LCT[gene] - ClinVar - NCBI

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	Variation	Gene (Protein Change)	Type (Consequence)	Condition	Classification, Review status
Select item 147544	GRCh38/hg38 2q14.3-22.1(chr2:123445762-140592538)x1	ACMSD, AMER3 +336 more	Copy number loss	See cases	GPathogenic
Select item 331154	NM_002299.4(LCT):c.*442GT[1]	LCT	Microsatellite (3 prime UTR variant)	Congenital lactase deficiency +1 more	GLikely benign
Select item 331155	NM_002299.4(LCT):c.*429A>C	LCT	Single nucleotide variant (3 prime UTR variant)	Lactose intolerance +1 more	GLikely benign
Select item 331156	NM_002299.4(LCT):c.*325G>C	LCT	Single nucleotide variant (3 prime UTR variant)	Lactose intolerance +1 more	GConflicting classifications of pathogenicity
Select item 894022	NM_002299.4(LCT):c.*275A>G	LCT	Single nucleotide variant (3 prime UTR variant)	Congenital lactase deficiency	GUncertain significance
Select item 331157	NM_002299.4(LCT):c.*251G>A	LCT	Single nucleotide variant (3 prime UTR variant)	Congenital lactase deficiency +1 more	GUncertain significance
Select item 894023	NM_002299.4(LCT):c.*239C>T	LCT	Single nucleotide variant (3 prime UTR variant)	Congenital lactase deficiency	GUncertain significance
Select item 894024	NM_002299.4(LCT):c.*235C>T	LCT	Single nucleotide variant (3 prime UTR variant)	Congenital lactase deficiency	GLikely benign
Select item 331158	NM_002299.4(LCT):c.*230T>C	LCT	Single nucleotide variant (3 prime UTR variant)	Congenital lactase deficiency +1 more	GUncertain significance
Select item 894025	NM_002299.4(LCT):c.*193C>T	LCT	Single nucleotide variant (3 prime UTR variant)	Congenital lactase deficiency	GUncertain significance
Select item 331159	NM_002299.4(LCT):c.*50G>C	LCT	Single nucleotide variant (3 prime UTR variant)	Congenital lactase deficiency +2 more	GBenign
Select item 331160	NM_002299.4(LCT):c.*10A>C	LCT	Single nucleotide variant (3 prime UTR variant)	Lactose intolerance +1 more	GUncertain significance
Select item 331161	NM_002299.4(LCT):c.5771T>C (p.Val1924Ala)	LCT (V1924A)	Single nucleotide variant (missense variant)	Congenital lactase deficiency +1 more	GUncertain significance
Select item 1626236	NM_002299.4(LCT):c.5769G>A (p.Pro1923=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 2347455	NM_002299.4(LCT):c.5768C>T (p.Pro1923Leu)	LCT (P1923L)	Single nucleotide variant (missense variant)	Inborn genetic diseases	GUncertain significance
Select item 331162	NM_002299.4(LCT):c.5768C>A (p.Pro1923Gln)	LCT (P1923Q)	Single nucleotide variant (missense variant)	not provided +3 more	GBenign/Likely benign
Select item 2113064	NM_002299.4(LCT):c.5766C>G (p.Ser1922Arg)	LCT (S1922R)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 1353227	NM_002299.4(LCT):c.5761T>G (p.Leu1921Val)	LCT (L1921V)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 1904681	NM_002299.4(LCT):c.5748A>C (p.Arg1916=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 1660625	NM_002299.4(LCT):c.5739A>G (p.Lys1913=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GBenign
Select item 1391315	NM_002299.4(LCT):c.5728A>C (p.Lys1910Gln)	LCT (K1910Q)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 2892659	NM_002299.4(LCT):c.5726C>G (p.Ser1909Cys)	LCT (S1909C)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 1160629	NM_002299.4(LCT):c.5724C>A (p.Arg1908=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 1032814	NM_002299.4(LCT):c.5723G>A (p.Arg1908His)	LCT (R1908H)	Single nucleotide variant (missense variant)	Congenital lactase deficiency	GUncertain significance
Select item 1722137	NM_002299.4(LCT):c.5722C>A (p.Arg1908Ser)	LCT (R1908S)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 1025930	NM_002299.4(LCT):c.5722C>T (p.Arg1908Cys)	LCT (R1908C)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 1395060	NM_002299.4(LCT):c.5712G>C (p.Lys1904Asn)	LCT (K1904N)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 2313987	NM_002299.4(LCT):c.5710A>C (p.Lys1904Gln)	LCT (K1904Q)	Single nucleotide variant (missense variant)	Inborn genetic diseases	GUncertain significance
Select item 1548435	NM_002299.4(LCT):c.5673G>A (p.Val1891=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 1406729	NM_002299.4(LCT):c.5669T>A (p.Leu1890His)	LCT (L1890H)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 2121256	NM_002299.4(LCT):c.5665dup (p.Ser1889fs)	LCT (S1889fs)	Duplication (frameshift variant)	not provided	GUncertain significance
