"GeneDx"[submitter] AND "NPHP3"[gene] - ClinVar - NCBI

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	Variation	Gene (Protein Change)	Type (Consequence)	Condition	Classification, Review status
Select item 152454	GRCh38/hg38 3q22.1-23(chr3:129817243-141425155)x1	A4GNT, ACAD11 +282 more	Copy number loss	See cases	GPathogenic
Select item 60091	GRCh38/hg38 3q22.1(chr3:132639520-132972626)x1	ACAD11, LOC129937585 +8 more	Copy number loss	See cases	GUncertain significance
Select item 57793	GRCh38/hg38 3q22.1(chr3:132662034-133263499)x3	LOC112903835, LOC112903836 +11 more	Copy number gain	See cases	GUncertain significance
Select item 343358	NM_153240.5(NPHP3):c.*815G>A	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	NPHP3-related Meckel-like syndrome +3 more	GConflicting classifications of pathogenicity
Select item 343359	NM_153240.5(NPHP3):c.*785G>A	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	Nephronophthisis 3 +3 more	GBenign/Likely benign
Select item 343361	NM_153240.5(NPHP3):c.*759G>A	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	Nephronophthisis 3 +3 more	GConflicting classifications of pathogenicity
Select item 2499840	NM_153240.5(NPHP3):c.*673C>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	not provided	GLikely benign
Select item 343363	NM_153240.5(NPHP3):c.*657C>T	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	NPHP3-related Meckel-like syndrome +3 more	GBenign
Select item 1264737	NM_153240.5(NPHP3):c.*651dup	NPHP3, NPHP3-ACAD11	Duplication (3 prime UTR variant)	not provided	GBenign
Select item 1259608	NM_153240.5(NPHP3):c.*651del	NPHP3, NPHP3-ACAD11	Deletion (3 prime UTR variant)	not provided	GBenign
Select item 343367	NM_153240.5(NPHP3):c.650_651del	NPHP3, NPHP3-ACAD11	Deletion (3 prime UTR variant)	Nephronophthisis +3 more	GConflicting classifications of pathogenicity
Select item 343369	NM_153240.5(NPHP3):c.*266G>A	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	NPHP3-related Meckel-like syndrome +3 more	GBenign/Likely benign
Select item 262714	NM_153240.5(NPHP3):c.3971T>C (p.Phe1324Ser)	NPHP3-ACAD11, NPHP3 (F1324S)	Single nucleotide variant (non-coding transcript variant +1 more)	not specified +3 more	GConflicting classifications of pathogenicity
Select item 594171	NM_153240.5(NPHP3):c.3964_3966del (p.Asn1322del)	NPHP3, NPHP3-ACAD11 (N1322del)	Deletion (non-coding transcript variant +1 more)	Nephronophthisis +1 more	GUncertain significance
Select item 188351	NM_153240.5(NPHP3):c.3941G>C (p.Ser1314Thr)	NPHP3-ACAD11, NPHP3 (S1314T)	Single nucleotide variant (non-coding transcript variant +1 more)	NPHP3-related Meckel-like syndrome +5 more	GBenign/Likely benign
Select item 218850	NM_153240.5(NPHP3):c.3913C>T (p.Arg1305Cys)	NPHP3, NPHP3-ACAD11 (R1305C)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis +6 more	GBenign/Likely benign
Select item 598130	NM_153240.5(NPHP3):c.3901A>C (p.Lys1301Gln)	NPHP3, NPHP3-ACAD11 (K1301Q)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis +4 more	GUncertain significance
Select item 673525	NM_153240.5(NPHP3):c.3812+290T>C	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 667705	NM_153240.5(NPHP3):c.3812+126C>T	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 1249561	NM_153240.5(NPHP3):c.3812+117T>C	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 2575788	NM_153240.5(NPHP3):c.3776G>A (p.Arg1259Gln)	NPHP3, NPHP3-ACAD11 (R1259Q)	Single nucleotide variant (non-coding transcript variant +1 more)	not provided	GUncertain significance
Select item 1706110	NM_153240.5(NPHP3):c.3764G>A (p.Arg1255Gln)	NPHP3, NPHP3-ACAD11 (R1255Q)	Single nucleotide variant (non-coding transcript variant +1 more)	not provided +1 more	GUncertain significance
Select item 262710	NM_153240.5(NPHP3):c.3759G>A (p.Leu1253=)	NPHP3, NPHP3-ACAD11	Single nucleotide variant (non-coding transcript variant +1 more)	not specified +5 more	GBenign
Select item 195996	NM_153240.5(NPHP3):c.3756C>G (p.Ser1252Arg)	NPHP3, NPHP3-ACAD11 (S1252R)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis +4 more	GConflicting classifications of pathogenicity
