NPHP3
MCID: NPH031
MIFTS: 41

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 2 and nephronophthisis 1, 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 37)
# Related Disease Score Top Affiliating Genes
1 nephronophthisis 2 32.1 NPHP1 NPHP3
2 nephronophthisis 1 31.6 NPHP1 NPHP3
3 juvenile nephronophthisis 31.5 NPHP1 NPHP3
4 nephronophthisis 18 31.5 NPHP1 NPHP3
5 nephronophthisis 11 31.5 NPHP1 NPHP3
6 senior-loken syndrome 1 31.4 NPHP1 NPHP3
7 cogan syndrome 31.4 NPHP1 NPHP3
8 nephronophthisis 9 31.4 NPHP1 NPHP3
9 visceral heterotaxy 31.0 NPHP1 NPHP3
10 leber congenital amaurosis 31.0 NPHP1 NPHP3 NRL
11 retinitis pigmentosa 30.4 CUL3 NPHP1 NPHP3 NRL
12 nephronophthisis 29.2 DNAJC13 NPHP1 NPHP3
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 polydactyly, postaxial, type a1 10.0
26 retinitis pigmentosa 2 10.0
27 caroli disease, isolated 10.0
28 polydactyly 10.0
29 nephronophthisis 16 10.0
30 caroli disease 10.0
31 kidney disease 10.0
32 situs inversus 10.0
33 retinal degeneration 10.0
34 renal dysplasia diffuse cystic 10.0
35 renal dysplasia 10.0
36 cervical cancer 9.9
37 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 enuresis 33 HP:0000805
6 tubular atrophy 33 HP:0000092
7 tubulointerstitial fibrosis 33 HP:0005576
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

GenomeRNAi Phenotypes related to Nephronophthisis 3 according to GeneCards Suite gene sharing:

27
# Description GenomeRNAi Source Accession Score Top Affiliating Genes
1 Increased viability with SS1P at EC90 GR00376-A-1 8.62 COL14A1 DNAJC13

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:

