NPHP3[gene] - ClinVar - NCBI

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	Variation	Gene (Protein Change)	Type (Consequence)	Condition	Classification, Review status
Select item 154258	GRCh38/hg38 3q11.1-24(chr3:93800620-145695381)x3	PDIA5, PHLDB2 +1344 more	Copy number gain	See cases	GPathogenic
Select item 145614	GRCh38/hg38 3q13.11-29(chr3:103426882-198110178)x3	LOC115995524, LOC115995525 +2647 more	Copy number gain	See cases	GPathogenic
Select item 153723	GRCh38/hg38 3q21.3-23(chr3:126106779-140918089)x3	LOC129937605, LOC129937606 +484 more	Copy number gain	See cases	GUncertain significance
Select item 154720	GRCh38/hg38 3q21.3-22.1(chr3:127607945-133566661)x1	LOC129937518, LOC129937519 +248 more	Copy number loss	See cases	GLikely pathogenic
Select item 152454	GRCh38/hg38 3q22.1-23(chr3:129817243-141425155)x1	A4GNT, ACAD11 +282 more	Copy number loss	See cases	GPathogenic
Select item 147358	GRCh38/hg38 3q22.1-24(chr3:129817243-143381624)x1	A4GNT, ACAD11 +345 more	Copy number loss	See cases	GPathogenic
Select item 150380	GRCh38/hg38 3q22.1-23(chr3:130401265-139005019)x1	A4GNT, ACAD11 +212 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 343352	NM_153240.5(NPHP3):c.*1213T>C	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	Renal-hepatic-pancreatic dysplasia 1 +2 more	GUncertain significance
Select item 903378	NM_153240.5(NPHP3):c.*1188A>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	Nephronophthisis 3 +2 more	GUncertain significance
Select item 903379	NM_153240.5(NPHP3):c.*1184A>T	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	Renal-hepatic-pancreatic dysplasia 1 +2 more	GUncertain significance
Select item 343353	NM_153240.5(NPHP3):c.*1176G>A	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	NPHP3-related Meckel-like syndrome +2 more	GConflicting classifications of pathogenicity
Select item 343354	NM_153240.5(NPHP3):c.*1121A>G	NPHP3-ACAD11, NPHP3	Single nucleotide variant (3 prime UTR variant)	NPHP3-related Meckel-like syndrome +2 more	GUncertain significance
Select item 343355	NM_153240.5(NPHP3):c.*1098C>T	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	NPHP3-related Meckel-like syndrome +2 more	GUncertain significance
Select item 900923	NM_153240.5(NPHP3):c.*1094A>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	Renal-hepatic-pancreatic dysplasia 1 +2 more	GUncertain significance
Select item 343356	NM_153240.5(NPHP3):c.*1078T>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	Nephronophthisis 3 +2 more	GUncertain significance
Select item 343357	NM_153240.5(NPHP3):c.*1020T>C	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	NPHP3-related Meckel-like syndrome +2 more	GConflicting classifications of pathogenicity
Select item 902586	NM_153240.5(NPHP3):c.*926C>T	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	Renal-hepatic-pancreatic dysplasia 1 +2 more	GConflicting classifications of pathogenicity
Select item 902587	NM_153240.5(NPHP3):c.*852C>A	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	Renal-hepatic-pancreatic dysplasia 1 +2 more	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 343360	NM_153240.5(NPHP3):c.*784C>T	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	Nephronophthisis 3 +2 more	GUncertain significance
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 343362	NM_153240.5(NPHP3):c.*692C>T	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	Renal-hepatic-pancreatic dysplasia 1 +2 more	GUncertain significance
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 343364	NM_153240.5(NPHP3):c.*654dup	NPHP3, NPHP3-ACAD11	Duplication (3 prime UTR variant)	Nephronophthisis +2 more	GUncertain significance
