NPHPL1
MCID: NPH037
MIFTS: 28

Nephronophthisis-Like Nephropathy 1 (NPHPL1)

Categories: Genetic diseases, Nephrological diseases, Neuronal diseases

Aliases & Classifications for Nephronophthisis-Like Nephropathy 1

MalaCards integrated aliases for Nephronophthisis-Like Nephropathy 1:

Name: Nephronophthisis-Like Nephropathy 1 57 12 75 29 13 6 15 73
Nphpl1 57 12 75
Nephronophthisis-Like Nephropathy, Type 1 40

Characteristics:

OMIM:

57
Inheritance:
autosomal recessive

Miscellaneous:
onset in childhood
two families with different phenotypes have been reported (as of september 2010)


HPO:

32
nephronophthisis-like nephropathy 1:
Inheritance autosomal recessive inheritance


Classifications:



Summaries for Nephronophthisis-Like Nephropathy 1

UniProtKB/Swiss-Prot : 75 Nephronophthisis-like nephropathy 1: A disorder with features of nephronophthisis, a cystic kidney disease leading to end-stage renal failure. Nephronophthisis is histologically characterized by modifications of the tubules with thickening of the basement membrane, interstitial fibrosis and, in the advanced stages, medullary cysts. Typical clinical manifestation are chronic renal failure, anemia, polyuria, polydipsia, isosthenuria, and growth retardation. Associations with extrarenal symptoms are frequent. In NPHPL1 patients, extrarenal symptoms include hypertension, essential tremor, sensorineural hearing loss and gout. Severely affected individuals can manifest a mitochondrial disorder with isolated complex I deficiency activity in muscle, seizures, mental retardation and hypertrophic dilated cardiomyopathy.

MalaCards based summary : Nephronophthisis-Like Nephropathy 1, also known as nphpl1, is related to nephronophthisis and senior-loken syndrome 1. An important gene associated with Nephronophthisis-Like Nephropathy 1 is XPNPEP3 (X-Prolyl Aminopeptidase 3). Affiliated tissues include kidney, liver and skeletal muscle, and related phenotypes are hypertension and intellectual disability

Disease Ontology : 12 A nephronophthisis that has material basis in homozygous mutation in the XPNPEP3 gene on chromosome 22q13.2.

OMIM : 57 Nephronophthisis is an autosomal recessive cystic kidney disease characterized by onset of end-stage renal failure in the first 3 decades of life. The disorder is often associated with extrarenal manifestations, including liver fibrosis, retinal degeneration, and central nervous system abnormalities (summary by O'Toole et al., 2010). For a general phenotypic description and a discussion of genetic heterogeneity of nephronophthisis, see NPHP1 (256100). (613159)

Related Diseases for Nephronophthisis-Like Nephropathy 1

Diseases related to Nephronophthisis-Like Nephropathy 1 via text searches within MalaCards or GeneCards Suite gene sharing:

# Related Disease Score Top Affiliating Genes
1 nephronophthisis 9.8 NPHP1 XPNPEP3
2 senior-loken syndrome 1 9.7 NPHP1 XPNPEP3
3 cystic kidney disease 9.6 NPHP1 XPNPEP3
4 nephronophthisis 11 9.6 LAP3 NPHP1 XPNPEP3
5 nephronophthisis 9 9.6 LAP3 NPHP1 XPNPEP3

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



Diseases related to Nephronophthisis-Like Nephropathy 1

Symptoms & Phenotypes for Nephronophthisis-Like Nephropathy 1

Symptoms via clinical synopsis from OMIM:

57
Genitourinary Kidneys:
nephronophthisis
tubular atrophy
interstitial fibrosis
end stage renal disease
tubular basement membrane disintegration
more
Head And Neck Ears:
sensorineural hearing loss (1 family)

Cardiovascular Vascular:
hypertension (1 family)

Abdomen Pancreas:
pancreatic cysts (1 patient)
chronic pancreatitis (1 patient)

Neurologic Central Nervous System:
seizures (1 family)
mental retardation (1 family)
essential tremor (1 family)
arachnoid cysts (1 patient)

