NPHPL1
MCID: NPH037
MIFTS: 35

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 72 29 13 6 15 70
Nphpl1 57 12 72
Nephronophthisis-Like Nephropathy, Type 1 39

Characteristics:

OMIM®:

57 (Updated 20-May-2021)
Inheritance:
autosomal recessive

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


HPO:

31
nephronophthisis-like nephropathy 1:
Inheritance autosomal recessive inheritance


Classifications:



Summaries for Nephronophthisis-Like Nephropathy 1

UniProtKB/Swiss-Prot : 72 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 19 and nephronophthisis 2. An important gene associated with Nephronophthisis-Like Nephropathy 1 is XPNPEP3 (X-Prolyl Aminopeptidase 3), and among its related pathways/superpathways is Protein export. Affiliated tissues include kidney, liver and skeletal muscle, and related phenotypes are intellectual disability and hypertension

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) (Updated 20-May-2021)

Related Diseases for Nephronophthisis-Like Nephropathy 1

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

Human phenotypes related to Nephronophthisis-Like Nephropathy 1:

31 (show all 13)
# Description HPO Frequency HPO Source Accession
1 intellectual disability 31 occasional (7.5%) HP:0001249
2 hypertension 31 occasional (7.5%) HP:0000822
3 sensorineural hearing impairment 31 occasional (7.5%) HP:0000407
4 pancreatic cysts 31 occasional (7.5%) HP:0001737
5 arachnoid cyst 31 occasional (7.5%) HP:0100702
6 chronic pancreatitis 31 occasional (7.5%) HP:0006280
7 seizure 31 occasional (7.5%) HP:0001250
8 nephronophthisis 31 HP:0000090
9 stage 5 chronic kidney disease 31 HP:0003774
10 renal tubular atrophy 31 HP:0000092
11 kinetic tremor 31 HP:0030186
12 renal corticomedullary cysts 31 HP:0000108
13 tubular basement membrane disintegration 31 HP:0005583

Symptoms via clinical synopsis from OMIM®:

57 (Updated 20-May-2021)
Genitourinary Kidneys:
nephronophthisis
tubular basement membrane disintegration
interstitial fibrosis
tubular atrophy
end stage renal disease
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 (Updated 20-May-2021)

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:

40
Kidney, Liver, Skeletal Muscle

Publications for Nephronophthisis-Like Nephropathy 1

Articles related to Nephronophthisis-Like Nephropathy 1:

# Title Authors PMID Year
1
Individuals with mutations in XPNPEP3, which encodes a mitochondrial protein, develop a nephronophthisis-like nephropathy. 57 6 61
20179356 2010

Variations for Nephronophthisis-Like Nephropathy 1

ClinVar genetic disease variations for Nephronophthisis-Like Nephropathy 1:

6 (show top 50) (show all 156)
# Gene Name Type Significance ClinVarId dbSNP ID Position
1 XPNPEP3 XPNPEP3, 4-BP DEL, 931AACA Deletion Pathogenic 52 GRCh37:
GRCh38:
2 XPNPEP3 NM_022098.4(XPNPEP3):c.1357G>T (p.Gly453Cys) SNV Pathogenic 51 rs267607179 GRCh37: 22:41320486-41320486
GRCh38: 22:40924482-40924482
3 XPNPEP3 NM_022098.4(XPNPEP3):c.1040G>A (p.Trp347Ter) SNV Pathogenic 1012365 GRCh37: 22:41310313-41310313
GRCh38: 22:40914309-40914309
4 XPNPEP3 NM_022098.4(XPNPEP3):c.645del (p.Ser216fs) Deletion Pathogenic 1012366 rs751910922 GRCh37: 22:41282372-41282372
GRCh38: 22:40886368-40886368
5 XPNPEP3 NM_022098.4(XPNPEP3):c.1243C>T (p.Arg415Ter) SNV Pathogenic 1031332 GRCh37: 22:41320372-41320372
GRCh38: 22:40924368-40924368
6 XPNPEP3 NM_022098.4(XPNPEP3):c.590-8A>G SNV Conflicting interpretations of pathogenicity 167851 rs143719656 GRCh37: 22:41282309-41282309
GRCh38: 22:40886305-40886305
7 XPNPEP3 NM_022098.4(XPNPEP3):c.817A>G (p.Ser273Gly) SNV Conflicting interpretations of pathogenicity 695160 rs138501598 GRCh37: 22:41303615-41303615
GRCh38: 22:40907611-40907611
8 XPNPEP3 NM_022098.4(XPNPEP3):c.597G>A (p.Thr199=) SNV Conflicting interpretations of pathogenicity 700347 rs151167805 GRCh37: 22:41282324-41282324
GRCh38: 22:40886320-40886320
9 XPNPEP3 NM_022098.4(XPNPEP3):c.1477C>G (p.Pro493Ala) SNV Conflicting interpretations of pathogenicity 538749 rs146023695 GRCh37: 22:41322392-41322392
GRCh38: 22:40926388-40926388
10 XPNPEP3 NM_022098.4(XPNPEP3):c.1376A>G (p.Asp459Gly) SNV Uncertain significance 900009 GRCh37: 22:41322291-41322291
GRCh38: 22:40926287-40926287
11 XPNPEP3 NM_022098.4(XPNPEP3):c.*2C>T SNV Uncertain significance 900010 GRCh37: 22:41322441-41322441
GRCh38: 22:40926437-40926437
12 XPNPEP3 NM_022098.4(XPNPEP3):c.*37T>C SNV Uncertain significance 900011 GRCh37: 22:41322476-41322476
GRCh38: 22:40926472-40926472
13 XPNPEP3 NM_022098.4(XPNPEP3):c.*150T>G SNV Uncertain significance 900012 GRCh37: 22:41322589-41322589
GRCh38: 22:40926585-40926585
14 XPNPEP3 NM_022098.4(XPNPEP3):c.*1470A>C SNV Uncertain significance 900077 GRCh37: 22:41323909-41323909
GRCh38: 22:40927905-40927905
15 XPNPEP3 NM_022098.4(XPNPEP3):c.*1265C>T SNV Uncertain significance 341696 rs548264406 GRCh37: 22:41323704-41323704
GRCh38: 22:40927700-40927700
16 XPNPEP3 NM_022098.4(XPNPEP3):c.*2779C>T SNV Uncertain significance 341719 rs886057532 GRCh37: 22:41325218-41325218
GRCh38: 22:40929214-40929214
17 XPNPEP3 NM_022098.4(XPNPEP3):c.1236+9C>T SNV Uncertain significance 341676 rs778161054 GRCh37: 22:41318526-41318526
GRCh38: 22:40922522-40922522
18 XPNPEP3 NM_022098.4(XPNPEP3):c.1085A>C (p.Glu362Ala) SNV Uncertain significance 341673 rs147185156 GRCh37: 22:41318366-41318366
GRCh38: 22:40922362-40922362
19 XPNPEP3 NM_022098.4(XPNPEP3):c.1244G>A (p.Arg415Gln) SNV Uncertain significance 199163 rs79385822 GRCh37: 22:41320373-41320373
GRCh38: 22:40924369-40924369
20 overlap with 13 genes NC_000022.10:g.(?_41264983)_(41729217_?)dup Duplication Uncertain significance 471411 GRCh37: 22:41264983-41729217
GRCh38: 22:40868979-41333213
21 XPNPEP3 NM_022098.4(XPNPEP3):c.1516G>A (p.Ala506Thr) SNV Uncertain significance 580250 rs139592817 GRCh37: 22:41322431-41322431
GRCh38: 22:40926427-40926427
22 XPNPEP3 NM_022098.4(XPNPEP3):c.119G>A (p.Arg40Lys) SNV Uncertain significance 641596 rs761750025 GRCh37: 22:41265057-41265057
GRCh38: 22:40869053-40869053
23 XPNPEP3 NM_022098.4(XPNPEP3):c.*1557C>G SNV Uncertain significance 900079 GRCh37: 22:41323996-41323996
GRCh38: 22:40927992-40927992
24 XPNPEP3 NM_022098.4(XPNPEP3):c.*1830G>A SNV Uncertain significance 900080 GRCh37: 22:41324269-41324269
GRCh38: 22:40928265-40928265
25 XPNPEP3 NM_022098.4(XPNPEP3):c.*3112T>C SNV Uncertain significance 900142 GRCh37: 22:41325551-41325551
GRCh38: 22:40929547-40929547
26 XPNPEP3 NM_022098.4(XPNPEP3):c.*3194G>A SNV Uncertain significance 900143 GRCh37: 22:41325633-41325633
GRCh38: 22:40929629-40929629
27 XPNPEP3 NM_022098.4(XPNPEP3):c.*4789C>T SNV Uncertain significance 900199 GRCh37: 22:41327228-41327228
GRCh38: 22:40931224-40931224
28 XPNPEP3 NM_022098.4(XPNPEP3):c.*5106T>G SNV Uncertain significance 900200 GRCh37: 22:41327545-41327545
GRCh38: 22:40931541-40931541
29 XPNPEP3 NM_022098.4(XPNPEP3):c.*5162C>G SNV Uncertain significance 900201 GRCh37: 22:41327601-41327601
GRCh38: 22:40931597-40931597
30 XPNPEP3 NM_022098.4(XPNPEP3):c.*5294C>T SNV Uncertain significance 900202 GRCh37: 22:41327733-41327733
GRCh38: 22:40931729-40931729
31 XPNPEP3 NM_022098.4(XPNPEP3):c.-28C>G SNV Uncertain significance 901104 GRCh37: 22:41253158-41253158
GRCh38: 22:40857154-40857154
32 XPNPEP3 NM_022098.4(XPNPEP3):c.112G>A (p.Glu38Lys) SNV Uncertain significance 901105 GRCh37: 22:41265050-41265050
GRCh38: 22:40869046-40869046
33 XPNPEP3 NM_022098.4(XPNPEP3):c.263A>G (p.Gln88Arg) SNV Uncertain significance 901106 GRCh37: 22:41277855-41277855
GRCh38: 22:40881851-40881851
34 XPNPEP3 NM_022098.4(XPNPEP3):c.388C>G (p.Pro130Ala) SNV Uncertain significance 798225 rs199693203 GRCh37: 22:41277980-41277980
GRCh38: 22:40881976-40881976
35 XPNPEP3 NM_022098.4(XPNPEP3):c.*1964G>T SNV Uncertain significance 901239 GRCh37: 22:41324403-41324403
GRCh38: 22:40928399-40928399
36 XPNPEP3 NM_022098.4(XPNPEP3):c.*1996T>G SNV Uncertain significance 901240 GRCh37: 22:41324435-41324435
GRCh38: 22:40928431-40928431
37 XPNPEP3 NM_022098.4(XPNPEP3):c.*2175C>T SNV Uncertain significance 901241 GRCh37: 22:41324614-41324614
GRCh38: 22:40928610-40928610
38 XPNPEP3 NM_022098.4(XPNPEP3):c.*2312G>A SNV Uncertain significance 901242 GRCh37: 22:41324751-41324751
GRCh38: 22:40928747-40928747
39 XPNPEP3 NM_022098.4(XPNPEP3):c.*2406C>T SNV Uncertain significance 901243 GRCh37: 22:41324845-41324845
GRCh38: 22:40928841-40928841
40 XPNPEP3 NM_022098.4(XPNPEP3):c.*3542A>G SNV Uncertain significance 901303 GRCh37: 22:41325981-41325981
GRCh38: 22:40929977-40929977
41 XPNPEP3 NM_022098.4(XPNPEP3):c.*3618A>G SNV Uncertain significance 901304 GRCh37: 22:41326057-41326057
GRCh38: 22:40930053-40930053
42 XPNPEP3 NM_022098.4(XPNPEP3):c.*3698G>T SNV Uncertain significance 901305 GRCh37: 22:41326137-41326137
GRCh38: 22:40930133-40930133
43 XPNPEP3 NM_022098.4(XPNPEP3):c.*3706T>G SNV Uncertain significance 901306 GRCh37: 22:41326145-41326145
GRCh38: 22:40930141-40930141
44 XPNPEP3 NM_022098.4(XPNPEP3):c.*3756A>G SNV Uncertain significance 901307 GRCh37: 22:41326195-41326195
GRCh38: 22:40930191-40930191
45 XPNPEP3 NM_022098.4(XPNPEP3):c.856-2A>G SNV Uncertain significance 632390 rs149609214 GRCh37: 22:41305124-41305124
GRCh38: 22:40909120-40909120
46 XPNPEP3 NM_022098.4(XPNPEP3):c.*5656G>A SNV Uncertain significance 901367 GRCh37: 22:41328095-41328095
GRCh38: 22:40932091-40932091
47 XPNPEP3 NM_022098.4(XPNPEP3):c.792+13T>C SNV Uncertain significance 901647 GRCh37: 22:41282532-41282532
GRCh38: 22:40886528-40886528
48 XPNPEP3 NM_022098.4(XPNPEP3):c.969+6T>C SNV Uncertain significance 901648 GRCh37: 22:41305245-41305245
GRCh38: 22:40909241-40909241
49 XPNPEP3 NM_022098.4(XPNPEP3):c.*869T>A SNV Uncertain significance 901723 GRCh37: 22:41323308-41323308
GRCh38: 22:40927304-40927304
50 XPNPEP3 NM_022098.4(XPNPEP3):c.*995T>C SNV Uncertain significance 901724 GRCh37: 22:41323434-41323434
GRCh38: 22:40927430-40927430

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

72
# Symbol AA change Variation ID SNP ID
1 XPNPEP3 p.Gly453Cys VAR_063820 rs267607179

Expression for Nephronophthisis-Like Nephropathy 1

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

Pathways for Nephronophthisis-Like Nephropathy 1

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

# Super pathways Score Top Affiliating Genes
1 9.98 SEC63 IMMP2L

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 9.46 XPNPEP3 PMPCA MIPEP IMMP2L
2 liver development GO:0001889 9.26 SEC63 PRKCSH
3 nitrogen compound metabolic process GO:0006807 8.96 SEC63 PRKCSH
4 protein processing involved in protein targeting to mitochondrion GO:0006627 8.8 PMPCA MIPEP IMMP2L

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

# Name GO ID Score Top Affiliating Genes
1 metalloendopeptidase activity GO:0004222 8.96 PMPCA MIPEP
2 peptidase activity GO:0008233 8.8 XPNPEP3 MIPEP IMMP2L

Sources for Nephronophthisis-Like Nephropathy 1

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
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35 IUPHAR
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44 MeSH
45 MESH via Orphanet
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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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