(show all 15)
# Title Authors Year
1
Thymosin β-4 is a novel regulator for primary cilium formation by nephronophthisis 3 in HeLa human cervical cancer cells. ( 31048733 )
2019
2
Transplantation for infantile nephronophthisis with loss-of-function mutation in NPHP3: Lesson from a case. ( 29869359 )
2018
3
Homozygous mutation in the NPHP3 gene causing foetal nephronophthisis. ( 28921755 )
2017
4
High mutation rate of NPHP3 in 18 Chinese infantile nephronophthisis patients. ( 26184788 )
2016
5
NPHP3 mutations are associated with neonatal onset multiorgan polycystic disease in two siblings. ( 24776604 )
2014
6
Caroli disease, bilateral diffuse cystic renal dysplasia, situs inversus, postaxial polydactyly, and preauricular fistulas: a ciliopathy caused by a homozygous NPHP3 mutation. ( 21845392 )
2013
7
ANKS6 is a central component of a nephronophthisis module linking NEK8 to INVS and NPHP3. ( 23793029 )
2013
8
Renal-hepatic-pancreatic dysplasia: a sibship with skeletal and central nervous system anomalies and NPHP3 mutation. ( 23686967 )
2013
9
Targeting of Nphp3 to the primary cilia is controlled by an N-terminal myristoylation site and coiled-coil domains. ( 22328406 )
2012
10
An ARL3-UNC119-RP2 GTPase cycle targets myristoylated NPHP3 to the primary cilium. ( 22085962 )
2011
11
Inv acts as a molecular anchor for Nphp3 and Nek8 in the proximal segment of primary cilia. ( 20169535 )
2010
12
Lethal cystic kidney disease in Amish neonates associated with homozygous nonsense mutation of NPHP3. ( 19303681 )
2009
13
Mutations of NPHP2 and NPHP3 in infantile nephronophthisis. ( 19177160 )
2009
14
Mutations in a novel gene, NPHP3, cause adolescent nephronophthisis, tapeto-retinal degeneration and hepatic fibrosis. ( 12872122 )
2003
15
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 36)
# Gene Variation Type Significance SNP ID Assembly Location
1 NPHP3 NM_153240.4(NPHP3): c.3824_3826delGAG (p.Gly1275del) deletion Pathogenic rs119456959 GRCh37 Chromosome 3, 132400921: 132400923
2 NPHP3 NM_153240.4(NPHP3): c.3824_3826delGAG (p.Gly1275del) deletion Pathogenic rs119456959 GRCh38 Chromosome 3, 132682077: 132682079
3 NPHP3 NM_153240.4(NPHP3): c.1079G> C (p.Ser360Thr) single nucleotide variant Pathogenic rs119456960 GRCh37 Chromosome 3, 132432009: 132432009
4 NPHP3 NM_153240.4(NPHP3): c.1079G> C (p.Ser360Thr) single nucleotide variant Pathogenic rs119456960 GRCh38 Chromosome 3, 132713165: 132713165
5 NPHP3 NM_153240.4(NPHP3): c.1381G> T (p.Glu461Ter) single nucleotide variant Pathogenic rs119456961 GRCh37 Chromosome 3, 132423185: 132423185
6 NPHP3 NM_153240.4(NPHP3): c.1381G> T (p.Glu461Ter) single nucleotide variant Pathogenic rs119456961 GRCh38 Chromosome 3, 132704341: 132704341
7 NPHP3 NM_153240.4(NPHP3): c.1729C> T (p.Arg577Ter) single nucleotide variant Pathogenic rs119456962 GRCh37 Chromosome 3, 132419192: 132419192
8 NPHP3 NM_153240.4(NPHP3): c.1729C> T (p.Arg577Ter) single nucleotide variant Pathogenic rs119456962 GRCh38 Chromosome 3, 132700348: 132700348
9 NPHP3 NM_153240.4(NPHP3): c.2104C> T (p.Arg702Ter) single nucleotide variant Pathogenic rs267606916 GRCh37 Chromosome 3, 132415642: 132415642
10 NPHP3 NM_153240.4(NPHP3): c.2104C> T (p.Arg702Ter) single nucleotide variant Pathogenic rs267606916 GRCh38 Chromosome 3, 132696798: 132696798
11 NPHP3 NM_153240.4(NPHP3): c.2369T> C (p.Leu790Pro) single nucleotide variant Likely pathogenic rs398124546 GRCh37 Chromosome 3, 132411604: 132411604
12 NPHP3 NM_153240.4(NPHP3): c.2369T> C (p.Leu790Pro) single nucleotide variant Likely pathogenic rs398124546 GRCh38 Chromosome 3, 132692760: 132692760
13 NPHP3 NM_153240.4(NPHP3): c.3373C> T (p.Arg1125Ter) single nucleotide variant Pathogenic rs368138001 GRCh37 Chromosome 3, 132403595: 132403595
14 NPHP3 NM_153240.4(NPHP3): c.3373C> T (p.Arg1125Ter) single nucleotide variant Pathogenic rs368138001 GRCh38 Chromosome 3, 132684751: 132684751
15 NPHP3 NM_153240.4(NPHP3): c.434_437delAAAG (p.Glu145Valfs) deletion Pathogenic rs763300393 GRCh37 Chromosome 3, 132438631: 132438634
