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Table 1 SNVs interrogated in BWS patients with loss of methylation at KCNQ1OT1 TSS-DMR

From: Genetic variation affecting DNA methylation and the human imprinting disorder, Beckwith-Wiedemann syndrome

Gene SNV_1 ID SNV_2 ID SNV_3 ID SNV_4 ID
MTHFR 677C>T Rs 1801133: C>T Rs 1801131: A>C Rs 2274976: G>A  
NM_005957.4: c.665C>T NM_005957.4: c.1286A>C NM_005957.4:c.1781G>A
NP_005948.3 p.Ala222Val NP_005948.3 p.Gln429Ala NP_005948.3 p.Arg594Gln
A = 0.24 G = 0.24 T = 0.075
MTRR Rs 1801394: A>G Rs 2287780: C>T Rs 10380: C>T  
NM_002454.2: c.66A>G NM_002454.2: c.1243C>T NM_024010.2: c.1864C>T
NP_002445.2 p.Ile22Met NP_002445.2 p.Arg415Cys NP_076915.2 p.His622Tyr
G = 0.36 GMAF, 0.47 ClinVar, 0.45 EXAC T = 0.0679 T = 0.219
MAT1A Rs 114494303: G>A Rs 72558181: G>A Rs 112848063: A>G Rs 116659053: G>A
NM_00429.2: c.530G>A NM_00429.2: c.791G>A NM_00429.2: c.1061A>G NM_00429.2: c.1066G>A
NP_00420.1 p.Arg177Gln NP_00420.1 p.Arg264His NP_00420.1 p.Asp354Gly NP_00420.1 p.Arg356Trp
A = 0.0002 A = 0.000009   A = 0.0002
MTR Rs 1805087: A>G    
NM_000254.2: c.2756A>G,
NP_000245.2 p.Asp919Gly
G = 0.218
CBS Rs 17849313: G>C Rs 117687681: C>T Rs 11700812: G>A/C  
NM_001178009.1: c.205G>C NM_001178009.1: c.1105C>T NM_000071.2: c.1106G>A, G>C
NP_000062.1 p.Ala69Pro NP_000062.1 p.Arg369Cys NP_001171479.1 p.Arg369His,
  A = 0.0012 NP_001171479.1 p.Arg369Pro.
   T/G = 0.00003
  1. Allele frequency data was obtained from dbSNP147 or other sources as indicated. Minor allele nucleotides on the forward genomic strand are shown. Where the alternate allele frequency is not shown, the SNV frequency is unknown. The MTHFR variant commonly referred to as c.677C>T is MTHFR: NM_005957.4 c.665C>T in HGVS format. Nucleotide numbering uses + 1 as the A of the ATG translation initiation codon
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Clinical Epigenetics

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