Select item 3367819	NM_153240.5(NPHP3):c.3728A>C (p.Glu1243Ala)	NPHP3, NPHP3-ACAD11 (E1243A)	Single nucleotide variant (non-coding transcript variant +1 more)	not provided	GUncertain significance
Select item 262709	NM_153240.5(NPHP3):c.3717G>A (p.Leu1239=)	NPHP3, NPHP3-ACAD11	Single nucleotide variant (non-coding transcript variant +1 more)	not specified +5 more	GConflicting classifications of pathogenicity
Select item 422589	NM_153240.5(NPHP3):c.3697-7del	NPHP3, NPHP3-ACAD11	Deletion (intron variant)	not provided +1 more	GBenign
Select item 1261340	NM_153240.5(NPHP3):c.3697-151C>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 262708	NM_153240.5(NPHP3):c.3664T>C (p.Leu1222=)	NPHP3, NPHP3-ACAD11	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis +2 more	GBenign/Likely benign
Select item 262707	NM_153240.5(NPHP3):c.3663C>T (p.Ala1221=)	NPHP3, NPHP3-ACAD11	Single nucleotide variant (non-coding transcript variant +1 more)	Renal-hepatic-pancreatic dysplasia 1 +6 more	GBenign/Likely benign
Select item 288174	NM_153240.5(NPHP3):c.3662C>T (p.Ala1221Val)	NPHP3-ACAD11, NPHP3 (A1221V)	Single nucleotide variant (non-coding transcript variant +1 more)	not specified +5 more	GConflicting classifications of pathogenicity
Select item 1313645	NM_153240.5(NPHP3):c.3627A>C (p.Lys1209Asn)	NPHP3, NPHP3-ACAD11 (K1209N)	Single nucleotide variant (non-coding transcript variant +1 more)	not provided	GUncertain significance
Select item 392050	NM_153240.5(NPHP3):c.3592C>T (p.Pro1198Ser)	NPHP3, NPHP3-ACAD11 (P1198S)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis +1 more	GUncertain significance
Select item 1218127	NM_153240.5(NPHP3):c.3571-73_3571-70del	NPHP3, NPHP3-ACAD11	Deletion (intron variant)	not provided	GLikely benign
Select item 1227758	NM_153240.5(NPHP3):c.3571-112dup	NPHP3, NPHP3-ACAD11	Duplication (intron variant)	not provided	GBenign
Select item 1189157	NM_153240.5(NPHP3):c.3570+181T>C	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 262706	NM_153240.5(NPHP3):c.3570+9G>T	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not specified +5 more	GConflicting classifications of pathogenicity
Select item 343375	NM_153240.5(NPHP3):c.3570+4A>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided +4 more	GUncertain significance
Select item 343376	NM_153240.5(NPHP3):c.3563A>G (p.Lys1188Arg)	NPHP3, NPHP3-ACAD11 (K1188R)	Single nucleotide variant (non-coding transcript variant +1 more)	NPHP3-related Meckel-like syndrome +4 more	GUncertain significance
Select item 167378	NM_153240.5(NPHP3):c.3550G>A (p.Ala1184Thr)	NPHP3-ACAD11, NPHP3 (A1184T)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis +6 more	GConflicting classifications of pathogenicity
Select item 262705	NM_153240.5(NPHP3):c.3500G>A (p.Arg1167His)	NPHP3, NPHP3-ACAD11 (R1167H)	Single nucleotide variant (non-coding transcript variant +1 more)	not specified +3 more	GConflicting classifications of pathogenicity
Select item 580774	NM_153240.5(NPHP3):c.3499C>T (p.Arg1167Cys)	NPHP3, NPHP3-ACAD11 (R1167C)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis +4 more	GUncertain significance
Select item 381594	NM_153240.5(NPHP3):c.3422T>C (p.Leu1141Pro)	NPHP3, NPHP3-ACAD11 (L1141P)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis +2 more	GConflicting classifications of pathogenicity
Select item 419574	NM_153240.5(NPHP3):c.3345dup (p.Leu1116fs)	NPHP3, NPHP3-ACAD11 (L1116fs)	Duplication (non-coding transcript variant +1 more)	not provided	GPathogenic
Select item 1525682	NM_153240.5(NPHP3):c.3339C>A (p.Asp1113Glu)	NPHP3, NPHP3-ACAD11 (D1113E)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis +1 more	GUncertain significance
Select item 2499220	NM_153240.5(NPHP3):c.3330-3C>T	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GUncertain significance
Select item 1250020	NM_153240.5(NPHP3):c.3329+198dup	NPHP3, NPHP3-ACAD11	Duplication (intron variant)	not provided	GBenign