Select item 343365	NM_153240.5(NPHP3):c.652_653del	NPHP3, NPHP3-ACAD11	Deletion (3 prime UTR variant)	Nephronophthisis +2 more	GUncertain significance
Select item 1264737	NM_153240.5(NPHP3):c.*651dup	NPHP3, NPHP3-ACAD11	Duplication (3 prime UTR variant)	not provided	GBenign
Select item 343366	NM_153240.5(NPHP3):c.*652del	NPHP3, NPHP3-ACAD11	Deletion (3 prime UTR variant)	Nephronophthisis +2 more	GUncertain significance
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 900989	NM_153240.5(NPHP3):c.*626C>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	Renal-hepatic-pancreatic dysplasia 1 +2 more	GUncertain significance
Select item 343368	NM_153240.5(NPHP3):c.*519C>T	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	Nephronophthisis 3 +2 more	GUncertain significance
Select item 900990	NM_153240.5(NPHP3):c.*437C>T	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	Nephronophthisis 3 +2 more	GUncertain significance
Select item 901547	NM_153240.5(NPHP3):c.*351A>T	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	Nephronophthisis 3 +2 more	GUncertain significance
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 343370	NM_153240.5(NPHP3):c.*231A>T	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	Nephronophthisis +2 more	GUncertain significance
Select item 903615	NM_153240.5(NPHP3):c.*178T>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	Nephronophthisis 3 +2 more	GUncertain significance
Select item 903616	NM_153240.5(NPHP3):c.*141T>C	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	Nephronophthisis 3 +3 more	GUncertain significance
Select item 343371	NM_153240.5(NPHP3):c.*139T>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	NPHP3-related Meckel-like syndrome +2 more	GUncertain significance
Select item 343372	NM_153240.5(NPHP3):c.121_123del	NPHP3, NPHP3-ACAD11	Deletion (3 prime UTR variant)	Nephronophthisis +2 more	GUncertain significance
Select item 1712471	NM_153240.5(NPHP3):c.*108G>A	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	Kidney disorder	GUncertain significance
Select item 343373	NM_153240.5(NPHP3):c.*46A>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (3 prime UTR variant)	NPHP3-related Meckel-like syndrome +2 more	GUncertain significance
Select item 1645505	NM_153240.5(NPHP3):c.3990G>A (p.Arg1330=)	NPHP3, NPHP3-ACAD11	Single nucleotide variant (synonymous variant)	Nephronophthisis	GLikely benign
Select item 262714	NM_153240.5(NPHP3):c.3971T>C (p.Phe1324Ser)	NPHP3, NPHP3-ACAD11 (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 1475504	NM_153240.5(NPHP3):c.3959C>A (p.Ser1320Tyr)	NPHP3, NPHP3-ACAD11 (S1320Y)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis	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 499391	NM_153240.5(NPHP3):c.3936G>A (p.Thr1312=)	NPHP3, NPHP3-ACAD11	Single nucleotide variant (non-coding transcript variant +1 more)	not provided	GUncertain significance
Select item 2140345	NM_153240.5(NPHP3):c.3935C>T (p.Thr1312Met)	NPHP3, NPHP3-ACAD11 (T1312M)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis	GUncertain significance
Select item 591966	NM_153240.5(NPHP3):c.3934del (p.Thr1312fs)	NPHP3, NPHP3-ACAD11 (T1312fs)	Deletion (non-coding transcript variant +1 more)	not provided	GUncertain significance
Select item 963751	NM_153240.5(NPHP3):c.3914G>A (p.Arg1305His)	NPHP3, NPHP3-ACAD11 (R1305H)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis	GUncertain significance
