Difference between revisions of "Rs2274976"

Latest revision as of 00:10, 2 August 2020

minus

Geno	Mag	Summary
(G;G)	0	common in complete genomics

Make rs2274976(A;A)

Make rs2274976(A;G)

Reference

GRCh38 38.1/141

Chromosome

1

Position

11790870

Gene

MTHFR

is a	snp
is	mentioned by
dbSNP	rs2274976
dbSNP (classic)	rs2274976
ClinGen	rs2274976
ebi	rs2274976
HLI	rs2274976
Exac	rs2274976
Gnomad	rs2274976
Varsome	rs2274976
LitVar	rs2274976
Map	rs2274976
PheGenI	rs2274976
Biobank	rs2274976
1000 genomes	rs2274976
hgdp	rs2274976
ensembl	rs2274976
geneview	rs2274976
scholar	rs2274976
google	rs2274976
pharmgkb	rs2274976
gwascentral	rs2274976
openSNP	rs2274976
23andMe	rs2274976
SNPshot	rs2274976
SNPdbe	rs2274976
MSV3d	rs2274976
GWAS Ctlg	rs2274976

GMAF

0.05096

Max Magnitude

0

?

(A;A) (A;G) (G;G)

28

[PMID 20863444] Associations between the genetic polymorphisms of MTHFR and outcomes of methotrexate treatment in rheumatoid arthritis

[PMID 22241680 ] Deep sequencing study of the MTHFR gene to identify variants associated with myelomeningocele

[PMID 17697348 ] Technology to accelerate pangenomic scanning for unknown point mutations in exonic sequences: cycling temperature capillary electrophoresis (CTCE).

[PMID 18191955 ] Correlating observed odds ratios from lung cancer case-control studies to SNP functional scores predicted by bioinformatic tools.

[PMID 19064578 ] No association of single nucleotide polymorphisms in one-carbon metabolism genes with prostate cancer risk.

[PMID 19190136 ] Association of thymidylate synthase gene with endometrial cancer risk in a Chinese population.

[PMID 19421414 ] Genetic variation in the methylenetetrahydrofolate reductase gene, MTHFR, does not alter the risk of visual failure in Leber's hereditary optic neuropathy.

[PMID 19493349 ] 118 SNPs of folate-related genes and risks of spina bifida and conotruncal heart defects.

[PMID 19591822] Prevalence of genetic thrombophilic polymorphisms in the Sri Lankan population--implications for association study design and clinical genetic testing services.

[PMID 20031578 ] Novel associations of CPS1, MUT, NOX4, and DPEP1 with plasma homocysteine in a healthy population: a genome-wide evaluation of 13 974 participants in the Women's Genome Health Study.

[PMID 20416077 ] Identification of type 2 diabetes-associated combination of SNPs using support vector machine.

[PMID 20458436] Early-onset ischaemic stroke: analysis of 58 polymorphisms in 17 genes involved in methionine metabolism.

[PMID 20890936] Maternal polymorphisms in folic acid metabolic genes are associated with nonsyndromic cleft lip and/or palate in the Brazilian population.

[PMID 21362212] [Detection of single nucleotide polymorphisms of mthfr and dpyd genes in leukemia cell lines K562 and K562/A02].

[PMID 24254627] MTHFR rs2274976 polymorphism is a risk marker for nonsyndromic cleft lip with or without cleft palate in the brazilian population

ClinVar
Risk	rs2274976(A;A)
Alt	rs2274976(A;A)
Reference	Rs2274976(G;G)
Significance	Other
Disease	not provided Neural tube defects not specified
Variation	info
Gene	MTHFR
CLNDBN	not provided Neural tube defects, folate-sensitive not specified
Reversed	1
HGVS	NC_000001.10:g.11850927C>T
CLNSRC	UniProtKB (protein)
CLNACC	RCV000174348.2, RCV000267830.1, RCV000433699.2,

[PMID 26522108] Methylenetetrahydrofolate reductase gene polymorphism in endometrial cancer: A systematic review and meta-analysis

[PMID 32117640 ] Single nucleotide polymorphism of MTHFR rs1801133 associated with elevated Hcy levels affects susceptibility to cerebral small vessel disease.

[PMID 32617779] Machine learning in prediction of genetic risk of nonsyndromic oral clefts in the Brazilian population.

[PMID 32682401 ] Association of ESR1 (rs2234693 and rs9340799), CETP (rs708272), MTHFR (rs1801133 and rs2274976) and MS (rs185087) polymorphisms with Coronary Artery Disease (CAD).

