NPHP1[gene] - ClinVar - NCBI

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	Variation	Gene (Protein Change)	Type (Consequence)	Condition	Classification, Review status
Select item 152537	GRCh38/hg38 2q11.1-13(chr2:94678532-110602409)x3	ACTR1B, ADRA2B +550 more	Copy number gain	See cases	GPathogenic
Select item 59147	GRCh38/hg38 2q11.2-13(chr2:97672522-110211318)x3	AFF3, C2orf15 +373 more	Copy number gain	See cases	GPathogenic
Select item 149662	GRCh38/hg38 2q11.2-13(chr2:101710825-110791418)x3	LOC129934515, LOC129934516 +241 more	Copy number gain	See cases	GPathogenic
Select item 152239	GRCh38/hg38 2q12.2-14.1(chr2:106428663-112379067)x3	ACOXL, ACOXL-AS1 +154 more	Copy number gain	See cases	GUncertain significance
Select item 150754	GRCh38/hg38 2q12.2-13(chr2:106516472-110576905)x3	CCDC138, CD8B2 +99 more	Copy number gain	See cases	GUncertain significance
Select item 59313	GRCh38/hg38 2q12.2-13(chr2:106696282-110223328)x3	CCDC138, EDAR +93 more	Copy number gain	See cases	GUncertain significance
Select item 148286	GRCh38/hg38 2q13(chr2:108719125-110611314)x3	CCDC138, EDAR +61 more	Copy number gain	See cases	GUncertain significance
Select item 3024348	GRCh38/hg38 2q13(chr2:109301667-110460985)	LOC112695115, LOC126806305 +33 more	Copy number gain	Autism spectrum disorder	GUncertain significance
Select item 144290	GRCh38/hg38 2q13(chr2:109623720-110207160)x1	LIMS3, LIMS3-LOC440895 +13 more	Copy number loss	See cases	GBenign
Select item 223120	Single allele	LIMS3, LIMS3-LOC440895 +15 more	Duplication	Autism spectrum disorder +1 more	GUncertain significance
Select item 59742	GRCh38/hg38 2q13(chr2:109936618-110452159)x1	LIMS3-LOC440895, LIMS4 +13 more	Copy number loss	See cases	GBenign
Select item 144831	GRCh38/hg38 2q13(chr2:109959903-110360538)x3	LIMS3-LOC440895, LIMS4 +12 more	Copy number gain	See cases	GBenign
Select item 152993	GRCh38/hg38 2q13(chr2:109975055-110207160)x1	LINC01123, LOC126806305 +5 more	Copy number loss	See cases	GBenign
Select item 148909	GRCh38/hg38 2q13(chr2:109975055-110576905)x3	LIMS4, LINC01106 +13 more	Copy number gain	See cases	GLikely benign
Select item 149500	GRCh38/hg38 2q13(chr2:109975072-110207198)x3	LINC01123, LOC126806305 +5 more	Copy number gain	See cases	GBenign
Select item 146098	GRCh38/hg38 2q13(chr2:110025459-110207301)x3	LOC126806305, LOC126806306 +4 more	Copy number gain	See cases	GBenign
Select item 144345	GRCh38/hg38 2q13(chr2:110025659-110207160)x3	LOC126806305, LOC126806306 +4 more	Copy number gain	See cases	GBenign
Select item 57545	GRCh38/hg38 2q13(chr2:110025659-110371270)x0	LOC129934555, LOC129934556 +10 more	Copy number loss	See cases	GPathogenic
Select item 34538	GRCh38/hg38 2q13(chr2:110025659-110207160)x1	LOC126806305, LOC126806306 +4 more	Copy number loss	See cases	GBenign
Select item 150752	GRCh38/hg38 2q13(chr2:110025674-110207198)x3	LOC126806305, LOC126806306 +4 more	Copy number gain	See cases	GLikely benign
Select item 145443	GRCh38/hg38 2q13(chr2:110025674-110321488)x3	LOC126806305, LOC126806306 +9 more	Copy number gain	See cases	GBenign