Select item 946581	NM_153240.5(NPHP3):c.3326T>G (p.Leu1109Arg)	NPHP3, NPHP3-ACAD11 (L1109R)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis +4 more	GUncertain significance
Select item 562245	NM_153240.5(NPHP3):c.3287T>C (p.Leu1096Pro)	NPHP3-ACAD11, NPHP3 (L1096P)	Single nucleotide variant (non-coding transcript variant +1 more)	not provided	GUncertain significance
Select item 195784	NM_153240.5(NPHP3):c.3281G>A (p.Arg1094Gln)	NPHP3, NPHP3-ACAD11 (R1094Q)	Single nucleotide variant (non-coding transcript variant +1 more)	not specified +5 more	GUncertain significance
Select item 262704	NM_153240.5(NPHP3):c.3252A>G (p.Thr1084=)	NPHP3, NPHP3-ACAD11	Single nucleotide variant (non-coding transcript variant +1 more)	Renal-hepatic-pancreatic dysplasia 1 +4 more	GConflicting classifications of pathogenicity
Select item 499991	NM_153240.5(NPHP3):c.3237G>C (p.Gln1079His)	NPHP3, NPHP3-ACAD11 (Q1079H)	Single nucleotide variant (non-coding transcript variant +1 more)	NPHP3-related Meckel-like syndrome +4 more	GUncertain significance
Select item 577594	NM_153240.5(NPHP3):c.3226C>T (p.Arg1076Trp)	NPHP3, NPHP3-ACAD11 (R1076W)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis +1 more	GConflicting classifications of pathogenicity
Select item 281975	NM_153240.5(NPHP3):c.3221G>A (p.Arg1074His)	NPHP3-ACAD11, NPHP3 (R1074H)	Single nucleotide variant (non-coding transcript variant +1 more)	not specified +2 more	GLikely benign
Select item 1183890	NM_153240.5(NPHP3):c.3205G>A (p.Gly1069Arg)	NPHP3, NPHP3-ACAD11 (G1069R)	Single nucleotide variant (non-coding transcript variant +1 more)	not provided +4 more	GUncertain significance
Select item 1216414	NM_153240.5(NPHP3):c.3202-100T>C	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 1275140	NM_153240.5(NPHP3):c.3202-106A>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 262703	NM_153240.5(NPHP3):c.3189A>G (p.Lys1063=)	NPHP3, NPHP3-ACAD11	Single nucleotide variant (non-coding transcript variant +1 more)	Renal-hepatic-pancreatic dysplasia 1 +6 more	GBenign/Likely benign
Select item 96515	NM_153240.5(NPHP3):c.3126-4del	NPHP3, NPHP3-ACAD11	Deletion (intron variant)	Nephronophthisis +2 more	GBenign
Select item 673892	NM_153240.5(NPHP3):c.3126-276A>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 1216236	NM_153240.5(NPHP3):c.3125+189A>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 262702	NM_153240.5(NPHP3):c.3125+7dup	NPHP3, NPHP3-ACAD11	Duplication (intron variant)	not specified +4 more	GBenign
Select item 2571847	NM_153240.5(NPHP3):c.3094G>A (p.Ala1032Thr)	NPHP3, NPHP3-ACAD11 (A1032T)	Single nucleotide variant (non-coding transcript variant +1 more)	not provided	GUncertain significance
Select item 262701	NM_153240.5(NPHP3):c.3093A>G (p.Glu1031=)	NPHP3, NPHP3-ACAD11	Single nucleotide variant (non-coding transcript variant +1 more)	Renal-hepatic-pancreatic dysplasia 1 +6 more	GConflicting classifications of pathogenicity
Select item 286995	NM_153240.5(NPHP3):c.3062C>T (p.Ala1021Val)	NPHP3, NPHP3-ACAD11 (A1021V)	Single nucleotide variant (non-coding transcript variant +1 more)	not provided +4 more	GUncertain significance
Select item 499254	NM_153240.5(NPHP3):c.3032C>T (p.Ala1011Val)	NPHP3, NPHP3-ACAD11 (A1011V)	Single nucleotide variant (non-coding transcript variant +1 more)	not provided +5 more	GUncertain significance
Select item 385384	NM_153240.5(NPHP3):c.2931A>G (p.Leu977=)	NPHP3, NPHP3-ACAD11	Single nucleotide variant (non-coding transcript variant +1 more)	NPHP3-related Meckel-like syndrome +4 more	GLikely benign
Select item 1190535	NM_153240.5(NPHP3):c.2883+60T>C	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 262700	NM_153240.5(NPHP3):c.2883+13G>C	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	Nephronophthisis +1 more	GBenign/Likely benign
Select item 343382	NM_153240.5(NPHP3):c.2881C>G (p.Gln961Glu)	NPHP3, NPHP3-ACAD11 (Q961E)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis 3 +4 more	GUncertain significance