16 NPHP3 NM_153240.4(NPHP3): c.434_437delAAAG (p.Glu145Valfs) deletion Pathogenic rs763300393 GRCh38 Chromosome 3, 132719787: 132719790
17 NPHP3 NM_153240.4(NPHP3): c.1817G> A (p.Trp606Ter) single nucleotide variant Pathogenic rs182135982 GRCh37 Chromosome 3, 132418832: 132418832
18 NPHP3 NM_153240.4(NPHP3): c.1817G> A (p.Trp606Ter) single nucleotide variant Pathogenic rs182135982 GRCh38 Chromosome 3, 132699988: 132699988
19 NPHP3 NM_153240.4(NPHP3): c.2694-2_2694-1delAG deletion Pathogenic rs751527253 GRCh38 Chromosome 3, 132689264: 132689265
20 NPHP3 NM_153240.4(NPHP3): c.2694-2_2694-1delAG deletion Pathogenic rs751527253 GRCh37 Chromosome 3, 132408108: 132408109
21 NPHP3 NM_153240.4(NPHP3): c.3896G> A (p.Gly1299Asp) single nucleotide variant Uncertain significance rs190548695 GRCh37 Chromosome 3, 132400851: 132400851
22 NPHP3 NM_153240.4(NPHP3): c.3896G> A (p.Gly1299Asp) single nucleotide variant Uncertain significance rs190548695 GRCh38 Chromosome 3, 132682007: 132682007
23 NPHP3 NM_153240.4(NPHP3): c.2881C> G (p.Gln961Glu) single nucleotide variant Uncertain significance rs144989330 GRCh38 Chromosome 3, 132689076: 132689076
24 NPHP3 NM_153240.4(NPHP3): c.2881C> G (p.Gln961Glu) single nucleotide variant Uncertain significance rs144989330 GRCh37 Chromosome 3, 132407920: 132407920
25 NPHP3 NM_153240.4(NPHP3): c.3608delC (p.Ala1203Valfs) deletion Pathogenic rs1060499938 GRCh38 Chromosome 3, 132683487: 132683487
26 NPHP3 NM_153240.4(NPHP3): c.3608delC (p.Ala1203Valfs) deletion Pathogenic rs1060499938 GRCh37 Chromosome 3, 132402331: 132402331
27 NPHP3 NM_153240.4(NPHP3): c.424C> T (p.Arg142Ter) single nucleotide variant Pathogenic rs771742823 GRCh38 Chromosome 3, 132719800: 132719800
28 NPHP3 NM_153240.4(NPHP3): c.424C> T (p.Arg142Ter) single nucleotide variant Pathogenic rs771742823 GRCh37 Chromosome 3, 132438644: 132438644
29 NPHP3 NM_153240.4(NPHP3): c.1082C> G (p.Ser361Cys) single nucleotide variant Uncertain significance rs146250226 GRCh37 Chromosome 3, 132432006: 132432006
30 NPHP3 NM_153240.4(NPHP3): c.1082C> G (p.Ser361Cys) single nucleotide variant Uncertain significance rs146250226 GRCh38 Chromosome 3, 132713162: 132713162
31 NPHP3 NM_153240.4(NPHP3): c.944A> T (p.Asp315Val) single nucleotide variant Uncertain significance rs149565564 GRCh37 Chromosome 3, 132433942: 132433942
32 NPHP3 NM_153240.4(NPHP3): c.944A> T (p.Asp315Val) single nucleotide variant Uncertain significance rs149565564 GRCh38 Chromosome 3, 132715098: 132715098
33 NPHP3 NM_153240.4(NPHP3): c.3570+2T> A single nucleotide variant Pathogenic rs1553771772 GRCh37 Chromosome 3, 132403396: 132403396
34 NPHP3 NM_153240.4(NPHP3): c.3570+2T> A single nucleotide variant Pathogenic rs1553771772 GRCh38 Chromosome 3, 132684552: 132684552
35 NPHP3 NM_153240.4(NPHP3): c.65C> T (p.Ala22Val) single nucleotide variant Uncertain significance rs369447363 GRCh37 Chromosome 3, 132441135: 132441135
36 NPHP3 NM_153240.4(NPHP3): c.65C> T (p.Ala22Val) single nucleotide variant Uncertain significance rs369447363 GRCh38 Chromosome 3, 132722291: 132722291

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 cilium GO:0005929 8.8 CUL3 NPHP1 NPHP3

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

(show all 11)
# Name GO ID Score Top Affiliating Genes
1 circadian rhythm GO:0007623 9.49 CRY1 CRY2
2 response to insulin GO:0032868 9.48 CRY1 CRY2
3 circadian regulation of gene expression GO:0032922 9.46 CRY1 CRY2
4 regulation of circadian rhythm GO:0042752 9.43 CRY1 CRY2
5 lipid storage GO:0019915 9.4 CRY1 CRY2
6 entrainment of circadian clock by photoperiod GO:0043153 9.37 CRY1 CRY2
7 protein-chromophore linkage GO:0018298 9.32 CRY1 CRY2
8 negative regulation of circadian rhythm GO:0042754 9.26 CRY1 CRY2
9 negative regulation of glucocorticoid receptor signaling pathway GO:2000323 9.16 CRY1 CRY2
10 blue light signaling pathway GO:0009785 8.96 CRY1 CRY2
11 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 9.4 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

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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