Select item 147196	GRCh38/hg38 2q13(chr2:110025681-110576905)x1	LIMS4, LINC01106 +12 more	Copy number loss	See cases	GBenign
Select item 149321	GRCh38/hg38 2q13(chr2:110049995-110576905)x3	LIMS4, LINC01106 +12 more	Copy number gain	See cases	GLikely benign
Select item 152160	GRCh38/hg38 2q13(chr2:110066680-110225841)x0	LOC126806305, LOC126806306 +7 more	Copy number loss	See cases	GPathogenic
Select item 152507	GRCh38/hg38 2q13(chr2:110076063-110209066)x3	LOC126806305, LOC126806306 +3 more	Copy number gain	See cases	GBenign
Select item 152506	GRCh38/hg38 2q13(chr2:110076063-110209066)x1	LOC126806305, LOC126806306 +3 more	Copy number loss	See cases	GBenign
Select item 144830	GRCh38/hg38 2q13(chr2:110076063-110257869)x3	LOC126806305, LOC126806306 +6 more	Copy number gain	See cases	GBenign
Select item 59744	GRCh38/hg38 2q13(chr2:110084138-110611314)x1	LIMS4, LINC01106 +12 more	Copy number loss	See cases	GBenign
Select item 59743	GRCh38/hg38 2q13(chr2:110084138-110212693)x1	LOC126806305, LOC126806306 +5 more	Copy number loss	See cases	GBenign
Select item 59745	GRCh38/hg38 2q13(chr2:110084194-110212693)x1	LOC126806305, LOC126806306 +5 more	Copy number loss	See cases	GBenign
Select item 2505162	GRCh38/hg38 2q13(chr2:110091573-110212811)	LOC126806305, LOC126806306 +5 more	Copy number loss	Nephronophthisis 1	GPathogenic
Select item 1676309	GRCh38/hg38 2q13(chr2:110091573-110205023)	LOC126806305, LOC126806306 +2 more	Copy number loss	Nephronophthisis 1	GPathogenic
Select item 453297	Single allele	LOC126806306, LOC126806305 +5 more	Deletion	Senior-loken syndrome 3 +1 more	GPathogenic
Select item 59746	GRCh38/hg38 2q13(chr2:110095383-110211318)x1	LOC126806305, LOC126806306 +2 more	Copy number loss	See cases	GBenign
Select item 438246	Single allele	LOC126806305, LOC126806306 +5 more	Deletion	Cone dystrophy	GLikely pathogenic
Select item 149342	GRCh38/hg38 2q13(chr2:110104897-110371270)x1	LIMS4, LOC126806305 +8 more	Copy number loss	See cases	GBenign
Select item 145407	GRCh38/hg38 2q13(chr2:110104897-110321488)x1	LOC126806306, LOC126806305 +7 more	Copy number loss	See cases	GBenign
Select item 144559	GRCh38/hg38 2q13(chr2:110104897-110207198)x1	LOC126806305, LOC126806306 +2 more	Copy number loss	See cases	GBenign/Likely benign
Select item 144557	GRCh38/hg38 2q13(chr2:110104897-110207198)x3	LOC126806305, LOC126806306 +2 more	Copy number gain	See cases	Gconflicting data from submitters
Select item 161069	GRCh38/hg38 2q13(chr2:110104900-110371270)x3	LIMS4, LOC126806305 +8 more	Copy number gain	See cases	GBenign
Select item 161023	GRCh38/hg38 2q13(chr2:110104900-110611314)x3	LIMS4, LINC01106 +11 more	Copy number gain	See cases	GBenign
Select item 161015	GRCh38/hg38 2q13(chr2:110104900-110207160)x1	LOC126806305, LOC126806306 +2 more	Copy number loss	See cases	GBenign
Select item 154483	GRCh38/hg38 2q13(chr2:110104900-110207160)x4	LOC126806305, LOC126806306 +2 more	Copy number gain	See cases	GBenign
