Disease associated variation - ClinVar Allele ID Type Name RS#dbSNP Phenotype IDs Chromosome Start Stop Reference Alternate 18546 single nucleotide variant NPHP1, IVS18, G-T, +1 -1 MedGen:C1855681,OMIM:256100 na -1 -1 na na 18547 deletion NPHP1, IVS14, 1-BP DEL, G, +1 -1 MedGen:C1855681,OMIM:256100 na -1 -1 na na 18548 single nucleotide variant NM_000272.3(NPHP1):c.80T>A (p.Leu27Ter) 121907898 MedGen:C0687120,SNOMED CT:C0687120;MedGen:C1855681,OMIM:256100 2 110959061 110959061 A T 18548 single nucleotide variant NM_000272.3(NPHP1):c.80T>A (p.Leu27Ter) 121907898 MedGen:C0687120,SNOMED CT:C0687120;MedGen:C1855681,OMIM:256100 2 110201484 110201484 A T 18549 single nucleotide variant NM_000272.3(NPHP1):c.1027G>A (p.Gly343Arg) 121907899 MedGen:C1855681,OMIM:256100 2 110920625 110920625 C T 18549 single nucleotide variant NM_000272.3(NPHP1):c.1027G>A (p.Gly343Arg) 121907899 MedGen:C1855681,OMIM:256100 2 110163048 110163048 C T 18550 deletion NPHP1, DEL -1 MedGen:C1846790,OMIM:609583;MedGen:C1855681,OMIM:256100;MedGen:C0403553,OMIM:266900 na -1 -1 na na 98623 duplication NM_000272.3(NPHP1):c.1184dupC (p.Leu396Serfs) 398123285 MedGen:C1855681,OMIM:256100;MedGen:CN221809 2 110917771 110917771 G GG 98623 duplication NM_000272.3(NPHP1):c.1184dupC (p.Leu396Serfs) 398123285 MedGen:C1855681,OMIM:256100;MedGen:CN221809 2 110160194 110160194 G GG 98624 single nucleotide variant NM_000272.3(NPHP1):c.133A>C (p.Ile45Leu) 145479679 MedGen:CN169374 2 110959008 110959008 T G 98624 single nucleotide variant NM_000272.3(NPHP1):c.133A>C (p.Ile45Leu) 145479679 MedGen:CN169374 2 110201431 110201431 T G 98625 single nucleotide variant NM_000272.3(NPHP1):c.1755T>C (p.Tyr585=) 398123286 MedGen:CN169374 2 110889311 110889311 A G 98625 single nucleotide variant NM_000272.3(NPHP1):c.1755T>C (p.Tyr585=) 398123286 MedGen:CN169374 2 110131734 110131734 A G 98626 single nucleotide variant NM_000272.3(NPHP1):c.654G>A (p.Glu218=) 11675767 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960;MedGen:CN169374 2 110922703 110922703 C T 98626 single nucleotide variant NM_000272.3(NPHP1):c.654G>A (p.Glu218=) 11675767 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960;MedGen:CN169374 2 110165126 110165126 C T 98627 single nucleotide variant NM_000272.3(NPHP1):c.773C>T (p.Ala258Val) 189320299 MedGen:CN169374 2 110922263 110922263 G A 98627 single nucleotide variant NM_000272.3(NPHP1):c.773C>T (p.Ala258Val) 189320299 MedGen:CN169374 2 110164686 110164686 G A 135258 single nucleotide variant NM_000272.3(NPHP1):c.793A>T (p.Asn265Tyr) 587780405 MedGen:CN169374 2 110922243 110922243 T A 135258 single nucleotide variant NM_000272.3(NPHP1):c.793A>T (p.Asn265Tyr) 587780405 MedGen:CN169374 2 110164666 110164666 T A 135259 single nucleotide variant NM_000272.3(NPHP1):c.115C>A (p.Pro39Thr) 33958626 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960;MedGen:CN169374 2 110959026 110959026 G T 135259 single nucleotide variant NM_000272.3(NPHP1):c.115C>A (p.Pro39Thr) 33958626 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960;MedGen:CN169374 2 110201449 110201449 G T 135260 single nucleotide variant NM_000272.3(NPHP1):c.14G>T (p.Arg5Leu) 190983114 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960;MedGen:CN169374 2 110962532 110962532 C A 135260 single nucleotide variant NM_000272.3(NPHP1):c.14G>T (p.Arg5Leu) 190983114 