chr14:64415662:A>G Detail (hg38) (MTHFD1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr14:64,882,380-64,882,380 View the variant detail on this assembly version. |
| hg38 | chr14:64,415,662-64,415,662 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | ||
| Ensemble | ENST00000545908.6:c.401A>G | ENST00000545908.6:p.Lys134Arg |
| 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 | |
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
| Descrption | Source | Links |
|---|---|---|
| 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
- hg38
- Position
- chr14:64,415,662-64,415,662
- 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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