthisis 3:

76
# Symbol AA change Variation ID SNP ID
1 NPHP3 p.Ser360Thr VAR_022815 rs119456960
2 NPHP3 p.Asn386Ser VAR_022816 rs142021049
3 NPHP3 p.Arg397His VAR_022817 rs755094682
4 NPHP3 p.Leu1141Pro VAR_022818 rs105752109
5 NPHP3 p.Ala1221Val VAR_022819 rs202048210
6 NPHP3 p.Ser1252Arg VAR_022820 rs143451766
7 NPHP3 p.Ser1314Thr VAR_022821 rs75316802

ClinVar genetic disease variations for Nephronophthisis 3:

6 (show all 24)
# Gene Variation Type Significance SNP ID Assembly Location
1 NPHP3 NM_153240.4(NPHP3): c.434_437delAAAG (p.Glu145Valfs) deletion Pathogenic rs763300393 GRCh37 Chromosome 3, 132438631: 132438634
2 NPHP3 NM_153240.4(NPHP3): c.434_437delAAAG (p.Glu145Valfs) deletion Pathogenic rs763300393 GRCh38 Chromosome 3, 132719787: 132719790
3 NPHP3 NM_153240.4(NPHP3): c.2694-2_2694-1delAG deletion Pathogenic rs751527253 GRCh38 Chromosome 3, 132689264: 132689265
4 NPHP3 NM_153240.4(NPHP3): c.2694-2_2694-1delAG deletion Pathogenic rs751527253 GRCh37 Chromosome 3, 132408108: 132408109
5 NPHP3 NM_153240.4(NPHP3): c.3824_3826delGAG (p.Gly1275del) deletion Pathogenic rs119456959 GRCh37 Chromosome 3, 132400921: 132400923
6 NPHP3 NM_153240.4(NPHP3): c.3824_3826delGAG (p.Gly1275del) deletion Pathogenic rs119456959 GRCh38 Chromosome 3, 132682077: 132682079
7 NPHP3 NM_153240.4(NPHP3): c.1079G> C (p.Ser360Thr) single nucleotide variant Pathogenic rs119456960 GRCh37 Chromosome 3, 132432009: 132432009
8 NPHP3 NM_153240.4(NPHP3): c.1079G> C (p.Ser360Thr) single nucleotide variant Pathogenic rs119456960 GRCh38 Chromosome 3, 132713165: 132713165
9 NPHP3 NM_153240.4(NPHP3): c.1381G> T (p.Glu461Ter) single nucleotide variant Pathogenic rs119456961 GRCh37 Chromosome 3, 132423185: 132423185
10 NPHP3 NM_153240.4(NPHP3): c.1381G> T (p.Glu461Ter) single nucleotide variant Pathogenic rs119456961 GRCh38 Chromosome 3, 132704341: 132704341
11 NPHP3 NM_153240.4(NPHP3): c.1729C> T (p.Arg577Ter) single nucleotide variant Pathogenic rs119456962 GRCh37 Chromosome 3, 132419192: 132419192
12 NPHP3 NM_153240.4(NPHP3): c.1729C> T (p.Arg577Ter) single nucleotide variant Pathogenic rs119456962 GRCh38 Chromosome 3, 132700348: 132700348
13 NPHP3 NM_153240.4(NPHP3): c.2104C> T (p.Arg702Ter) single nucleotide variant Pathogenic rs267606916 GRCh37 Chromosome 3, 132415642: 132415642
14 NPHP3 NM_153240.4(NPHP3): c.2104C> T (p.Arg702Ter) single nucleotide variant Pathogenic rs267606916 GRCh38 Chromosome 3, 132696798: 132696798
15 NPHP3 NM_153240.4(NPHP3): c.2369T> C (p.Leu790Pro) single nucleotide variant Likely pathogenic rs398124546 GRCh37 Chromosome 3, 132411604: 132411604
16 NPHP3 NM_153240.4(NPHP3): c.2369T> C (p.Leu790Pro) single nucleotide variant Likely pathogenic rs398124546 GRCh38 Chromosome 3, 132692760: 132692760
17 NPHP3 NM_153240.4(NPHP3): c.3373C> T (p.Arg1125Ter) single nucleotide variant Pathogenic rs368138001 GRCh37 Chromosome 3, 132403595: 132403595
18 NPHP3 NM_153240.4(NPHP3): c.3373C> T (p.Arg1125Ter) single nucleotide variant Pathogenic rs368138001 GRCh38 Chromosome 3, 132684751: 132684751
19 NPHP3 NM_153240.4(NPHP3): c.3608delC (p.Ala1203Valfs) deletion Pathogenic rs1060499938 GRCh38 Chromosome 3, 132683487: 132683487
20 NPHP3 NM_153240.4(NPHP3): c.3608delC (p.Ala1203Valfs) deletion Pathogenic rs1060499938 GRCh37 Chromosome 3, 132402331: 132402331
21 NPHP3 NM_153240.4(NPHP3): c.424C> T (p.Arg142Ter) single nucleotide variant Pathogenic rs771742823 GRCh38 Chromosome 3, 132719800: 132719800
22 NPHP3 NM_153240.4(NPHP3): c.424C> T (p.Arg142Ter) single nucleotide variant Pathogenic rs771742823 GRCh37 Chromosome 3, 132438644: 132438644
23 NPHP3 NM_153240.4(NPHP3): c.3570+2T> A single nucleotide variant Pathogenic rs1553771772 GRCh37 Chromosome 3, 132403396: 132403396
24 NPHP3 NM_153240.4(NPHP3): c.3570+2T> A single nucleotide variant Pathogenic rs1553771772 GRCh38 Chromosome 3, 132684552: 132684552