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960;MedGen:CN169374 2 110204955 110204955 C A 135261 single nucleotide variant NM_000272.3(NPHP1):c.810C>T (p.Cys270=) 73954628 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960;MedGen:CN169374 2 110922226 110922226 G A 135261 single nucleotide variant NM_000272.3(NPHP1):c.810C>T (p.Cys270=) 73954628 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960;MedGen:CN169374 2 110164649 110164649 G A 154432 copy number gain GRCh38/hg38 2q13(chr2:110123094-110207198)x3 -1 - 2 110880671 110964775 na na 154432 copy number gain GRCh38/hg38 2q13(chr2:110123094-110207198)x3 -1 - 2 110123094 110207198 na na 154432 copy number gain GRCh38/hg38 2q13(chr2:110123094-110207198)x3 -1 - 2 110237960 110322064 na na 157691 copy number gain GRCh38/hg38 2q13(chr2:110123660-110207160)x3 -1 - 2 110881237 110964737 na na 157691 copy number gain GRCh38/hg38 2q13(chr2:110123660-110207160)x3 -1 - 2 110123660 110207160 na na 157691 copy number gain GRCh38/hg38 2q13(chr2:110123660-110207160)x3 -1 - 2 110238526 110322026 na na 166175 duplication NM_000272.3(NPHP1):c.625-3dupT 200118387 MedGen:C0339527,Orphanet:ORPHA65,SNOMED CT:C0339527 2 110165158 110165158 A AA 166175 duplication NM_000272.3(NPHP1):c.625-3dupT 200118387 MedGen:C0339527,Orphanet:ORPHA65,SNOMED CT:C0339527 2 110922735 110922735 A AA 177328 single nucleotide variant NM_000272.3(NPHP1):c.232T>C (p.Tyr78His) 140446520 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960;MedGen:CN169374 2 110936097 110936097 A G 177328 single nucleotide variant NM_000272.3(NPHP1):c.232T>C (p.Tyr78His) 140446520 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960;MedGen:CN169374 2 110178520 110178520 A G 190731 single nucleotide variant NM_000272.3(NPHP1):c.1109C>G (p.Ala370Gly) 375317119 MedGen:CN169374 2 110919193 110919193 G C 190731 single nucleotide variant NM_000272.3(NPHP1):c.1109C>G (p.Ala370Gly) 375317119 MedGen:CN169374 2 110161616 110161616 G C 190732 single nucleotide variant NM_000272.3(NPHP1):c.1035A>G (p.Gln345=) 371112962 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960;MedGen:CN169374 2 110919267 110919267 T C 190732 single nucleotide variant NM_000272.3(NPHP1):c.1035A>G (p.Gln345=) 371112962 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960;MedGen:CN169374 2 110161690 110161690 T C 190733 single nucleotide variant NM_000272.3(NPHP1):c.1080A>G (p.Gln360=) 794726975 MedGen:CN169374 2 110919222 110919222 T C 190733 single nucleotide variant NM_000272.3(NPHP1):c.1080A>G (p.Gln360=) 794726975 MedGen:CN169374 2 110161645 110161645 T C 190967 single nucleotide variant NM_000272.3(NPHP1):c.1154T>C (p.Ile385Thr) 794727018 MedGen:CN169374 2 110917801 110917801 A G 190967 single nucleotide variant NM_000272.3(NPHP1):c.1154T>C (p.Ile385Thr) 794727018 MedGen:CN169374 2 110160224 110160224 A G 191490 single nucleotide variant NM_000272.3(NPHP1):c.1438-4C>T 151204566 MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN169374 2 110904416 110904416 G A 191490 single nucleotide variant NM_000272.3(NPHP1):c.1438-4C>T 151204566 MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN169374 2 110146839 110146839 G A 194813 deletion NM_000272.3(NPHP1):c.421_426delGAAGAG (p.Glu141_Glu142del) 777574728 MedGen:CN169374 2 110927479 110927484 CTCTTC - 194813 deletion NM_000272.3(NPHP1):c.421_426delGAAGAG (p.Glu141_Glu142del) 777574728 MedGen:CN169374 