Select item 289555	NM_153240.5(NPHP3):c.2769C>T (p.Phe923=)	NPHP3, NPHP3-ACAD11	Single nucleotide variant (non-coding transcript variant +1 more)	not provided +5 more	GConflicting classifications of pathogenicity
Select item 220868	NM_153240.5(NPHP3):c.2694-2_2694-1del	NPHP3, NPHP3-ACAD11	Deletion (splice acceptor variant)	Renal-hepatic-pancreatic dysplasia 1 +4 more	GPathogenic/Likely pathogenic
Select item 1221243	NM_153240.5(NPHP3):c.2693+295G>A	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 1193801	NM_153240.5(NPHP3):c.2693+233A>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 1186230	NM_153240.5(NPHP3):c.2693+130A>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 1212669	NM_153240.5(NPHP3):c.2693+115A>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 262699	NM_153240.5(NPHP3):c.2693+17A>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	Renal-hepatic-pancreatic dysplasia 1 +4 more	GBenign/Likely benign
Select item 96513	NM_153240.5(NPHP3):c.2610G>A (p.Pro870=)	NPHP3, NPHP3-ACAD11	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis 3 +5 more	GBenign
Select item 3369547	NM_153240.5(NPHP3):c.2574G>A (p.Gln858=)	NPHP3, NPHP3-ACAD11	Single nucleotide variant (non-coding transcript variant +1 more)	not provided	GUncertain significance
Select item 96512	NM_153240.5(NPHP3):c.2571-7T>C	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	Nephronophthisis 3 +6 more	GBenign/Likely benign
Select item 675000	NM_153240.5(NPHP3):c.2571-103G>T	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 1029229	NM_153240.5(NPHP3):c.2570+1G>T	NPHP3, NPHP3-ACAD11	Single nucleotide variant (splice donor variant)	not provided +1 more	GPathogenic/Likely pathogenic
Select item 571559	NM_153240.5(NPHP3):c.2563C>T (p.Gln855Ter)	NPHP3, NPHP3-ACAD11 (Q855*)	Single nucleotide variant (non-coding transcript variant +1 more)	not provided +4 more	GPathogenic/Likely pathogenic
Select item 646548	NM_153240.5(NPHP3):c.2531A>G (p.Tyr844Cys)	NPHP3, NPHP3-ACAD11 (Y844C)	Single nucleotide variant (non-coding transcript variant +1 more)	not provided +4 more	GUncertain significance
Select item 674999	NM_153240.5(NPHP3):c.2476-72T>C	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 674998	NM_153240.5(NPHP3):c.2476-84A>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 1194646	NM_153240.5(NPHP3):c.2476-262T>C	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 1215613	NM_153240.5(NPHP3):c.2475+309A>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 1181634	NM_153240.5(NPHP3):c.2475+280A>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 194799	NM_153240.5(NPHP3):c.2442T>C (p.Tyr814=)	NPHP3, NPHP3-ACAD11	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis +1 more	GConflicting classifications of pathogenicity
Select item 500644	NM_153240.5(NPHP3):c.2346G>A (p.Val782=)	NPHP3, NPHP3-ACAD11	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis 3 +4 more	GConflicting classifications of pathogenicity
Select item 1706153	NM_153240.5(NPHP3):c.2310+27del	NPHP3, NPHP3-ACAD11	Deletion (intron variant)	not provided	GLikely benign
Select item 1305077	NM_153240.5(NPHP3):c.2258A>G (p.His753Arg)	NPHP3, NPHP3-ACAD11 (H753R)	Single nucleotide variant (non-coding transcript variant +1 more)	not provided	GUncertain significance
Select item 194681	NM_153240.5(NPHP3):c.2172-4A>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	Nephronophthisis +4 more	GConflicting classifications of pathogenicity
Select item 1219650	NM_153240.5(NPHP3):c.2172-65del	NPHP3, NPHP3-ACAD11	Deletion (intron variant)	not provided	GLikely benign
Select item 1293900	NM_153240.5(NPHP3):c.2172-66C>T	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 1293811	NM_153240.5(NPHP3):c.2172-78G>A	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 667700	NM_153240.5(NPHP3):c.2172-132T>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 670771	NM_153240.5(NPHP3):c.2172-187A>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 667698	NM_153240.5(NPHP3):c.2171+151A>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GBenign

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