Select item 1619930	NM_002299.4(LCT):c.5664T>C (p.Phe1888=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 331163	NM_002299.4(LCT):c.5656G>A (p.Val1886Ile)	LCT (V1886I)	Single nucleotide variant (missense variant)	Inborn genetic diseases +2 more	GUncertain significance
Select item 894422	NM_002299.4(LCT):c.5655C>T (p.Tyr1885=)	LCT	Single nucleotide variant (synonymous variant)	not provided +1 more	GConflicting classifications of pathogenicity
Select item 1387993	NM_002299.4(LCT):c.5647G>A (p.Ala1883Thr)	LCT (A1883T)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 1346607	NM_002299.4(LCT):c.5626G>A (p.Gly1876Ser)	LCT (G1876S)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 2190879	NM_002299.4(LCT):c.5625C>T (p.Leu1875=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 2280363	NM_002299.4(LCT):c.5620A>G (p.Met1874Val)	LCT (M1874V)	Single nucleotide variant (missense variant)	Inborn genetic diseases	GUncertain significance
Select item 1662291	NM_002299.4(LCT):c.5619A>G (p.Leu1873=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 2772816	NM_002299.4(LCT):c.5598G>A (p.Glu1866=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 1652740	NM_002299.4(LCT):c.5589G>C (p.Val1863=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 1543420	NM_002299.4(LCT):c.5586C>T (p.Pro1862=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 1716686	NM_002299.4(LCT):c.5581A>G (p.Ser1861Gly)	LCT (S1861G)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 1489795	NM_002299.4(LCT):c.5572C>T (p.Pro1858Ser)	LCT (P1858S)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 331164	NM_002299.4(LCT):c.5568T>C (p.Ala1856=)	LCT	Single nucleotide variant (synonymous variant)	Lactose intolerance +2 more	GBenign
Select item 2813681	NM_002299.4(LCT):c.5564-7C>A	LCT	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 1627907	NM_002299.4(LCT):c.5564-17G>A	LCT	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 2992270	NM_002299.4(LCT):c.5564-20C>T	LCT	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 1252509	NM_002299.4(LCT):c.5564-37G>A	LCT	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 1234374	NM_002299.4(LCT):c.5563+214G>A	LCT	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 1266259	NM_002299.4(LCT):c.5563+74T>C	LCT	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 894423	NM_002299.4(LCT):c.5563+7T>C	LCT	Single nucleotide variant (intron variant)	Congenital lactase deficiency	GUncertain significance
Select item 2200841	NM_002299.4(LCT):c.5544C>T (p.His1848=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 331165	NM_002299.4(LCT):c.5529C>T (p.Pro1843=)	LCT	Single nucleotide variant (synonymous variant)	Lactose intolerance +2 more	GConflicting classifications of pathogenicity
Select item 2662435	NM_002299.4(LCT):c.5516G>A (p.Gly1839Asp)	LCT (G1839D)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 2696336	NM_002299.4(LCT):c.5514del (p.Asn1838fs)	LCT (N1838fs)	Deletion (frameshift variant)	not provided	GUncertain significance
Select item 2105594	NM_002299.4(LCT):c.5511C>T (p.Cys1837=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 1564254	NM_002299.4(LCT):c.5505C>T (p.Val1835=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 331166	NM_002299.4(LCT):c.5493C>T (p.Tyr1831=)	LCT	Single nucleotide variant (synonymous variant)	not provided +2 more	GConflicting classifications of pathogenicity
Select item 1416790	NM_002299.4(LCT):c.5486A>G (p.Lys1829Arg)	LCT (K1829R)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 1666245	NM_002299.4(LCT):c.5484G>A (p.Ala1828=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 2909848	NM_002299.4(LCT):c.5460G>A (p.Leu1820=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 1719517	NM_002299.4(LCT):c.5459T>G (p.Leu1820Arg)	LCT (L1820R)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 1471626	NM_002299.4(LCT):c.5448T>G (p.Ser1816Arg)	LCT (S1816R)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 1393156	NM_002299.4(LCT):c.5404A>G (p.Thr1802Ala)	LCT (T1802A)	Single nucleotide variant (missense variant)	not provided +1 more	GUncertain significance
Select item 892984	NM_002299.4(LCT):c.5391T>C (p.Asn1797=)	LCT	Single nucleotide variant (synonymous variant)	not provided +1 more	GConflicting classifications of pathogenicity