2 110169902 110169907 CTCTTC - 194814 single nucleotide variant NM_000272.3(NPHP1):c.330-4G>A 774162169 MedGen:CN169374 2 110927579 110927579 C T 194814 single nucleotide variant NM_000272.3(NPHP1):c.330-4G>A 774162169 MedGen:CN169374 2 110170002 110170002 C T 195571 duplication NM_000272.3(NPHP1):c.644_646dupAAG (p.Glu215_Gly216insGlu) 777677768 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960;MedGen:CN169374 2 110922711 110922713 CTT CTTCTT 195571 duplication NM_000272.3(NPHP1):c.644_646dupAAG (p.Glu215_Gly216insGlu) 777677768 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960;MedGen:CN169374 2 110165134 110165136 CTT CTTCTT 195864 single nucleotide variant NM_000272.3(NPHP1):c.830G>A (p.Arg277Gln) 143174377 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960;MedGen:CN169374 2 110922206 110922206 C T 195864 single nucleotide variant NM_000272.3(NPHP1):c.830G>A (p.Arg277Gln) 143174377 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960;MedGen:CN169374 2 110164629 110164629 C T 195865 single nucleotide variant NM_000272.3(NPHP1):c.905G>A (p.Gly302Glu) 140151060 MedGen:CN169374 2 110922131 110922131 C T 195865 single nucleotide variant NM_000272.3(NPHP1):c.905G>A (p.Gly302Glu) 140151060 MedGen:CN169374 2 110164554 110164554 C T 196163 single nucleotide variant NM_000272.3(NPHP1):c.940-17G>A 146343637 MedGen:CN169374 2 110920729 110920729 C T 196163 single nucleotide variant NM_000272.3(NPHP1):c.940-17G>A 146343637 MedGen:CN169374 2 110163152 110163152 C T 212118 single nucleotide variant NM_000272.3(NPHP1):c.2081A>G (p.Gln694Arg) 186950965 MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN169374 2 110881489 110881489 T C 212118 single nucleotide variant NM_000272.3(NPHP1):c.2081A>G (p.Gln694Arg) 186950965 MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN169374 2 110123912 110123912 T C 212119 single nucleotide variant NM_000272.3(NPHP1):c.2029G>C (p.Glu677Gln) 780427871 MedGen:C0687120,SNOMED CT:C0687120 2 110881541 110881541 C G 212119 single nucleotide variant NM_000272.3(NPHP1):c.2029G>C (p.Glu677Gln) 780427871 MedGen:C0687120,SNOMED CT:C0687120 2 110123964 110123964 C G 212120 deletion NM_000272.3(NPHP1):c.728+8delA 863224357 MedGen:C0687120,SNOMED CT:C0687120 2 110165044 110165044 T - 212120 deletion NM_000272.3(NPHP1):c.728+8delA 863224357 MedGen:C0687120,SNOMED CT:C0687120 2 110922621 110922621 T - 213503 duplication NM_000272.3(NPHP1):c.(?_-1)_(*1_?)dup -1 MedGen:C0687120,SNOMED CT:C0687120 na -1 -1 na na 221114 single nucleotide variant NM_000272.3(NPHP1):c.2118G>A (p.Leu706=) 144850331 MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN169374 2 110881452 110881452 C T 221114 single nucleotide variant NM_000272.3(NPHP1):c.2118G>A (p.Leu706=) 144850331 MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN169374 2 110123875 110123875 C T 226829 deletion NM_000272.3(NPHP1):c.(?_-1)_(*1_?)del -1 MedGen:C0687120,SNOMED CT:C0687120 na -1 -1 na na 237153 single nucleotide variant NM_000272.3(NPHP1):c.689C>T (p.Ala230Val) 113450177 MedGen:CN221809;MedGen:CN169374 2 110165091 110165091 G A 237153 single nucleotide variant NM_000272.3(NPHP1):c.689C>T (p.Ala230Val) 113450177 MedGen:CN221809;MedGen:CN169374 2 110922668 110922668 G A 238354 deletion NM_000272.3(NPHP1):c.-94-?_*455+?del -1 MedGen:C0687120,SNOMED CT:C0687120 na -1 -1 na na 243912 deletion 2q13 deletion (290 kb) -1 MedGen:C0687120,SNOMED CT:C0687120 na -1 -1 na na 247889 copy number loss NC_000002.11:g.