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NPHP3

Synonyms
CFAP31, MKS7, NPH3, RHPD, RHPD1, SLSN3
External resources
Summary
This gene encodes a protein containing a coiled-coil (CC) domain, a tubulin-tyrosine ligase (TTL) domain, and a tetratrico peptide repeat (TPR) domain. The encoded protein interacts with nephrocystin, it is required for normal ciliary development, and it functions in renal tubular development. Mutations in this gene are associated with nephronophthisis type 3, and also with renal-hepatic-pancreatic dysplasia, and Meckel syndrome type 7. Naturally occurring read-through transcripts exist between this gene and the downstream ACAD11 (acyl-CoA dehydrogenase family, member 11) 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
25
Likely pathogenic
15
VUS
10,622
Likely benign
6,792
Benign
601

Patient phenotypes

Proportions of phenotypes among 39 patients carring pathogenic or likely pathogenic variants on NPHP3 gene are displayed below.

Phenotype class
Patients in 3billion (%)
Abnormality of the nervous system
38.5%
Abnormality of the genitourinary system
33.3%
Abnormality of the musculoskeletal system
25.6%
Abnormality of the eye
23.1%
Abnormality of head or neck
20.5%
Abnormality of the ear
12.8%
Abnormality of the endocrine system
12.8%
Abnormality of the integument
10.3%
Growth abnormality
10.3%
Abnormality of limbs
7.7%
Abnormality of the digestive system
7.7%
Neoplasm
7.7%
Abnormality of the cardiovascular system
5.1%
Abnormality of blood and blood-forming tissues
2.6%
Abnormality of prenatal development or birth
2.6%
Abnormality of the respiratory system
2.6%
Abnormal cellular phenotype
0%
Abnormality of metabolism homeostasis
0%
Abnormality of the breast
0%
Abnormality of the immune system
0%
Abnormality of the thoracic cavity
0%
Abnormality of the voice
0%
Constitutional symptom
0%

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