Skip to main content

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