NPHP1

nephrocystin 1

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. [provided by RefSeq, Jul 2008]

Known Variants716 total

rsid	Position (GRCh37)	Alleles	Class	ClinVar
rs960612307	2:110,880,908	A/T	—	uncertain significance
rs886054752	2:110,881,046	T/C	—	uncertain significance
rs150558683	2:110,881,118	G/A	—	uncertain significance
rs897567205	2:110,881,130	A/G	—	uncertain significance
rs139901700	2:110,881,162	G/C	—	likely benign
rs1679131109	2:110,881,169	T/C	—	uncertain significance
rs189472793	2:110,881,174	A/G	—	conflicting classifications of pathogenicity
rs376898832	2:110,881,367	G/A	—	uncertain significance
rs2467116396	2:110,881,371	C/G	—	likely benign
rs2467116521	2:110,881,381	T/C	—	uncertain significance
rs2104408356	2:110,881,383	T/G	—	uncertain significance
rs753549193	2:110,881,384	C/T	—	uncertain significance
rs1679144907	2:110,881,385	T/G	—	likely benign
rs759211123	2:110,881,392	A/G	—	likely benign
rs151120697	2:110,881,395	C/T	—	likely benign
rs1301634267	2:110,881,404	A/G	—	likely benign
rs2467116884	2:110,881,407	G/A	—	likely benign
rs1679147532	2:110,881,408	G/A	—	uncertain significance
rs1679151001	2:110,881,436	G/A	—	uncertain significance
rs781531545	2:110,881,442	C/T	—	uncertain significance
rs751440951	2:110,881,443	G/A	—	likely benign
rs1679153432	2:110,881,447	G/A	—	uncertain significance
rs756468448	2:110,881,449	T/A	—	likely benign
rs144850331	2:110,881,452	C/T	—	conflicting classifications of pathogenicity
rs935465878	2:110,881,454	G/A	—	likely benign
rs779089046	2:110,881,459	G/C	—	uncertain significance
rs748152745	2:110,881,466	G/A	—	uncertain significance
rs201077898	2:110,881,469	C/T	—	uncertain significance
rs200631256	2:110,881,470	G/A	—	uncertain significance
rs760619900	2:110,881,472	C/G	missense variant	pathogenic
rs1553479835	2:110,881,473	C/T	—	likely benign
rs2467117743	2:110,881,476	G/A	—	likely benign
rs2467117760	2:110,881,479	T/C	—	likely benign
rs186950965	2:110,881,489	T/C	—	conflicting classifications of pathogenicity
rs2104409055	2:110,881,503	A/G	—	likely benign
rs764769662	2:110,881,505	T/C	—	uncertain significance
rs1212945698	2:110,881,507	A/G	—	uncertain significance
rs1486711364	2:110,881,511	C/A	—	uncertain significance
rs1311042980	2:110,881,516	C/T	—	pathogenic
rs2467118321	2:110,881,518	C/T	—	likely benign
rs768137941	2:110,881,519	C/T	—	uncertain significance
rs141686332	2:110,881,520	G/A	—	uncertain significance
rs1157663897	2:110,881,521	T/C	—	likely benign
rs1574045410	2:110,881,530	A/T	—	likely benign
rs1418617951	2:110,881,535	C/G	—	uncertain significance
rs2467118580	2:110,881,536	T/C	—	likely benign
rs2467118613	2:110,881,539	T/G	—	uncertain significance
rs780427871	2:110,881,541	C/G	—	conflicting classifications of pathogenicity
rs1473345628	2:110,881,545	C/T	—	conflicting classifications of pathogenicity
rs1679169552	2:110,881,548	C/T	—	likely benign
rs2467118749	2:110,881,554	T/G	—	likely benign
rs1559039003	2:110,881,557	G/A	—	likely benign
rs778988243	2:110,881,560	T/C	—	likely benign
rs1383805122	2:110,881,563	G/A	—	likely benign
rs566866150	2:110,881,564	C/T	—	uncertain significance
rs543675502	2:110,881,565	G/A	—	uncertain significance
rs2104409447	2:110,881,567	G/A	—	uncertain significance
rs549736636	2:110,881,570	G/A	—	uncertain significance
rs570047408	2:110,881,575	G/A	—	likely benign
rs2467119188	2:110,881,586	G/A	—	uncertain significance
rs770956057	2:110,881,589	C/T	—	uncertain significance
rs2104409598	2:110,881,592	A/C	—	uncertain significance
rs745639828	2:110,881,595	C/A	—	uncertain significance
rs2467119328	2:110,881,596	A/G	—	likely benign
rs1291356538	2:110,881,597	T/C	—	uncertain significance
rs538690900	2:110,881,598	G/C	—	uncertain significance
rs1004757413	2:110,881,614	C/T	—	likely benign
rs201460699	2:110,881,615	G/A	—	conflicting classifications of pathogenicity
rs2467119480	2:110,881,618	G/A	—	uncertain significance
rs1679177926	2:110,881,628	A/G	—	uncertain significance
rs2467119578	2:110,881,629	C/T	—	likely benign
rs896252440	2:110,881,637	C/T	—	uncertain significance
rs2467119676	2:110,881,638	T/C	—	likely benign
rs2104409792	2:110,881,641	C/T	—	uncertain significance
rs1224236164	2:110,881,652	C/G	—	likely benign
rs1023737876	2:110,881,655	C/T	—	likely benign
rs2467119864	2:110,881,659	C/A	—	likely benign
rs79332992	2:110,881,736	G/A	—	likely benign
rs139209422	2:110,882,126	G/C	—	benign
rs764393095	2:110,883,194	T/C	—	likely benign
rs2467131587	2:110,883,195	G/A	—	likely benign
rs2467131620	2:110,883,199	A/G	—	likely benign
rs2104415404	2:110,883,200	G/A	—	likely benign
rs2467131727	2:110,883,207	A/G	—	likely benign
rs201030203	2:110,883,209	T/G	—	uncertain significance
rs757410501	2:110,883,220	T/G	—	likely benign
rs2104415458	2:110,883,222	A/G	—	uncertain significance
rs1188653340	2:110,883,228	T/C	—	uncertain significance
rs1408406395	2:110,883,236	C/T	—	uncertain significance
rs779746002	2:110,883,241	T/C	—	likely benign
rs1679301117	2:110,883,250	C/T	—	pathogenic
rs2467132150	2:110,883,251	C/T	—	likely pathogenic
rs778531895	2:110,883,253	C/T	—	likely benign
rs138181219	2:110,883,254	G/A	—	uncertain significance
rs370205671	2:110,883,259	C/A	—	likely pathogenic
rs1679303713	2:110,883,263	A/C	—	uncertain significance
rs1574049081	2:110,883,264	G/A	—	likely benign
rs41295841	2:110,883,266	G/A	—	likely benign
rs1574049110	2:110,883,270	A/G	—	likely benign
rs780438944	2:110,886,743	T/C	—	likely benign

Showing 100 of 716 variants. Use the SNP search for the full list.

Gene information from NCBI Gene. Variant classifications from ClinVar.