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NPHP1

Synonyms
JBTS4, NPH1, SLSN1
External resources
Summary
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.

Variant counts

Variant classification counts according to ACMG guideline on all identified variants among our tested samples are listed. The variants with over 5% variant frequency in population genome databases ( gnomAD, dbSNP, etc) are excluded.

Pathogenic
13
Likely pathogenic
0
VUS
2,459
Likely benign
2,072
Benign
263

Patient phenotypes

Proportions of phenotypes among 13 patients carring pathogenic or likely pathogenic variants on NPHP1 gene are displayed below.

Phenotype class
Patients in 3billion (%)
Abnormality of the musculoskeletal system
61.5%
Abnormality of the nervous system
53.8%
Abnormality of the eye
38.5%
Abnormality of head or neck
30.8%
Abnormality of limbs
15.4%
Growth abnormality
15.4%
Abnormality of prenatal development or birth
7.7%
Abnormality of the breast
7.7%
Abnormality of the digestive system
7.7%
Abnormality of the ear
7.7%
Abnormality of the endocrine system
7.7%
Abnormality of the genitourinary system
7.7%
Abnormality of the integument
7.7%
Abnormal cellular phenotype
0%
Abnormality of blood and blood-forming tissues
0%
Abnormality of metabolism homeostasis
0%
Abnormality of the cardiovascular system
0%
Abnormality of the immune system
0%
Abnormality of the respiratory system
0%
Abnormality of the thoracic cavity
0%
Abnormality of the voice
0%
Constitutional symptom
0%
Neoplasm
0%

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