Table 2.
Comparison of genotype distributions between omphalocele cases and controls.
| Gene symbol; name | Protein function | SNP | Description | Allelesa | Control Genotypesb | Case Genotypesb | Adjusted odds ratio (95% Confidence Interval)c | |
|---|---|---|---|---|---|---|---|---|
| Heterozygous | Homozygous for minor allele | |||||||
| MTHFR; Methylenetetrahydrofolate reductase (NAD(P)H) | Converts 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate | rs1801131 | c.1298A>C | A/C | 463/259/37 | 93/61/15 | 1.17 (0.81, 1.70) | 2.04 (1.06, 3.94) |
| rs1801133 | c.677C>T | C/T | 342/316/101 | 81/76/12 | 1.02 (0.71, 1.48) | 0.52 (0.27, 1.02) | ||
| MTR; Methionine synthase | Converts homocysteine and 5-methyltetrahydrofolate to methionine and tetrahydrofolate | rs1805087 | p.D919G | A/G | 465/250/41 | 110/43/11 | 0.73 (0.49, 1.07) | 1.10 (0.54, 2.26) |
| MTRR; Methionine synthase reductase | Regenerates functional methionine synthase via reductive methylation | rs1801394 | p.I22M | A/G | 288/327/146 | 60/74/34 | 1.08 (0.73, 1.58) | 1.12 (0.68, 1.82) |
| rs1532268 | p.S175 L | G/A | 378/311/65 | 82/68/13 | 0.97 (0.68, 1.40) | 0.93 (0.48, 1.78) | ||
| BHMT; Betaine-homocysteine S-methyl-transferase | Converts betaine and homocysteine to dimethylglycine and methionine | rs3733890 | p.R239Q | G/A | 413/282/66 | 80/71/13 | 1.34 (0.94, 1.93) | 1.02 (0.53, 1.96) |
| FOLH1 (also known as GCPII); Folate hydrolase (folylpoly-glutamate carboxy-peptidase) | Hydrolyzes folate polyglutamates | rs61886492 | p.H475Y | C/T | 714/40/3 | 152/14/1 | 1.58 (0.82, 3.05) | 1.56 (0.16, 15.22) |
| MTHFD1; Methylene tetrahydrofolate dehydrogenase (NADP+ dependent) 1 | C1-synthase trifunctional enzyme catalyzing the interconversion of 1-carbon derivatives of tetrahydrofolate | rs2236225 | p.R653Q | C/T | 282/327/150 | 68/67/29 | 0.85 (0.58, 1.26) | 0.81 (0.49, 1.34) |
| PEMT; Phosphatidyl-ethanolamine N-methyl-transferase | Converts phosphatidyl-ethanolamine to phosphatidyl-choline by sequential methylation | rs7946 | p.V175M | T/C | 271/315/169 | 57/73/37 | 1.14 (0.76, 1.70) | 1.11 (0.67, 1.85) |
| rs897453 | c.V58I | G/A | 388/278/89 | 84/61/21 | 1.01 (0.68, 1.50) | 1.16 (0.65, 2.07) | ||
| rs12325817 | p.744C>G | C/G | 362/301/96 | 80/68/18 | 1.04 (0.71, 1.54) | 0.87 (0.48, 1.59) | ||
| SHMT1; Serine hydroxymethyl-transferase 1 (soluble) | Converts serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate | rs1979277 | p.L474F | G/A | 391/304/59 | 84/71/9 | 1.05 (0.74, 1.50) | 0.64 (0.30, 1.37) |
| PCFT (also known as SLC46A1); Proton-coupled folate transporter | Transport of folate across cell membranes under specific pH conditions | rs9909629 | A>T (5′ near gene) | A/T | 615/132/14 | 142/25/2 | 0.84 (0.52, 1.34) | 0.61 (0.13, 2.80) |
| rs11080058 | G>A (5′ near gene) | G/A | 344/333/83 | 79/71/17 | 0.92 (0.64, 1.32) | 0.92 (0.51, 1.65) | ||
| BRCA1; Breast cancer 1, early onset | Involved in transcription, DNA repair of double-stranded breaks, and recombination; acts as tumor suppressor | rs3737559 | G>A (intron) | G/A | 673/81/7 | 146/19/1 | 1.08 (0.63, 1.84) | - |
| TCblR (also known as CD320); Transcobalamin receptor | Facilitates the uptake of transcobalamin-bound vitamin B12 into tissues | rs173665 | C>T (3′ near gene) | G/A | 600/153/8 | 133/29/5 | 0.87 (0.56, 1.35) | 3.10 (0.95, 10.13) |
| rs2227288 | G>C (5′ near gene) | G/C | 536/207/17 | 122/38/8 | 0.83 (0.56, 1.25) | 2.06 (0.85, 4.95) | ||
| rs2336573 | p.G220R | C/T | 593/145/22 | 127/31/9 | 0.98 (0.62, 1.55) | 1.99 (0.84, 4.74) | ||
| rs2232775 | p.Q8R | A/G | 544/180/33 | 112/35/18 | 1.02 (0.64, 1.61) | 3.20 (1.55, 6.62) | ||
| RFC1 (also known as SLC19A1); Reduced folate carrier | Facilitates the transport of reduced folates into cells | rs1051266 | p.H27R | G/A | 216/359/184 | 40/76/49 | 1.16 (0.76, 1.78) | 1.43 (0.89, 2.31) |
| TCN2; Transcobalamin II | Binds cobalamin and mediates its transport into cells | rs9606756 | p.I23V | A/G | 571/173/17 | 117/46/4 | 1.32 (0.90, 1.94) | 1.23 (0.40, 3.76) |
| rs1801198 | p.P259R | C/G | 315/340/101 | 62/77/26 | 1.16 (0.79, 1.70) | 1.35 (0.79, 2.30) | ||
| rs9621049 | p.S348F | C/T | 574/172/14 | 118/46/2 | 1.30 (0.89, 1.92) | 0.72 (0.16, 3.21) | ||
a
Major allele is listed first
b
Genotypevalues are numbers of individuals with homozygous major allele/heterozygous/homozygous minor allele
c
Homozygous for major allele was reference category; adjustment for maternal race, maternal education, and in vitro fertilization/assisted reproductive technique