Select item 151434	GRCh38/hg38 2q13(chr2:110104900-110257869)x1	LOC126806305, LOC126806306 +5 more	Copy number loss	See cases	GLikely benign
Select item 146191	GRCh38/hg38 2q13(chr2:110104900-110207160)x3	LOC126806305, LOC126806306 +2 more	Copy number gain	See cases	GBenign
Select item 146178	GRCh38/hg38 2q13(chr2:110104900-110611314)x1	LIMS4, LINC01106 +11 more	Copy number loss	See cases	GBenign
Select item 146137	GRCh38/hg38 2q13(chr2:110104900-110201550)x1	LOC126806305, LOC126806306 +2 more	Copy number loss	See cases	GConflicting classifications of pathogenicity
Select item 144826	GRCh38/hg38 2q13(chr2:110104900-110209066)x1	LOC126806305, LOC126806306 +2 more	Copy number loss	See cases	GBenign/Likely benign
Select item 144825	GRCh38/hg38 2q13(chr2:110104900-110209066)x3	LOC126806305, LOC126806306 +2 more	Copy number gain	See cases	GLikely benign
Select item 144426	GRCh38/hg38 2q13(chr2:110104900-110321480)x1	LOC126806305, LOC126806306 +7 more	Copy number loss	See cases	GBenign
Select item 144125	GRCh38/hg38 2q13(chr2:110104900-110207160)x1	LOC126806305, LOC126806306 +2 more	Copy number loss	See cases	GBenign
Select item 34228	GRCh38/hg38 2q13(chr2:110104900-110201550)x3	LOC126806305, LOC126806306 +2 more	Copy number gain	See cases	GBenign
Select item 32789	GRCh38/hg38 2q13(chr2:110104900-110207160)x0	LOC126806305, LOC126806306 +2 more	Copy number loss	See cases	GPathogenic
Select item 32161	GRCh38/hg38 2q13(chr2:110104900-110371270)x3	LIMS4, LOC126806305 +8 more	Copy number gain	See cases	GBenign
Select item 144681	GRCh38/hg38 2q13(chr2:110123094-110207198)x3	LOC126806306, NPHP1	Copy number gain	See cases	GBenign
Select item 2579194	GRCh38/hg38 2q13(chr2:110123182-110205164)x0	LOC126806306, NPHP1	Copy number loss	Nephronophthisis 1	GPathogenic
Select item 893357	NM_000272.4(NPHP1):c.*460T>A	NPHP1	Single nucleotide variant	Nephronophthisis 1 +2 more	GUncertain significance
Select item 237627	NM_000272.5(NPHP1):c.(?_-45)_(*443_?)del	LOC126806306, NPHP1	Deletion	Nephronophthisis +1 more	GPathogenic
Select item 330724	NM_001128178.3(NPHP1):c.*333AAC[1]	NPHP1	Microsatellite (3 prime UTR variant)	Renal dysplasia and retinal aplasia +2 more	GUncertain significance
Select item 330725	NM_001128178.3(NPHP1):c.*322A>G	NPHP1	Single nucleotide variant (3 prime UTR variant)	Joubert syndrome with renal defect +2 more	GUncertain significance
Select item 330726	NM_001128178.3(NPHP1):c.*250C>T	NPHP1	Single nucleotide variant (3 prime UTR variant)	Nephronophthisis 1 +2 more	GUncertain significance
Select item 894188	NM_001128178.3(NPHP1):c.*238T>C	NPHP1	Single nucleotide variant (3 prime UTR variant)	Joubert syndrome with renal defect +2 more	GUncertain significance
Select item 2651263	NM_001128178.3(NPHP1):c.*206C>G	NPHP1	Single nucleotide variant (3 prime UTR variant)	not provided	GLikely benign
Select item 894189	NM_001128178.3(NPHP1):c.*199A>G	NPHP1	Single nucleotide variant (3 prime UTR variant)	Joubert syndrome with renal defect +2 more	GUncertain significance