Expression for Nephronophthisis 3

Search GEO for disease gene expression data for Nephronophthisis 3.

Pathways for Nephronophthisis 3

Pathways related to Nephronophthisis 3 according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1 10.95 CRY1 CRY2
2
Show member pathways
10.79 CRY1 CRY2
3 10.52 CRY1 CRY2
4
Show member pathways
9.7 CRY1 CRY2

GO Terms for Nephronophthisis 3

Cellular components related to Nephronophthisis 3 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 cytosol GO:0005829 9.17 CRY2 CUL3 DNAJC13 KHK NPHP1 NPHP3
2 cilium GO:0005929 9.13 CUL3 NPHP1 NPHP3

Biological processes related to Nephronophthisis 3 according to GeneCards Suite gene sharing:

(show all 13)
# Name GO ID Score Top Affiliating Genes
1 response to stimulus GO:0050896 9.7 CRY1 CRY2 NRL
2 glucose homeostasis GO:0042593 9.51 CRY1 CRY2
3 circadian rhythm GO:0007623 9.49 CRY1 CRY2
4 circadian regulation of gene expression GO:0032922 9.48 CRY1 CRY2
5 regulation of circadian rhythm GO:0042752 9.46 CRY1 CRY2
6 lipid storage GO:0019915 9.43 CRY1 CRY2
7 entrainment of circadian clock by photoperiod GO:0043153 9.4 CRY1 CRY2
8 protein-chromophore linkage GO:0018298 9.37 CRY1 CRY2
9 response to insulin GO:0032868 9.33 CRY1 CRY2 KHK
10 negative regulation of circadian rhythm GO:0042754 9.32 CRY1 CRY2
11 negative regulation of glucocorticoid receptor signaling pathway GO:2000323 9.26 CRY1 CRY2
12 blue light signaling pathway GO:0009785 8.96 CRY1 CRY2
13 negative regulation of glucocorticoid secretion GO:2000850 8.62 CRY1 CRY2

Molecular functions related to Nephronophthisis 3 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 kinase binding GO:0019900 9.43 CRY1 CRY2
2 phosphatase binding GO:0019902 9.37 CRY1 CRY2
3 nuclear hormone receptor binding GO:0035257 9.32 CRY1 CRY2
4 photoreceptor activity GO:0009881 9.26 CRY1 CRY2
5 blue light photoreceptor activity GO:0009882 9.16 CRY1 CRY2
6 deoxyribodipyrimidine photo-lyase activity GO:0003904 8.96 CRY1 CRY2
7 DNA (6-4) photolyase activity GO:0003914 8.62 CRY1 CRY2
8 protein binding GO:0005515 10.01 CRY1 CRY2 CUL3 DNAJC13 KHK NPHP1

Sources for Nephronophthisis 3

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
20 FMA
29 GO
30 GTR
31 HGMD
32 HMDB
33 HPO
34 ICD10
35 ICD10 via Orphanet
36 ICD9CM
37 IUPHAR
38 KEGG
39 LifeMap
41 LOVD
43 MedGen
45 MeSH
46 MESH via Orphanet
47 MGI
50 NCI
51 NCIt
52 NDF-RT
55 NINDS
56 Novoseek
58 OMIM
59 OMIM via Orphanet
63 PubMed
65 QIAGEN
70 SNOMED-CT via HPO
71 SNOMED-CT via Orphanet
72 TGDB
73 Tocris
74 UMLS
75 UMLS via Orphanet
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