(?_110881237)_(110963848_?)del -1 - 2 110881237 110963848 na na 250085 single nucleotide variant NM_000272.3(NPHP1):c.1697+19C>T 112090979 MedGen:CN169374 2 110901100 110901100 G A 250085 single nucleotide variant NM_000272.3(NPHP1):c.1697+19C>T 112090979 MedGen:CN169374 2 110143523 110143523 G A 250086 single nucleotide variant NM_000272.3(NPHP1):c.1521-47T>C 1509419 MedGen:CN169374 2 110902193 110902193 A G 250086 single nucleotide variant NM_000272.3(NPHP1):c.1521-47T>C 1509419 MedGen:CN169374 2 110144616 110144616 A G 250087 single nucleotide variant NM_000272.3(NPHP1):c.1437+9G>A 13414551 MedGen:CN169374 2 110905484 110905484 C T 250087 single nucleotide variant NM_000272.3(NPHP1):c.1437+9G>A 13414551 MedGen:CN169374 2 110147907 110147907 C T 250088 single nucleotide variant NM_000272.3(NPHP1):c.1028-47G>A 2271244 MedGen:CN169374 2 110919321 110919321 C T 250088 single nucleotide variant NM_000272.3(NPHP1):c.1028-47G>A 2271244 MedGen:CN169374 2 110161744 110161744 C T 250089 single nucleotide variant NM_000272.3(NPHP1):c.1027+34A>C 79943015 MedGen:CN169374 2 110920591 110920591 T G 250089 single nucleotide variant NM_000272.3(NPHP1):c.1027+34A>C 79943015 MedGen:CN169374 2 110163014 110163014 T G 250090 single nucleotide variant NM_000272.3(NPHP1):c.829C>A (p.Arg277=) 367600757 MedGen:CN169374 2 110164630 110164630 G T 250090 single nucleotide variant NM_000272.3(NPHP1):c.829C>A (p.Arg277=) 367600757 MedGen:CN169374 2 110922207 110922207 G T 267761 duplication NM_000272.3(NPHP1):c.555dupA (p.Pro186Thrfs) 886042650 MedGen:C1855681,OMIM:256100 2 110926098 110926098 T TT 267761 duplication NM_000272.3(NPHP1):c.555dupA (p.Pro186Thrfs) 886042650 MedGen:C1855681,OMIM:256100 2 110168521 110168521 T TT 271173 single nucleotide variant NM_000272.3(NPHP1):c.329+1G>A 376974221 MedGen:CN221809 2 110935999 110935999 C T 271173 single nucleotide variant NM_000272.3(NPHP1):c.329+1G>A 376974221 MedGen:CN221809 2 110178422 110178422 C T 271425 single nucleotide variant NM_000272.3(NPHP1):c.184G>A (p.Ala62Thr) 886043591 MedGen:CN169374 2 110937221 110937221 C T 271425 single nucleotide variant NM_000272.3(NPHP1):c.184G>A (p.Ala62Thr) 886043591 MedGen:CN169374 2 110179644 110179644 C T 271582 single nucleotide variant NM_000272.3(NPHP1):c.1121C>T (p.Thr374Ile) 140469160 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960;MedGen:CN169374 2 110919181 110919181 G A 271582 single nucleotide variant NM_000272.3(NPHP1):c.1121C>T (p.Thr374Ile) 140469160 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960;MedGen:CN169374 2 110161604 110161604 G A 272606 single nucleotide variant NM_000272.3(NPHP1):c.971T>C (p.Met324Thr) 114250691 MedGen:CN169374 2 110920681 110920681 A G 272606 single nucleotide variant NM_000272.3(NPHP1):c.971T>C (p.Met324Thr) 114250691 MedGen:CN169374 2 110163104 110163104 A G 272766 single nucleotide variant NM_000272.3(NPHP1):c.1955C>T (p.Thr652Met) 201460699 MedGen:CN169374 2 110881615 110881615 G A 272766 single nucleotide variant NM_000272.3(NPHP1):c.1955C>T (p.Thr652Met) 201460699 MedGen:CN169374 2 110124038 110124038 G A 274617 single nucleotide variant NM_000272.3(NPHP1):c.979A>G (p.Ile327Val) 750291966 MedGen:CN169374 2 110920673 110920673 T C 274617 single nucleotide variant NM_000272.3(NPHP1):c.979A>G (p.Ile327Val) 750291966 MedGen:CN169374 2 110163096 110163096 T C 275479 single nucleotide variant NM_000272.3(NPHP1):c.50A>G (p.Asn17Ser) 200480007 MedGen:CN169374 2 110962496 110962496 T C 275479 single nucleotide variant NM_000272.3(NPHP1):c.50A>G (p.Asn17Ser) 200480007 MedGen:CN169374 2 110204919 110204919 T C 275484 single nucleotide variant NM_000272.3(NPHP1):c.1309T>G (p.Trp437Gly) 755958462 MedGen:CN169374 2 110907776 110907776 A C 275484 single nucleotide variant NM_000272.3(NPHP1):c.1309T>G (p.Trp437Gly) 755958462 MedGen:CN169374 2 110150199 110150199 A C 275519 single nucleotide variant NM_000272.3(NPHP1):c.619C>G (p.Leu207Val) 144088139 MedGen:CN169374 2 110926034 110926034 G C 275519 single nucleotide variant NM_000272.3(NPHP1):c.619C>G (p.Leu207Val) 144088139 MedGen:CN169374 2 110168457 110168457 G C 281544 deletion NM_000272.3(NPHP1):c.*336_*338delAAC 555468187 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110123453 110123455 GTT - 281544 deletion NM_000272.3(NPHP1):c.*336_*338delAAC 555468187 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110881030 110881032 GTT - 281552 single nucleotide variant NM_000272.3(NPHP1):c.*322A>G 886054752 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110123469 110123469 T C 281552 single nucleotide variant NM_000272.3(NPHP1):c.*322A>G 886054752 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110881046 110881046 T C 281554 single nucleotide variant NM_000272.3(NPHP1):c.2100C>T (p.Gly700=) 200631256 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110123893 110123893 G A 281554 single nucleotide variant NM_000272.3(NPHP1):c.2100C>T (p.Gly700=) 200631256 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110881470 110881470 G A 281560 single nucleotide variant NM_000272.3(NPHP1):c.1889C>T (p.Ser630Leu) 138181219 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110125677 110125677 G A 281560 single nucleotide variant NM_000272.3(NPHP1):c.1889C>T (p.Ser630Leu) 138181219 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110883254 110883254 G A 281574 single nucleotide variant NM_000272.3(NPHP1):c.1690G>C (p.Val564Leu) 573192954 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110143549 110143549 C G 281574 single nucleotide variant NM_000272.3(NPHP1):c.1690G>C (p.Val564Leu) 573192954 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110901126 110901126 C G 281578 single nucleotide variant NM_000272.3(NPHP1):c.1637G>A (p.Arg546Lys) 149887461 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110143602 110143602 C T 281578 single nucleotide variant NM_000272.3(NPHP1):c.1637G>A (p.Arg546Lys) 149887461 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110901179 110901179 C T 282227 single nucleotide variant NM_000272.3(NPHP1):c.1447G>C (p.Glu483Gln) 886054753 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110146826 110146826 C G 282227 single nucleotide variant NM_000272.3(NPHP1):c.1447G>C (p.Glu483Gln) 886054753 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110904403 110904403 C G 282229 single nucleotide variant NM_000272.3(NPHP1):c.860A>G (p.Asn287Ser) 139787582 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110164599 110164599 T C 282229 single nucleotide variant NM_000272.3(NPHP1):c.860A>G (p.Asn287Ser) 139787582 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110922176 110922176 T C 282230 single