Cardiovascular Heart:
hypertrophic dilated cardiomyopathy (1 family)

Abdomen Liver:
hepatopathy (1 patient)

Muscle Soft Tissue:
skeletal muscle biopsy showed mitochondrial complex i deficiency (1 family)


Clinical features from OMIM:

613159

Human phenotypes related to Nephronophthisis-Like Nephropathy 1:

32 (show all 13)
# Description HPO Frequency HPO Source Accession
1 hypertension 32 occasional (7.5%) HP:0000822
2 intellectual disability 32 occasional (7.5%) HP:0001249
3 seizures 32 occasional (7.5%) HP:0001250
4 sensorineural hearing impairment 32 occasional (7.5%) HP:0000407
5 pancreatic cysts 32 occasional (7.5%) HP:0001737
6 nephronophthisis 32 HP:0000090
7 arachnoid cyst 32 occasional (7.5%) HP:0100702
8 stage 5 chronic kidney disease 32 HP:0003774
9 tubular atrophy 32 HP:0000092
10 kinetic tremor 32 HP:0030186
11 chronic pancreatitis 32 occasional (7.5%) HP:0006280
12 tubular basement membrane disintegration 32 HP:0005583
13 renal corticomedullary cysts 32 HP:0000108

Drugs & Therapeutics for Nephronophthisis-Like Nephropathy 1

Search Clinical Trials , NIH Clinical Center for Nephronophthisis-Like Nephropathy 1

Genetic Tests for Nephronophthisis-Like Nephropathy 1

Genetic tests related to Nephronophthisis-Like Nephropathy 1:

# Genetic test Affiliating Genes
1 Nephronophthisis-Like Nephropathy 1 29 XPNPEP3

Anatomical Context for Nephronophthisis-Like Nephropathy 1

MalaCards organs/tissues related to Nephronophthisis-Like Nephropathy 1:

41
Kidney, Liver, Skeletal Muscle

Publications for Nephronophthisis-Like Nephropathy 1

Variations for Nephronophthisis-Like Nephropathy 1

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

75
# Symbol AA change Variation ID SNP ID
1 XPNPEP3 p.Gly453Cys VAR_063820 rs267607179

ClinVar genetic disease variations for Nephronophthisis-Like Nephropathy 1:

