chr17:18328782:G>A Detail (hg38) (SHMT1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr17:18,232,096-18,232,096 View the variant detail on this assembly version. |
| hg38 | chr17:18,328,782-18,328,782 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_004169.4:c.1420C>T | NP_004160.3:p.Leu474Phe |
| NM_148918.2:c.1303C>T | NP_683718.1:p.Leu435Phe | |
| Ensemble | ENST00000316694.8:c.1420C>T | ENST00000316694.8:p.Leu474Phe |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.081 |
| ToMMo:0.088 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.169 |
Prediction
ClinVar
| Clinical Significance |
Uncertain significance
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Uncertain significance
|
no assertion criteria provided | gastrointestinal stromal tumor |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| <0.001 | Cancer of Head and Neck | We conducted a case-control study (265 HNSCC cases and 466 non-cancer controls) ... | BeFree | 22051736 | Detail |
| 0.003 | Cancer of Head and Neck | We conducted a case-control study (265 HNSCC cases and 466 non-cancer controls) ... | BeFree | 22051736 | Detail |
| 0.128 | Lymphoma, