NPHP1 Chromosome 2
Nephrocystin 1
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What This Gene Does
This gene encodes a protein with src homology domain 3 (SH3) patterns. This protein interacts with Crk-associated substrate, and it appears to function in the control of cell division, as well as in cell-cell and cell-matrix adhesion signaling, likely as part of a multifunctional complex localized in actin- and microtubule-based structures. Mutations in this gene cause familial juvenile nephronophthisis type 1, a kidney disorder involving both tubules and glomeruli. Defects in this gene are also associated with Senior-Loken syndrome type 1, also referred to as juvenile nephronophthisis with Leber amaurosis, which is characterized by kidney and eye disease, and with Joubert syndrome type 4, which is characterized by cerebellar ataxia, oculomotor apraxia, psychomotor delay and neonatal breathing abnormalities, sometimes including retinal dystrophy and renal disease. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Gene Info
Gene Group
NPHP complex
Locus Type
gene with protein product
Location
2q13
Ensembl
ENSG00000144061
Associated Conditions (15)
Nephronophthisis 1
Joubert syndrome with renal defect
Senior-Loken syndrome 1
Retinal dystrophy
Nephronophthisis
NPHP1-related disorder
Inborn genetic diseases
Joubert syndrome and related disorders
Leber congenital amaurosis
Thyroid cancer
nonmedullary
1
Ovarian serous cystadenocarcinoma
Clear cell carcinoma of kidney
Congenital anomaly of kidney and urinary tract
Key Variants
RS114250691
Conflicting classifications of pathogenicity
Nephronophthisis 1, Joubert syndrome with renal defect, Senior-Loken syndrome 1
Health Risk
RS1253817401
Conflicting classifications of pathogenicity
Nephronophthisis, Nephronophthisis
Health Risk
RS1266229950
Conflicting classifications of pathogenicity
Nephronophthisis, Nephronophthisis 1, Joubert syndrome with renal defect
Health Risk
RS1280756117
Conflicting classifications of pathogenicity
Nephronophthisis, NPHP1-related disorder, Nephronophthisis
Health Risk
RS1365022834
Conflicting classifications of pathogenicity
Joubert syndrome with renal defect, Nephronophthisis 1, Senior-Loken syndrome 1
Health Risk
RS139787582
Conflicting classifications of pathogenicity
Joubert syndrome with renal defect, Nephronophthisis, Senior-Loken syndrome 1
Health Risk
RS140151060
Conflicting classifications of pathogenicity
Nephronophthisis, Inborn genetic diseases, NPHP1-related disorder
Health Risk
RS140446520
Conflicting classifications of pathogenicity
Nephronophthisis, Joubert syndrome with renal defect, Senior-Loken syndrome 1
Health Risk
RS140469160
Conflicting classifications of pathogenicity
Senior-Loken syndrome 1, Joubert syndrome with renal defect, Nephronophthisis
Health Risk
RS141763330
Conflicting classifications of pathogenicity
Senior-Loken syndrome 1, Nephronophthisis, Joubert syndrome with renal defect
Health Risk
RS143163969
Conflicting classifications of pathogenicity
Joubert syndrome with renal defect, Senior-Loken syndrome 1, Nephronophthisis 1
Health Risk
RS144217506
Conflicting classifications of pathogenicity
Nephronophthisis, Nephronophthisis
Health Risk
All Variants (157)
| RSID | Category | Clinical Significance | Conditions |
|---|---|---|---|
| RS1193790186 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Joubert syndrome with renal defect |
| RS1327440899 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Joubert syndrome with renal defect |
| RS1336978749 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Joubert syndrome with renal defect |
| RS1454994826 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Joubert syndrome with renal defect |
| RS1482130141 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Joubert syndrome with renal defect |
| RS1482624366 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Joubert syndrome with renal defect |
| RS1559043866 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Joubert syndrome with renal defect |
| RS1681356752 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Joubert syndrome with renal defect |
| RS1683656584 | Health Risk | Likely pathogenic | Nephronophthisis, Nephronophthisis |
| RS2104548702 | Health Risk | Likely pathogenic | Nephronophthisis 1, Nephronophthisis 1 |
| RS2467132150 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Joubert syndrome with renal defect |
| RS2467132343 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Joubert syndrome with renal defect |
| RS2467238709 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Joubert syndrome with renal defect |
| RS2467251149 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Nephronophthisis, Joubert syndrome with renal defect |
| RS2467251453 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Joubert syndrome with renal defect |
| RS2467251559 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Joubert syndrome with renal defect |
| RS2467251817 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Thyroid cancer, nonmedullary |
| RS2467252177 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Joubert syndrome with renal defect |
| RS2467259873 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Joubert syndrome with renal defect |
| RS2467272833 | Health Risk | Likely pathogenic | Nephronophthisis, Nephronophthisis |
| RS2467272890 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Joubert syndrome with renal defect |
| RS2467273765 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Joubert syndrome with renal defect |
| RS2467332716 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Joubert syndrome with renal defect |
| RS2467344481 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Joubert syndrome with renal defect |
| RS2467345309 | Health Risk | Likely pathogenic | Nephronophthisis, Nephronophthisis |
| RS2467354598 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Joubert syndrome with renal defect |
| RS2467370218 | Health Risk | Likely pathogenic | Nephronophthisis, Joubert syndrome with renal defect, Nephronophthisis |
| RS2467370400 | Health Risk | Likely pathogenic | Nephronophthisis, Nephronophthisis |
| RS2467395269 | Health Risk | Likely pathogenic | Nephronophthisis, Nephronophthisis |
| RS2467403268 | Health Risk | Likely pathogenic | Nephronophthisis, Nephronophthisis, NPHP1-related disorder |
| RS2467405206 | Health Risk | Likely pathogenic | Nephronophthisis 1, Nephronophthisis 1 |
| RS2467598236 | Health Risk | Likely pathogenic | Nephronophthisis, Nephronophthisis |
| RS2467599107 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Nephronophthisis, Joubert syndrome with renal defect |
| RS370205671 | Health Risk | Likely pathogenic | Nephronophthisis, Nephronophthisis |
| RS564605452 | Health Risk | Likely pathogenic | Joubert syndrome and related disorders, Joubert syndrome with renal defect, Joubert syndrome and related disorders |
| RS745806504 | Health Risk | Likely pathogenic | Nephronophthisis, Nephronophthisis 1, Senior-Loken syndrome 1 |
| RS752708835 | Health Risk | Likely pathogenic | Joubert syndrome and related disorders, Joubert syndrome with renal defect, Nephronophthisis |
| RS753607290 | Health Risk | Likely pathogenic | — |
| RS760619900 | Health Risk | Likely pathogenic | — |
| RS762322858 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Joubert syndrome with renal defect |
| RS773781058 | Health Risk | Likely pathogenic | Nephronophthisis, Joubert syndrome with renal defect, Nephronophthisis 1 |
| RS774810198 | Health Risk | Likely pathogenic | Joubert syndrome with renal defect, Joubert syndrome with renal defect |
| RS1017750255 | Health Risk | Pathogenic | Nephronophthisis, Joubert syndrome and related disorders, Joubert syndrome with renal defect |
| RS1204764976 | Health Risk | Pathogenic | Nephronophthisis, Nephronophthisis |
| RS121907898 | Health Risk | Pathogenic | Nephronophthisis 1, Nephronophthisis, Nephronophthisis 1 |
| RS121907899 | Health Risk | Pathogenic | Nephronophthisis 1, Nephronophthisis, NPHP1-related disorder |
| RS1328879943 | Health Risk | Pathogenic | Nephronophthisis, Nephronophthisis |
| RS1374365071 | Health Risk | Pathogenic | Nephronophthisis, Nephronophthisis |
| RS1388373598 | Health Risk | Pathogenic | Nephronophthisis, Nephronophthisis 1, Senior-Loken syndrome 1 |
| RS1458494785 | Health Risk | Pathogenic | Nephronophthisis, NPHP1-related disorder, Nephronophthisis 1 |