Select item 56392	NM_002299.4(LCT):c.5387del (p.Asp1796fs)	LCT (D1796fs)	Deletion (frameshift variant)	Congenital lactase deficiency	GLikely pathogenic
Select item 2421429	NM_002299.4(LCT):c.5382G>A (p.Ala1794=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 1405609	NM_002299.4(LCT):c.5381C>T (p.Ala1794Val)	LCT (A1794V)	Single nucleotide variant (missense variant)	not provided +1 more	GConflicting classifications of pathogenicity
Select item 2476975	NM_002299.4(LCT):c.5360G>C (p.Arg1787Pro)	LCT (R1787P)	Single nucleotide variant (missense variant)	Inborn genetic diseases	GUncertain significance
Select item 1554533	NM_002299.4(LCT):c.5346C>T (p.Asp1782=)	LCT	Single nucleotide variant (synonymous variant)	not provided +1 more	GLikely benign
Select item 2768078	NM_002299.4(LCT):c.5336-14C>T	LCT	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 1629073	NM_002299.4(LCT):c.5336-14C>A	LCT	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 1279576	NM_002299.4(LCT):c.5336-115C>T	LCT	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 1175484	NM_002299.4(LCT):c.5335+112C>G	LCT	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 1264901	NM_002299.4(LCT):c.5335+59T>C	LCT	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 1259500	NM_002299.4(LCT):c.5335+36C>T	LCT	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 1222663	NM_002299.4(LCT):c.5335+22C>A	LCT	Single nucleotide variant (intron variant)	not provided	GBenign
Select item 1936226	NM_002299.4(LCT):c.5335+13C>A	LCT	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 892985	NM_002299.4(LCT):c.5335+5G>A	LCT	Single nucleotide variant (intron variant)	Congenital lactase deficiency	GUncertain significance
Select item 3061665	NM_002299.4(LCT):c.5321A>G (p.Asn1774Ser)	LCT (N1774S)	Single nucleotide variant (missense variant)	LCT-related disorder	GUncertain significance
Select item 2785262	NM_002299.4(LCT):c.5316C>T (p.Tyr1772=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 2911668	NM_002299.4(LCT):c.5304C>T (p.Tyr1768=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 2513666	NM_002299.4(LCT):c.5302T>C (p.Tyr1768His)	LCT (Y1768H)	Single nucleotide variant (missense variant)	Inborn genetic diseases	GUncertain significance
Select item 1664265	NM_002299.4(LCT):c.5280C>T (p.Leu1760=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 1625004	NM_002299.4(LCT):c.5250T>C (p.Asn1750=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 3022584	NM_002299.4(LCT):c.5211G>A (p.Lys1737=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 2009726	NM_002299.4(LCT):c.5187C>T (p.Phe1729=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GUncertain significance
Select item 2171517	NM_002299.4(LCT):c.5175G>A (p.Thr1725=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GLikely benign
Select item 2045585	NM_002299.4(LCT):c.5175G>C (p.Thr1725=)	LCT	Single nucleotide variant (synonymous variant)	not provided	GUncertain significance
Select item 2260242	NM_002299.4(LCT):c.5174C>T (p.Thr1725Met)	LCT (T1725M)	Single nucleotide variant (missense variant)	Inborn genetic diseases	GUncertain significance
Select item 1362629	NM_002299.4(LCT):c.5170A>G (p.Met1724Val)	LCT (M1724V)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 2264504	NM_002299.4(LCT):c.5135G>A (p.Arg1712His)	LCT (R1712H)	Single nucleotide variant (missense variant)	Inborn genetic diseases	GUncertain significance
Select item 1358107	NM_002299.4(LCT):c.5128G>A (p.Ala1710Thr)	LCT (A1710T)	Single nucleotide variant (missense variant)	not provided	GUncertain significance
Select item 1915401	NM_002299.4(LCT):c.5112-3T>C	LCT	Single nucleotide variant (intron variant)	not provided	GUncertain significance
Select item 1252910	NM_002299.4(LCT):c.5111+23C>T	LCT	Single nucleotide variant (intron variant)	not provided +1 more	GBenign
Select item 1655129	NM_002299.4(LCT):c.5111+20G>T	LCT	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 2040722	NM_002299.4(LCT):c.5111+7C>A	LCT	Single nucleotide variant (intron variant)	not provided	GLikely benign
Select item 1424083	NM_002299.4(LCT):c.5111+4A>G	LCT	Single nucleotide variant (intron variant)	not provided	GUncertain significance
Select item 1408255	NM_002299.4(LCT):c.5111+1del	LCT	Deletion (splice donor variant)	not provided	GPathogenic

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