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 1637947	NM_153240.5(NPHP3):c.3912A>G (p.Ser1304=)	NPHP3, NPHP3-ACAD11	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis	GLikely benign
Select item 951359	NM_153240.5(NPHP3):c.3907C>T (p.Pro1303Ser)	NPHP3, NPHP3-ACAD11 (P1303S)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis 3 +3 more	GUncertain significance
Select item 3201650	NM_153240.5(NPHP3):c.3904G>T (p.Ala1302Ser)	NPHP3, NPHP3-ACAD11 (A1302S)	Single nucleotide variant (non-coding transcript variant +1 more)	Inborn genetic diseases	GUncertain significance
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 1512935	NM_153240.5(NPHP3):c.3898G>A (p.Gly1300Arg)	NPHP3, NPHP3-ACAD11 (G1300R)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis +3 more	GUncertain significance
Select item 291194	NM_153240.5(NPHP3):c.3896G>A (p.Gly1299Asp)	NPHP3-ACAD11, NPHP3 (G1299D)	Single nucleotide variant (non-coding transcript variant +1 more)	Renal-hepatic-pancreatic dysplasia 1 +4 more	GConflicting classifications of pathogenicity
Select item 2753357	NM_153240.5(NPHP3):c.3892T>C (p.Leu1298=)	NPHP3, NPHP3-ACAD11	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis	GLikely benign
Select item 1092723	NM_153240.5(NPHP3):c.3891C>T (p.Leu1297=)	NPHP3, NPHP3-ACAD11	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis	GLikely benign
Select item 1930116	NM_153240.5(NPHP3):c.3884C>T (p.Thr1295Ile)	NPHP3, NPHP3-ACAD11 (T1295I)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis	GUncertain significance
Select item 949854	NM_153240.5(NPHP3):c.3872AAG[1] (p.Glu1292del)	NPHP3, NPHP3-ACAD11 (E1292del)	Microsatellite (non-coding transcript variant +1 more)	Nephronophthisis	GUncertain significance
Select item 343374	NM_153240.5(NPHP3):c.3875A>C (p.Glu1292Ala)	NPHP3, NPHP3-ACAD11 (E1292A)	Single nucleotide variant (non-coding transcript variant +1 more)	NPHP3-related Meckel-like syndrome +3 more	GUncertain significance
Select item 1387373	NM_153240.5(NPHP3):c.3866A>C (p.Glu1289Ala)	NPHP3, NPHP3-ACAD11 (E1289A)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis	GUncertain significance
Select item 598708	NM_153240.5(NPHP3):c.3863T>C (p.Met1288Thr)	NPHP3-ACAD11, NPHP3 (M1288T)	Single nucleotide variant (non-coding transcript variant +1 more)	not provided	GUncertain significance
Select item 1994428	NM_153240.5(NPHP3):c.3858G>T (p.Arg1286Ser)	NPHP3, NPHP3-ACAD11 (R1286S)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis	GUncertain significance
Select item 1471104	NM_153240.5(NPHP3):c.3857G>A (p.Arg1286Lys)	NPHP3, NPHP3-ACAD11 (R1286K)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis	GUncertain significance
Select item 2117132	NM_153240.5(NPHP3):c.3846A>G (p.Glu1282=)	NPHP3, NPHP3-ACAD11	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis	GLikely benign
Select item 1400739	NM_153240.5(NPHP3):c.3841G>A (p.Ala1281Thr)	NPHP3, NPHP3-ACAD11 (A1281T)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis	GUncertain significance
Select item 1925405	NM_153240.5(NPHP3):c.3838G>A (p.Ala1280Thr)	NPHP3, NPHP3-ACAD11 (A1280T)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis	GUncertain significance
Select item 591582	NM_153240.5(NPHP3):c.3837dup (p.Ala1280fs)	NPHP3-ACAD11, NPHP3 (A1280fs)	Duplication (non-coding transcript variant +1 more)	Nephronophthisis 3 +1 more	GConflicting classifications of pathogenicity
Select item 1056181	NM_153240.5(NPHP3):c.3833A>T (p.Glu1278Val)	NPHP3, NPHP3-ACAD11 (E1278V)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis +3 more	GUncertain significance