Select item 894599	NM_001128178.3(NPHP1):c.*194T>C	NPHP1	Single nucleotide variant (3 prime UTR variant)	Joubert syndrome with renal defect +2 more	GConflicting classifications of pathogenicity
Select item 147940	GRCh38/hg38 2q13(chr2:110123660-110207160)x3	LOC126806306, NPHP1	Copy number gain	See cases	GBenign
Select item 462703	Single allele	LOC126806306, NPHP1	Duplication	Nephronophthisis	GBenign
Select item 462702	NC_000002.12:g.(?_110123771)_(110204988_?)del	LOC126806306, NPHP1	Deletion	Nephronophthisis	GPathogenic
Select item 502508	NM_001128178.3(NPHP1):c.*1C>T	NPHP1	Single nucleotide variant (3 prime UTR variant)	not provided	GUncertain significance
Select item 583935	NC_000002.12:g.(?_110123791)_(110204968_?)del	LOC126806306, NPHP1	Deletion	Nephronophthisis	GPathogenic
Select item 2834720	NM_001128178.3(NPHP1):c.2031G>C (p.Val677=)	NPHP1	Single nucleotide variant (synonymous variant +1 more)	Nephronophthisis	GLikely benign
Select item 3033403	NM_001128178.3(NPHP1):c.2021A>G (p.Lys674Arg)	NPHP1 (K611R +4 more)	Single nucleotide variant (missense variant +1 more)	NPHP1-related condition	GUncertain significance
Select item 1508616	NM_001128178.3(NPHP1):c.2019A>C (p.Arg673Ser)	NPHP1 (R728S +4 more)	Single nucleotide variant (missense variant +1 more)	Nephronophthisis	GUncertain significance
Select item 968322	NM_001128178.3(NPHP1):c.2018G>A (p.Arg673Lys)	NPHP1 (R673K +4 more)	Single nucleotide variant (missense variant +1 more)	Senior-Loken syndrome 1 +4 more	GUncertain significance
Select item 2807898	NM_001128178.3(NPHP1):c.2017A>C (p.Arg673=)	NPHP1	Single nucleotide variant (synonymous variant +1 more)	Nephronophthisis	GLikely benign
Select item 1549768	NM_001128178.3(NPHP1):c.2010T>C (p.Gly670=)	NPHP1	Single nucleotide variant (synonymous variant +1 more)	Nephronophthisis	GLikely benign
Select item 1062140	NM_001128178.3(NPHP1):c.2007G>A (p.Leu669=)	NPHP1	Single nucleotide variant (synonymous variant +1 more)	Senior-Loken syndrome 1 +3 more	GConflicting classifications of pathogenicity
Select item 2858130	NM_001128178.3(NPHP1):c.1998T>C (p.Tyr666=)	NPHP1	Single nucleotide variant (synonymous variant +1 more)	Nephronophthisis	GLikely benign
Select item 2864163	NM_001128178.3(NPHP1):c.1995C>T (p.Thr665=)	NPHP1	Single nucleotide variant (synonymous variant +1 more)	Nephronophthisis	GLikely benign
Select item 2420503	NM_001128178.3(NPHP1):c.1994C>T (p.Thr665Ile)	NPHP1 (T602I +4 more)	Single nucleotide variant (missense variant +1 more)	Nephronophthisis	GUncertain significance
Select item 2126960	NM_001128178.3(NPHP1):c.1990dup (p.Gln664fs)	NPHP1 (Q663fs +4 more)	Duplication (frameshift variant +1 more)	Nephronophthisis	GUncertain significance
Select item 854284	NM_001128178.3(NPHP1):c.1977del (p.Phe659fs)	NPHP1 (F658fs +4 more)	Deletion (frameshift variant +1 more)	Nephronophthisis	GPathogenic
Select item 1384670	NM_001128178.3(NPHP1):c.1966C>T (p.His656Tyr)	NPHP1 (H655Y +4 more)	Single nucleotide variant (missense variant +1 more)	Nephronophthisis	GUncertain significance