6 (show all 23)
# Gene Variation Type Significance SNP ID Assembly Location
1 XPNPEP3 NM_022098.3(XPNPEP3): c.1357G> T (p.Gly453Cys) single nucleotide variant Pathogenic rs267607179 GRCh37 Chromosome 22, 41320486: 41320486
2 XPNPEP3 NM_022098.3(XPNPEP3): c.1357G> T (p.Gly453Cys) single nucleotide variant Pathogenic rs267607179 GRCh38 Chromosome 22, 40924482: 40924482
3 XPNPEP3 XPNPEP3, 4-BP DEL, 931AACA deletion Pathogenic
4 XPNPEP3 NM_022098.3(XPNPEP3): c.590-8A> G single nucleotide variant Conflicting interpretations of pathogenicity rs143719656 GRCh37 Chromosome 22, 41282309: 41282309
5 XPNPEP3 NM_022098.3(XPNPEP3): c.590-8A> G single nucleotide variant Conflicting interpretations of pathogenicity rs143719656 GRCh38 Chromosome 22, 40886305: 40886305
6 XPNPEP3 NM_022098.3(XPNPEP3): c.1244G> A (p.Arg415Gln) single nucleotide variant Uncertain significance rs79385822 GRCh37 Chromosome 22, 41320373: 41320373
7 XPNPEP3 NM_022098.3(XPNPEP3): c.1244G> A (p.Arg415Gln) single nucleotide variant Uncertain significance rs79385822 GRCh38 Chromosome 22, 40924369: 40924369
8 XPNPEP3 NM_022098.3(XPNPEP3): c.891T> G (p.Ile297Met) single nucleotide variant Uncertain significance rs746834434 GRCh37 Chromosome 22, 41305161: 41305161
9 XPNPEP3 NM_022098.3(XPNPEP3): c.891T> G (p.Ile297Met) single nucleotide variant Uncertain significance rs746834434 GRCh38 Chromosome 22, 40909157: 40909157
10 XPNPEP3 NM_022098.3(XPNPEP3): c.1122C> T (p.Leu374=) single nucleotide variant Likely benign rs761504767 GRCh37 Chromosome 22, 41318403: 41318403
11 XPNPEP3 NM_022098.3(XPNPEP3): c.1122C> T (p.Leu374=) single nucleotide variant Likely benign rs761504767 GRCh38 Chromosome 22, 40922399: 40922399
12 XPNPEP3 NM_022098.3(XPNPEP3): c.970-9T> C single nucleotide variant Benign/Likely benign rs117568682 GRCh37 Chromosome 22, 41310234: 41310234
13 XPNPEP3 NM_022098.3(XPNPEP3): c.970-9T> C single nucleotide variant Benign/Likely benign rs117568682 GRCh38 Chromosome 22, 40914230: 40914230
14 XPNPEP3 NM_022098.3(XPNPEP3): c.111A> G (p.Pro37=) single nucleotide variant Benign/Likely benign rs1894658 GRCh38 Chromosome 22, 40869045: 40869045
15 XPNPEP3 NM_022098.3(XPNPEP3): c.111A> G (p.Pro37=) single nucleotide variant Benign/Likely benign rs1894658 GRCh37 Chromosome 22, 41265049: 41265049
16 XPNPEP3 NM_022098.3(XPNPEP3): c.963C> T (p.Leu321=) single nucleotide variant Likely benign rs759612541 GRCh37 Chromosome 22, 41305233: 41305233
17 XPNPEP3 NM_022098.3(XPNPEP3): c.963C> T (p.Leu321=) single nucleotide variant Likely benign rs759612541 GRCh38 Chromosome 22, 40909229: 40909229
18 subset of 12 genes:EP300 NC_000022.11: g.(?_40868979)_(41333213_?)dup duplication Uncertain significance GRCh38 Chromosome 22, 40868979: 41333213
19 subset of 12 genes:EP300 NC_000022.11: g.(?_40868979)_(41333213_?)dup duplication Uncertain significance GRCh37 Chromosome 22, 41264983: 41729217
20 XPNPEP3 NM_022098.3(XPNPEP3): c.1477C> G (p.Pro493Ala) single nucleotide variant Benign rs146023695 GRCh38 Chromosome 22, 40926388: 40926388
21 XPNPEP3 NM_022098.3(XPNPEP3): c.1477C> G (p.Pro493Ala) single nucleotide variant Benign rs146023695 GRCh37 Chromosome 22, 41322392: 41322392
22 XPNPEP3 NM_022098.3(XPNPEP3): c.1516G> A (p.Ala506Thr) single nucleotide variant Uncertain significance rs139592817 GRCh38 Chromosome 22, 40926427: 40926427
23 XPNPEP3 NM_022098.3(XPNPEP3): c.1516G> A (p.Ala506Thr) single nucleotide variant Uncertain significance rs139592817 GRCh37 Chromosome 22, 41322431: 41322431

Expression for Nephronophthisis-Like Nephropathy 1

Search GEO for disease gene expression data for Nephronophthisis-Like Nephropathy 1.

Pathways for Nephronophthisis-Like Nephropathy 1

GO Terms for Nephronophthisis-Like Nephropathy 1

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

# Name GO ID Score Top Affiliating Genes
1 proteolysis GO:0006508 8.62 LAP3 XPNPEP3

Molecular functions related to Nephronophthisis-Like Nephropathy 1 according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 peptidase activity GO:0008233 9.16 LAP3 XPNPEP3
2 manganese ion binding GO:0030145 8.96 LAP3 XPNPEP3
3 aminopeptidase activity GO:0004177 8.62 LAP3 XPNPEP3

Sources for Nephronophthisis-Like Nephropathy 1

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