chr14:64882380:A>G Detail (hg19) (MTHFD1)

Information

Genome

Assembly Position
hg19 chr14:64,882,380-64,882,380
hg38 chr14:64,415,662-64,415,662 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq
Ensemble ENST00000557539.2:c.158A>G ENST00000557539.2:p.Lys53Arg
ENST00000554768.6:c.158A>G ENST00000554768.6:p.Lys53Arg
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.780
ToMMo:0.785
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.674

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 172460 OMIM
HGNC 7432 HGNC
Ensembl ENSG00000100714 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv51073502 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2021-12-03 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2024-02-01 criteria provided, single submitter not provided germline Detail
Benign 2021-09-05 criteria provided, single submitter Combined immunodeficiency and megaloblastic anemia with or without hyperhomocysteinemia germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.004 Non-small cell lung carcinoma Variant alleles were significantly associated with favorable survivals of NSCLC ... BeFree 20737570 Detail
0.003 Non-small cell lung carcinoma Variant alleles were significantly associated with favorable survivals of NSCLC ... BeFree 20737570 Detail
0.003 Non-small cell lung carcinoma Variant alleles were significantly associated with favorable survivals of NSCLC ... BeFree 20737570 Detail
0.003 Non-small cell lung carcinoma Variant alleles were significantly associated with favorable survivals of NSCLC ... BeFree 20737570 Detail
0.112 colorectal cancer Statistically significant associations were observed between CRC risk and functi... BeFree 26108676 Detail
0.001 colorectal carcinoma Statistically significant associations were observed between CRC risk and functi... BeFree 26108676 Detail
0.004 colorectal cancer Statistically significant associations were observed between CRC risk and functi... BeFree 26108676 Detail
<0.001 colorectal cancer Statistically significant associations were observed between CRC risk and functi... BeFree 26108676 Detail
<0.001 colorectal carcinoma Statistically significant associations were observed between CRC risk and functi... BeFree 26108676 Detail
0.033 colorectal carcinoma Statistically significant associations were observed between CRC risk and functi... BeFree 26108676 Detail
0.015 colorectal cancer Statistically significant associations were observed between CRC risk and functi... BeFree 26108676 Detail
0.036 colorectal cancer Statistically significant associations were observed between CRC risk and functi... BeFree 26108676 Detail
<0.001 colorectal carcinoma Statistically significant associations were observed between CRC risk and functi... BeFree 26108676 Detail
0.002 colorectal carcinoma Statistically significant associations were observed between CRC risk and functi... BeFree 26108676 Detail
0.005 Migraine Disorders Association study of MTHFD1 coding polymorphisms R134K and R653Q with migraine s... BeFree 25039261 Detail
<0.001 colon carcinoma Meanwhile, the MTHFD1 G401A might play a protective role in the development of c... BeFree 23894459 Detail
<0.001 ovarian carcinoma Lack of association between MTHFD1 G401A polymorphism and ovarian cancer suscept... BeFree 24287951 Detail
0.003 Malignant neoplasm of ovary [We sought to replicate associations for DPYD rs1801265, DNMT3A rs13420827, MTHF... GAD 20570913 Detail
<0.001 Malignant tumor of colon Meanwhile, the MTHFD1 G401A might play a protective role in the development of c... BeFree 23894459 Detail
<0.001 Common Migraine The R134K and R653Q variants in MTHFD1 were genotyped in an Australian cohort of... BeFree 25039261 Detail
0.003 Malignant neoplasm of ovary Lack of association between MTHFD1 G401A polymorphism and ovarian cancer suscept... BeFree 24287951 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_005956.4(MTHFD1):c.401A>G (p.Lys134Arg) AND not specified ClinVar Detail
NM_005956.4(MTHFD1):c.401A>G (p.Lys134Arg) AND not provided ClinVar Detail
NM_005956.4(MTHFD1):c.401A>G (p.Lys134Arg) AND Combined immunodeficiency and megaloblastic anemia wi... ClinVar Detail
Variant alleles were significantly associated with favorable survivals of NSCLC for MTR rs3768160 A&... DisGeNET Detail
Variant alleles were significantly associated with favorable survivals of NSCLC for MTR rs3768160 A&... DisGeNET Detail
Variant alleles were significantly associated with favorable survivals of NSCLC for MTR rs3768160 A&... DisGeNET Detail
Variant alleles were significantly associated with favorable survivals of NSCLC for MTR rs3768160 A&... DisGeNET Detail
Statistically significant associations were observed between CRC risk and functionally defined candi... DisGeNET Detail
Statistically significant associations were observed between CRC risk and functionally defined candi... DisGeNET Detail
Statistically significant associations were observed between CRC risk and functionally defined candi... DisGeNET Detail
Statistically significant associations were observed between CRC risk and functionally defined candi... DisGeNET Detail
Statistically significant associations were observed between CRC risk and functionally defined candi... DisGeNET Detail
Statistically significant associations were observed between CRC risk and functionally defined candi... DisGeNET Detail
Statistically significant associations were observed between CRC risk and functionally defined candi... DisGeNET Detail
Statistically significant associations were observed between CRC risk and functionally defined candi... DisGeNET Detail
Statistically significant associations were observed between CRC risk and functionally defined candi... DisGeNET Detail
Statistically significant associations were observed between CRC risk and functionally defined candi... DisGeNET Detail
Association study of MTHFD1 coding polymorphisms R134K and R653Q with migraine susceptibility. DisGeNET Detail
Meanwhile, the MTHFD1 G401A might play a protective role in the development of colon cancer. DisGeNET Detail
Lack of association between MTHFD1 G401A polymorphism and ovarian cancer susceptibility. DisGeNET Detail
[We sought to replicate associations for DPYD rs1801265, DNMT3A rs13420827, MTHFD1 rs1950902, MTHFS ... DisGeNET Detail
Meanwhile, the MTHFD1 G401A might play a protective role in the development of colon cancer. DisGeNET Detail
The R134K and R653Q variants in MTHFD1 were genotyped in an Australian cohort of 520 unrelated migra... DisGeNET Detail
Lack of association between MTHFD1 G401A polymorphism and ovarian cancer susceptibility. DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs1950902 dbSNP
Genome
hg19
Position
chr14:64,882,380-64,882,380
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1207
Mean of sample read depth (HGVD)
112.92
Standard deviation of sample read depth (HGVD)
47.97
Number of reference allele (HGVD)
529
Number of alternative allele (HGVD)
1881
Allele Frequency (HGVD)
0.7804979253112033
Gene Symbol (HGVD)
MTHFD1
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs1950902
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.7851
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
13158
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8626
East Asian Allele Counts (ExAC)
5817
East Asian Heterozygous Counts (ExAC)
1857
East Asian Homozygous Counts (ExAC)
1980
East Asian Allele Frequency (ExAC)
0.6743565963366566
Chromosome Counts in All Race (ExAC)
121292
Allele Counts in All Race (ExAC)
101046
Heterozygous Counts in All Race (ExAC)
16418
Homozygous Counts in All Race (ExAC)
42314
Allele Frequency in All Race (ExAC)
0.8330804999505326
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