Select item 1429265	NM_001128178.3(NPHP1):c.1960G>A (p.Gly654Arg)	NPHP1 (G591R +4 more)	Single nucleotide variant (missense variant +1 more)	Nephronophthisis +3 more	GUncertain significance
Select item 1116415	NM_001128178.3(NPHP1):c.1959C>T (p.Asp653=)	NPHP1	Single nucleotide variant (synonymous variant +1 more)	Nephronophthisis	GLikely benign
Select item 2166217	NM_001128178.3(NPHP1):c.1955C>T (p.Pro652Leu)	NPHP1 (P651L +4 more)	Single nucleotide variant (missense variant +1 more)	Nephronophthisis	GUncertain significance
Select item 2707816	NM_001128178.3(NPHP1):c.1953A>T (p.Ser651=)	NPHP1	Single nucleotide variant (synonymous variant +1 more)	Nephronophthisis	GLikely benign
Select item 2841552	NM_001128178.3(NPHP1):c.1950G>T (p.Leu650=)	NPHP1	Single nucleotide variant (synonymous variant +1 more)	Nephronophthisis	GLikely benign
Select item 1980945	NM_001128178.3(NPHP1):c.1950G>C (p.Leu650=)	NPHP1	Single nucleotide variant (synonymous variant +1 more)	Nephronophthisis	GLikely benign
Select item 219983	NM_001128178.3(NPHP1):c.1950G>A (p.Leu650=)	NPHP1	Single nucleotide variant (synonymous variant +1 more)	NPHP1-related condition +2 more	GConflicting classifications of pathogenicity
Select item 1122157	NM_001128178.3(NPHP1):c.1948C>T (p.Leu650=)	NPHP1	Single nucleotide variant (synonymous variant +1 more)	Nephronophthisis	GLikely benign
Select item 2506582	NM_001128178.3(NPHP1):c.1943C>T (p.Ala648Val)	NPHP1 (A585V +4 more)	Single nucleotide variant (missense variant +1 more)	Joubert syndrome with renal defect	GUncertain significance
Select item 1442883	NM_001128178.3(NPHP1):c.1943C>G (p.Ala648Gly)	NPHP1 (A585G +4 more)	Single nucleotide variant (missense variant +1 more)	Nephronophthisis	GUncertain significance
Select item 1990537	NM_001128178.3(NPHP1):c.1936C>T (p.Leu646Phe)	NPHP1 (L583F +4 more)	Single nucleotide variant (missense variant +1 more)	Nephronophthisis	GUncertain significance
Select item 1030711	NM_001128178.3(NPHP1):c.1933G>A (p.Ala645Thr)	NPHP1 (A644T +4 more)	Single nucleotide variant (missense variant +1 more)	Nephronophthisis +3 more	GUncertain significance
Select item 330727	NM_001128178.3(NPHP1):c.1932C>T (p.Gly644=)	NPHP1	Single nucleotide variant (synonymous variant +1 more)	Senior-Loken syndrome 1 +5 more	GConflicting classifications of pathogenicity
Select item 425213	NM_001128178.3(NPHP1):c.1930G>C (p.Gly644Arg)	NPHP1 (G700R +4 more)	Single nucleotide variant (missense variant +1 more)	not provided	GLikely pathogenic
Select item 531637	NM_001128178.3(NPHP1):c.1929G>A (p.Gln643=)	NPHP1	Single nucleotide variant (synonymous variant +1 more)	Nephronophthisis	GLikely benign
Select item 2028313	NM_001128178.3(NPHP1):c.1926C>T (p.Asn642=)	NPHP1	Single nucleotide variant (synonymous variant +1 more)	Nephronophthisis	GLikely benign
Select item 2763764	NM_001128178.3(NPHP1):c.1923A>G (p.Glu641=)	NPHP1	Single nucleotide variant (synonymous variant +1 more)	Nephronophthisis	GLikely benign

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