NPHP1
MCID: NPH019
MIFTS: 43

Nephronophthisis 1 (NPHP1)

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

Aliases & Classifications for Nephronophthisis 1

MalaCards integrated aliases for Nephronophthisis 1:

Name: Nephronophthisis 1 57 12 75 29 6 15
Nphp1 57 12 75 55
Nephronophthisis, Familial Juvenile 57 73
Nephronophthisis 1, Juvenile 57 13
Nph1 57 12
Familial Juvenile Nephronophthisis 1 75
Juvenile Nephronophthisis 1 12

Characteristics:

OMIM:

57
Inheritance:
autosomal recessive

Miscellaneous:
medial onset of end stage renal disease 13 years
allelic to senior-loken syndrome 1 and joubert syndrome 4


HPO:

32
nephronophthisis 1:
Inheritance autosomal recessive inheritance


Classifications:



Summaries for Nephronophthisis 1

OMIM : 57 Nephronophthisis is an autosomal recessive cystic kidney disease that leads to renal failure in childhood or adolescence. It is the most frequent genetic cause of renal failure in children. NPHP may be combined with extrarenal manifestations, such as liver fibrosis, situs inversus, or cardiac malformations. When nephronophthisis is combined with retinitis pigmentosa, the disorder is known as Senior-Loken syndrome (SLSN1; 266900); when it is combined with cerebellar vermis hypoplasia, the disorder is known as Joubert syndrome (JBTS1; 213300); and when it is combined with multiple developmental and neurologic abnormalities, the disorder is often known as Meckel-Gruber syndrome (MKS1; 249000). Because most NPHP gene products localize to the cilium or its associated structures, nephronophthisis and the related syndromes have been termed 'ciliopathies' (summary by Hoff et al., 2013). Clinical features of familial juvenile nephronophthisis include anemia, polyuria, polydipsia, isosthenuria, and death in uremia. Simms et al. (2009) provided a detailed review of nephronophthisis, including a discussion of clinical features and molecular genetics. (256100)

MalaCards based summary : Nephronophthisis 1, also known as nphp1, is related to apraxia and nephronophthisis 18, and has symptoms including polydipsia and polyuria. An important gene associated with Nephronophthisis 1 is NPHP1 (Nephrocystin 1), and among its related pathways/superpathways are Organelle biogenesis and maintenance and Cargo trafficking to the periciliary membrane. Affiliated tissues include kidney and liver, and related phenotypes are hypertension and polydipsia

Disease Ontology : 12 A nephronophthisis that has material basis in homozygous or compound heterozygous mutation in or deletion of the NPHP1 gene on chromosome 2q13.

UniProtKB/Swiss-Prot : 75 Nephronophthisis 1: An autosomal recessive inherited disease characterized by anemia, polyuria, polydipsia, isosthenuria and death in uremia. Symmetrical destruction of the kidneys involving both tubules and glomeruli occurs. The underlying pathology is a chronic tubulo-interstitial nephropathy with characteristic tubular basement membrane thickening and medullary cyst formation. Associations with extrarenal symptoms, especially ocular lesions, are frequent. The age at death ranges from about 4 to 15 years.