Select item 1386294	NM_153240.5(NPHP3):c.3832G>C (p.Glu1278Gln)	NPHP3, NPHP3-ACAD11 (E1278Q)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis	GUncertain significance
Select item 2632	NM_153240.5(NPHP3):c.3821GAG[1] (p.Gly1275del)	NPHP3, NPHP3-ACAD11 (G1275del)	Microsatellite (non-coding transcript variant +1 more)	Nephronophthisis 3 +3 more	GPathogenic/Likely pathogenic
Select item 959343	NM_153240.5(NPHP3):c.3820G>T (p.Gly1274Ter)	NPHP3, NPHP3-ACAD11 (G1274*)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis	GPathogenic
Select item 1104909	NM_153240.5(NPHP3):c.3816T>C (p.Tyr1272=)	NPHP3, NPHP3-ACAD11	Single nucleotide variant (non-coding transcript variant +1 more)	not provided +4 more	GLikely benign
Select item 2142601	NM_153240.5(NPHP3):c.3813-12TC[2]	NPHP3, NPHP3-ACAD11	Microsatellite (intron variant)	Nephronophthisis	GUncertain significance
Select item 1164133	NM_153240.5(NPHP3):c.3813-10T>C	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	Nephronophthisis +3 more	GBenign/Likely benign
Select item 1661602	NM_153240.5(NPHP3):c.3813-12del	NPHP3, NPHP3-ACAD11	Deletion (intron variant)	Nephronophthisis	GBenign
Select item 2902688	NM_153240.5(NPHP3):c.3813-18_3813-17del	NPHP3, NPHP3-ACAD11	Deletion (intron variant)	Nephronophthisis	GLikely benign
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 262711	NM_153240.5(NPHP3):c.3812+42C>T	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided +1 more	GBenign
Select item 2077390	NM_153240.5(NPHP3):c.3812+16_3812+17del	NPHP3, NPHP3-ACAD11	Deletion (intron variant)	Nephronophthisis	GLikely benign
Select item 1624399	NM_153240.5(NPHP3):c.3812+16A>G	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	Nephronophthisis 3 +3 more	GLikely benign
Select item 594073	NM_153240.5(NPHP3):c.3812+9T>C	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	not provided	GUncertain significance
Select item 1998949	NM_153240.5(NPHP3):c.3812+4A>T	NPHP3, NPHP3-ACAD11	Single nucleotide variant (intron variant)	Nephronophthisis	GUncertain significance
Select item 2634638	NM_153240.5(NPHP3):c.3812+2dup	NPHP3, NPHP3-ACAD11	Duplication (splice donor variant)	NPHP3-related disorder	GPathogenic
Select item 944911	NM_153240.5(NPHP3):c.3812+1G>T	NPHP3, NPHP3-ACAD11	Single nucleotide variant (splice donor variant)	Nephronophthisis	GPathogenic
Select item 2740922	NM_153240.5(NPHP3):c.3810dup (p.Ser1271Ter)	NPHP3, NPHP3-ACAD11 (S1271*)	Duplication (non-coding transcript variant +1 more)	Nephronophthisis	GPathogenic
Select item 195995	NM_153240.5(NPHP3):c.3809T>C (p.Leu1270Pro)	NPHP3, NPHP3-ACAD11 (L1270P)	Single nucleotide variant (non-coding transcript variant +1 more)	not provided +4 more	GUncertain significance
Select item 2905125	NM_153240.5(NPHP3):c.3807G>A (p.Val1269=)	NPHP3, NPHP3-ACAD11	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis	GLikely benign
Select item 942300	NM_153240.5(NPHP3):c.3805G>A (p.Val1269Met)	NPHP3, NPHP3-ACAD11 (V1269M)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis 3 +3 more	GUncertain significance
Select item 3066093	NM_153240.5(NPHP3):c.3800T>C (p.Leu1267Ser)	NPHP3, NPHP3-ACAD11 (L1267S)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis 3	GUncertain significance
Select item 1452823	NM_153240.5(NPHP3):c.3787del (p.Thr1263fs)	NPHP3, NPHP3-ACAD11 (T1263fs)	Deletion (non-coding transcript variant +1 more)	Nephronophthisis	GPathogenic
Select item 1022804	NM_153240.5(NPHP3):c.3787A>G (p.Thr1263Ala)	NPHP3, NPHP3-ACAD11 (T1263A)	Single nucleotide variant (non-coding transcript variant +1 more)	Nephronophthisis	GUncertain significance

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