@@ Line 13: / Line 13: @@
 |geno3=(G;G)
 |Gene_s=MTHFR
+|StabilizedOrientation=minus
 }}{{ population diversity
 | geno1=(A;A)
@@ Line 30: / Line 31: @@
 | TSI | 0.0 | 2.9 | 97.1
 | HapMapRevision=28
-}}{{PharmGKB
-|RSID=rs2274976
-|Name_s=MTHFR:1793G>A; MTHFR:Arg594Gln; G1793A
-|Gene_s=C1orf167, MTHFR
-|Feature=NA, Exon/NonSyn
-|Evidence=PubMed ID:15643524
-|Annotation=In a case control study of Asian gastric cancer (n=633), individuals with 6 variant alleles of three MTHFR common variants (i.e. C677T, A1298C and G1793A) were at increased risk for gastric cardia adenocarcinoma (OR =4.64, 95% CI =1.34-16.01) compared with those having 0-2 variants.
-|Drugs=
-|Drug Classes=
-|Diseases=Stomach Neoplasms
-|Curation Level=Curated
-|PharmGKB Accession ID=PA164918204
 }}
@@ Line 123: / Line 112: @@
 }}
-{{GET Evidence
+{{PMID Auto
-|gene=MTHFR
+|PMID=24254627
-|aa_change=Arg594Gln
+|Title=MTHFR rs2274976 polymorphism is a risk marker for nonsyndromic cleft lip with or without cleft palate in the brazilian population
-|aa_change_short=R594Q
+}}
-|impact=pharmacogenetic
-|qualified_impact=Insufficiently evaluated pharmacogenetic
+{{ClinVar
-|inheritance=unknown
+|ALT=T
-|quality_scores=Array
+|CAF=0.9255; 0.07448
-|dbsnp_id=rs2274976
+|CHROM=1
-|overall_frequency_n=435
+|CLNACC=RCV000174348.2; RCV000267830.1; RCV000433699.2
-|overall_frequency_d=10758
+|CLNALLE=1
-|overall_frequency=0.040435
+|CLNDBN=not provided; Neural tube defects, folate-sensitive; not specified
-|n_genomes=2
+|CLNDSDB=MedGen; MedGen:OMIM
-|n_genomes_annotated=0
+|CLNDSDBID=CN221809; C1866558:601634; CN169374
-|n_haplomes=3
+|CLNHGVS=NC_000001.10:g.11850927C>T
-|n_articles=1
+|CLNORIGIN=1
-|n_articles_annotated=1
+|CLNREVSTAT=single; mult
-|gene_in_genetests=Y
+|CLNSIG=255
-|in_pharmgkb=Y
+|COMMON=1
-|genetests_testable=Y
+|Disease=not provided; Neural tube defects; not specified
-|nblosum100=0
+|FwdALT=A
-|autoscore=4
+|FwdREF=G
-|webscore=N
+|GENEINFO=MTHFR:4524
-|n_web_uneval=10
+|GENE_ID=4524
+|GENE_NAME=MTHFR
+|REF=C
+|RSPOS=11850927
+|Reversed=1
+|SAO=0
+|SSR=0
+|Tags=RV;PM;TPA;PMC;SLO;NSM;REF;INT;ASP;VLD;G5;HD;GNO;KGPhase1;KGPhase3
+|VC=SNV
+|VP=0x050138080a05150537000101
+|WGT=1
+|dbSNPBuildID=100
+|rsid=2274976
+|CLNSRC=UniProtKB (protein)
+|CLNSRCID=P42898#VAR_018859
 }}
 {{PMID Auto
-|PMID=24254627
+|PMID=26522108
-|Title=MTHFR rs2274976 polymorphism is a risk marker for nonsyndromic cleft lip with or without cleft palate in the brazilian population
+|Title=Methylenetetrahydrofolate reductase gene polymorphism in endometrial cancer: A systematic review and meta-analysis
+}}
+{{PMID Auto
+|PMID=32117640
+|Title=Single nucleotide polymorphism of MTHFR rs1801133 associated with elevated Hcy levels affects susceptibility to cerebral small vessel disease.
+|OA=1
+}}
+{{PMID Auto
+|PMID=32617779
+|Title=Machine learning in prediction of genetic risk of nonsyndromic oral clefts in the Brazilian population.
 }}
+{{PMID Auto
+|PMID=32682401
+|Title=Association of ESR1 (rs2234693 and rs9340799), CETP (rs708272), MTHFR (rs1801133 and rs2274976) and MS (rs185087) polymorphisms with Coronary Artery Disease (CAD).
+|OA=1
+}}
 {{on chip | 23andMe v1}}
 {{on chip | 23andMe v2}}
 {{on chip | 23andMe v3}}
 {{on chip | 23andMe v4}}
+{{on chip | 23andMe v5}}
+{{on chip | Ancestry v2c}}
+{{on chip | Ancestry v2d}}
+{{on chip | Ancestry v2}}
 {{on chip | FTDNA2}}
 {{on chip | HumanOmni1Quad}}
 {{on chip | Illumina Human 1M}}