Related Diseases for Nephronophthisis 1

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

(show top 50) (show all 56)
# Related Disease Score Top Affiliating Genes
1 apraxia 32.2 NPHP1 NPHP4
2 nephronophthisis 18 31.8 INVS NPHP1 NPHP3 NPHP4
3 nephronophthisis 9 31.8 INVS NPHP1 NPHP3 NPHP4
4 juvenile nephronophthisis 31.8 INVS NPHP1 NPHP3 NPHP4
5 nephronophthisis 4 31.7 NPHP1 NPHP4
6 bardet-biedl syndrome 31.6 INVS NPHP1 NPHP4 PKD1
7 nephronophthisis 3 31.6 NPHP1 NPHP3
8 nephronophthisis 19 31.6 NPHP1 NPHP4
9 retinal aplasia 31.5 NPHP1 NPHP4
10 joubert syndrome 3 31.5 AHI1 NPHP1
11 joubert syndrome 6 31.5 AHI1 NPHP1
12 nephronophthisis 13 31.4 INVS NPHP1
13 cogan syndrome 31.4 NPHP1 NPHP3 NPHP4
14 nephronophthisis 7 31.3 INVS NPHP1
15 polycystic liver disease 1 with or without kidney cysts 31.3 NPHP1 NPHP4 PKD1
16 chronic kidney failure 31.2 INVS NPHP1 PKD1
17 nephronophthisis 2 31.1 INVS NPHP1 NPHP3 NPHP4
18 senior-loken syndrome 1 31.0 AHI1 INVS NPHP1 NPHP3 NPHP4
19 nephronophthisis 11 31.0 AHI1 NPHP1 NPHP3 NPHP4
20 leber congenital amaurosis 31.0 AHI1 NPHP1 NPHP3 NPHP4
21 visceral heterotaxy 30.9 INVS NPHP1 NPHP3
22 cystic kidney disease 30.9 INVS NPHP1 NPHP3 NPHP4 PKD1
23 meckel syndrome, type 6 30.8 AHI1 INVS NPHP1 NPHP4
24 meckel syndrome, type 1 30.8 AHI1 INVS NPHP1 NPHP4
25 retinitis pigmentosa 30.7 AHI1 INVS NPHP1 NPHP3 NPHP4
26 joubert syndrome 1 28.9 AHI1 INVS NPHP1 NPHP3 NPHP4
27 nephronophthisis 28.9 AHI1 INVS NPHP1 NPHP3 NPHP4 PKD1
28 joubert syndrome 4 11.7
29 nephronophthisis-like nephropathy 1 11.6
30 ocular motor apraxia 11.4
31 pontine tegmental cap dysplasia 11.3
32 medullary cystic kidney disease 1 11.3
33 kidney disease 11.2
34 nephronophthisis 20 11.0
35 hyperuricemic nephropathy, familial juvenile, 1 11.0
36 meckel syndrome, type 3 11.0
37 joubert syndrome 2 11.0
38 joubert syndrome 17 11.0
39 nephronophthisis 16 11.0
40 senior-loken syndrome 3 10.9
41 fundus dystrophy 10.9
42 joubert syndrome with renal anomalies 10.9
43 autism 10.1
44 autism spectrum disorder 10.1
45 infertility 10.1
46 alacrima, achalasia, and mental retardation syndrome 10.0
47 bardet-biedl syndrome 2 10.0
48 bardet-biedl syndrome 10 10.0
49 bardet-biedl syndrome 11 10.0
50 bardet-biedl syndrome 12 10.0

Graphical network of the top 20 diseases related to Nephronophthisis 1:



Diseases related to Nephronophthisis 1

Symptoms & Phenotypes for Nephronophthisis 1

Symptoms via clinical synopsis from OMIM:

57
Metabolic Features:
polydipsia
polyuria
absence of hypertension

Genitourinary Kidneys:
nephronophthisis
tubular atrophy
interstitial fibrosis
end stage renal disease
tubular basement membrane disintegration
more
Laboratory Abnormalities:
hyposthenuria (inability to concentrate urine normally)

Hematology:
anemia

Growth Other:
growth retardation


Clinical features from OMIM:

256100

Human phenotypes related to Nephronophthisis 1:

32 (show all 12)
# Description HPO Frequency HPO Source Accession
1 hypertension 32 HP:0000822
2 polydipsia 32 HP:0001959
3 anemia 32 HP:0001903
4 growth delay 32 HP:0001510
5 nephronophthisis 32 HP:0000090
6 stage 5 chronic kidney disease 32 HP:0003774
7 tubular atrophy 32 HP:0000092
8 tubulointerstitial fibrosis 32 HP:0005576
9 hyposthenuria 32 HP:0003158
10 polyuria 32 HP:0000103
11 tubular basement membrane disintegration 32 HP:0005583
12 renal corticomedullary cysts 32 HP:0000108

UMLS symptoms related to Nephronophthisis 1:


polydipsia, polyuria

MGI Mouse Phenotypes related to Nephronophthisis 1:

46
# Description MGI Source Accession Score Top Affiliating Genes
1 cellular MP:0005384 9.63 AHI1 INVS NPHP1 NPHP3 NPHP4 PKD1
2 nervous system MP:0003631 9.35 AHI1 NPHP1 NPHP3 NPHP4 PKD1
3 renal/urinary system MP:0005367 9.1 AHI1 INVS NPHP1 NPHP3 NPHP4 PKD1

Drugs & Therapeutics for Nephronophthisis 1

Interventional clinical trials:


# Name Status NCT ID Phase Drugs
1 Assessment of the Prevalence of Genes AHI1, NPHP1 and CEP290 in Joubert Syndrome Completed NCT00873678
2 Nephronophthisis : Clinical and Genetic Study Completed NCT01022957 Not Applicable
3 Hereditary Tubulointerstitial Nephritis Completed NCT01312727 Not Applicable