nucleotide variant NM_000272.3(NPHP1):c.456A>G (p.Ser152=) 143163969 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110169872 110169872 T C 282230 single nucleotide variant NM_000272.3(NPHP1):c.456A>G (p.Ser152=) 143163969 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110927449 110927449 T C 283553 single nucleotide variant NM_000272.3(NPHP1):c.1333C>T (p.Arg445Cys) 375907280 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110148020 110148020 G A 283553 single nucleotide variant NM_000272.3(NPHP1):c.1333C>T (p.Arg445Cys) 375907280 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110905597 110905597 G A 283554 single nucleotide variant NM_000272.3(NPHP1):c.969G>A (p.Thr323=) 141763330 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110163106 110163106 C T 283554 single nucleotide variant NM_000272.3(NPHP1):c.969G>A (p.Thr323=) 141763330 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110920683 110920683 C T 283555 single nucleotide variant NM_000272.3(NPHP1):c.593A>G (p.Asn198Ser) 886054756 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110168483 110168483 T C 283555 single nucleotide variant NM_000272.3(NPHP1):c.593A>G (p.Asn198Ser) 886054756 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110926060 110926060 T C 283689 single nucleotide variant NM_000272.3(NPHP1):c.*250C>T 150558683 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110123541 110123541 G A 283689 single nucleotide variant NM_000272.3(NPHP1):c.*250C>T 150558683 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110881118 110881118 G A 283710 single nucleotide variant NM_000272.3(NPHP1):c.988G>C (p.Gly330Arg) 886054754 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110163087 110163087 C G 283710 single nucleotide variant NM_000272.3(NPHP1):c.988G>C (p.Gly330Arg) 886054754 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110920664 110920664 C G 283715 single nucleotide variant NM_000272.3(NPHP1):c.669C>T (p.Gly223=) 886054755 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110165111 110165111 G A 283715 single nucleotide variant NM_000272.3(NPHP1):c.669C>T (p.Gly223=) 886054755 MedGen:C0431399,Orphanet:ORPHA475,SNOMED CT:C0431399;MedGen:C0687120,SNOMED CT:C0687120;MedGen:CN117960,Orphanet:ORPHA3156,SNOMED CT:CN117960 2 110922688 110922688 G A

Disease associated variation - GWASdb Chr Pos SNP ID(dbSNP 142) Ref Alt Ori SNP ID P-value Drug Name Drug Anno GWAS Trait HPO ID DO ID AA Type Trait or Drug 2 110958329 rs17463266 C T rs17463266 9.06E-04 Amyotrophic lateral sclerosis (sporadic) HPOID:0007354 DOID:332 C intron GWASdb_trait 2 110959008 rs145479679 T G rs145479679 0.000000084 Breast cancer(er negative) HPOID:0003002 DOID:1612 T missense GWASdb_trait

Disease associated variation - GWAS Central Study Name Source Marker Accession Chromosome Marker Start Marker Stop Alleles Gene Section P-value -log(p-value) GWAS of prostate cancer rs3789735 2 110886142 110886142 intronic 0.858812 0.0661018958876603 GWAS of prostate cancer rs2864665 2 110900895 110900895 intronic 0.818746 0.0868508087493772 GWAS of prostate cancer rs11240790 2 110889108 110889108 intronic 0.816188 0.0882097947282636 GWAS of prostate cancer rs10496435 2 110929173 110929173 intronic 0.695509 0.15769724579408

Disease associated variation - OMIM Ensembl_gene_ID Approved Gene Symbol MIM Number ENSG00000144061.12 NPHP1 607100