Search NIH Clinical Center for Nephronophthisis 1

Genetic Tests for Nephronophthisis 1

Genetic tests related to Nephronophthisis 1:

# Genetic test Affiliating Genes
1 Nephronophthisis 1 29 NPHP1

Anatomical Context for Nephronophthisis 1

MalaCards organs/tissues related to Nephronophthisis 1:

41
Kidney, Liver

Publications for Nephronophthisis 1

Articles related to Nephronophthisis 1:

# Title Authors Year
1
NPHP1 (Nephrocystin-1) Gene Deletions Cause Adult-Onset ESRD. ( 29654215 )
2018
2
QMPSF is sensitive and specific in the detection of NPHP1 heterozygous deletions. ( 28002029 )
2017
3
Recurrent 2q13 microduplication encompassing MALL, NPHP1, RGPD6, and BUB1 associated with autism spectrum disorder, intellectual disability, and liver disorder. ( 28254236 )
2017
4
Copy number analysis of the low-copy repeats at the primate NPHP1 locus by array comparative genomic hybridization. ( 27222811 )
2016
5
Recurrent CNVs and SNVs at the NPHP1 locus contribute pathogenic alleles to Bardet-Biedl syndrome. ( 24746959 )
2014
6
Duplication of the NPHP1 gene in patients with autism spectrum disorder and normal intellectual ability: a case series. ( 25126106 )
2014
7
Identification of a novel polymorphism--the duplication of the NPHP1 (nephronophthisis 1) gene. ( 16892302 )
2006
8
Lack of large, homozygous deletions of the nephronophthisis 1 region in Joubert syndrome type B. APN Study Group. Arbeitsgemeinschaft fA1r PAodiatrische Nephrologie. ( 9502560 )
1998

Variations for Nephronophthisis 1

UniProtKB/Swiss-Prot genetic disease variations for Nephronophthisis 1:

75
# Symbol AA change Variation ID SNP ID
1 NPHP1 p.Gly342Arg VAR_012160 rs121907899

ClinVar genetic disease variations for Nephronophthisis 1:

6 (show all 20)
# Gene Variation Type Significance SNP ID Assembly Location
1 NPHP1 NM_000272.3(NPHP1): c.1884+1G> T single nucleotide variant Pathogenic GRCh38 Chromosome 2, 110129185: 110129185
2 NPHP1 NM_000272.3(NPHP1): c.1884+1G> T single nucleotide variant Pathogenic GRCh37 Chromosome 2, 110886762: 110886762
3 NPHP1 NM_000272.3(NPHP1): c.80T> A (p.Leu27Ter) single nucleotide variant Pathogenic rs121907898 GRCh37 Chromosome 2, 110959061: 110959061
4 NPHP1 NM_000272.3(NPHP1): c.80T> A (p.Leu27Ter) single nucleotide variant Pathogenic rs121907898 GRCh38 Chromosome 2, 110201484: 110201484
5 NPHP1 NM_000272.3(NPHP1): c.1027G> A (p.Gly343Arg) single nucleotide variant Pathogenic rs121907899 GRCh37 Chromosome 2, 110920625: 110920625
6 NPHP1 NM_000272.3(NPHP1): c.1027G> A (p.Gly343Arg) single nucleotide variant Pathogenic rs121907899 GRCh38 Chromosome 2, 110163048: 110163048
7 NPHP1 NPHP1, DEL deletion Pathogenic
8 NPHP1 NM_000272.3(NPHP1): c.1184dupC (p.Leu396Serfs) duplication Pathogenic rs398123285 GRCh37 Chromosome 2, 110917771: 110917771
9 NPHP1 NM_000272.3(NPHP1): c.1184dupC (p.Leu396Serfs) duplication Pathogenic rs398123285 GRCh38 Chromosome 2, 110160194: 110160194
10 NPHP1 NM_000272.3(NPHP1): c.625-3dupT duplication Uncertain significance rs200118387 GRCh38 Chromosome 2, 110165158: 110165158
11 NPHP1 NM_000272.3(NPHP1): c.625-3dupT duplication Uncertain significance rs200118387 GRCh37 Chromosome 2, 110922735: 110922735
12 NPHP1 NM_000272.3(NPHP1): c.232T> C (p.Tyr78His) single nucleotide variant Conflicting interpretations of pathogenicity rs140446520 GRCh37 Chromosome 2, 110936097: 110936097
13 NPHP1 NM_000272.3(NPHP1): c.232T> C (p.Tyr78His) single nucleotide variant Conflicting interpretations of pathogenicity rs140446520 GRCh38 Chromosome 2, 110178520: 110178520
14 NPHP1 NM_000272.3(NPHP1): c.555dupA (p.Pro186Thrfs) duplication Pathogenic rs886042650 GRCh37 Chromosome 2, 110926098: 110926098
15 NPHP1 NM_000272.3(NPHP1): c.555dupA (p.Pro186Thrfs) duplication Pathogenic rs886042650 GRCh38 Chromosome 2, 110168521: 110168521
16 NPHP1 NM_000272.3(NPHP1): c.1529_1530delAG (p.Glu510Alafs) deletion Pathogenic GRCh37 Chromosome 2, 110902137: 110902138
17 NPHP1 NM_000272.3(NPHP1): c.1529_1530delAG (p.Glu510Alafs) deletion Pathogenic GRCh38 Chromosome 2, 110144560: 110144561
18 NPHP1 NC_000002.11: g.110852960_110975102del122143 deletion Pathogenic GRCh37 Chromosome 2, 110852960: 110975102
19 NPHP1 NM_000272.3(NPHP1): c.1520+1delG deletion Pathogenic rs747861275 GRCh37 Chromosome 2, 110904329: 110904329
20 NPHP1 NM_000272.3(NPHP1): c.1520+1delG deletion Pathogenic rs747861275 GRCh38 Chromosome 2, 110146752: 110146752

Expression for Nephronophthisis 1

Search GEO for disease gene expression data for Nephronophthisis 1.

Pathways for Nephronophthisis 1

Pathways related to Nephronophthisis 1 according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1
Show member pathways
11.75 AHI1 NPHP1 NPHP3 NPHP4 PKD1
2
Show member pathways
10.99 NPHP3 PKD1

GO Terms for Nephronophthisis 1

Cellular components related to Nephronophthisis 1 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 cytoskeleton GO:0005856 9.67 AHI1 INVS NPHP1 NPHP4
2 motile cilium GO:0031514 9.48 NPHP1 PKD1
3 ciliary basal body GO:0036064 9.46 AHI1 NPHP4
4 bicellular tight junction GO:0005923 9.43 NPHP1 NPHP4
5 cell projection GO:0042995 9.43 AHI1 INVS NPHP1 NPHP3 NPHP4 PKD1
6 adherens junction GO:0005912 9.4 AHI1 NPHP1
7 cell-cell junction GO:0005911 9.33 AHI1 NPHP1 NPHP4
8 photoreceptor connecting cilium GO:0032391 9.32 NPHP1 NPHP4
9 non-motile cilium GO:0097730 9.26 AHI1 NPHP4
10 cilium GO:0005929 9.1 AHI1 INVS NPHP1 NPHP3 NPHP4 PKD1

Biological processes related to Nephronophthisis 1 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 cell-cell adhesion GO:0098609 9.54 NPHP1 NPHP4 PKD1
2 negative regulation of canonical Wnt signaling pathway GO:0090090 9.5 INVS NPHP3 NPHP4
3 kidney development GO:0001822 9.48 NPHP3 PKD1
4 retina development in camera-type eye GO:0060041 9.46 NPHP1 NPHP4
5 heart looping GO:0001947 9.43 AHI1 NPHP3
6 photoreceptor cell maintenance GO:0045494 9.4 NPHP3 NPHP4
7 ciliary basal body-plasma membrane docking GO:0097711 9.33 AHI1 NPHP1 NPHP4
8 photoreceptor cell outer segment organization GO:0035845 9.26 AHI1 NPHP4
9 visual behavior GO:0007632 8.96 NPHP1 NPHP4
10 positive regulation of bicellular tight junction assembly GO:1903348 8.62 NPHP1 NPHP4

Sources for Nephronophthisis 1

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 ExPASy
19 FMA
28 GO
29 GTR
30 HGMD
31 HMDB
32 HPO
33 ICD10
34 ICD10 via Orphanet
35 ICD9CM
36 IUPHAR
37 KEGG
38 LifeMap
40 LOVD
42 MedGen
44 MeSH
45 MESH via Orphanet
46 MGI
49 NCI
50 NCIt
51 NDF-RT
54 NINDS
55 Novoseek
57 OMIM
58 OMIM via Orphanet
62 PubMed
64 QIAGEN
69 SNOMED-CT via HPO
70 SNOMED-CT via Orphanet
71 TGDB
72 Tocris
73 UMLS
74 UMLS via Orphanet
Content
Loading form....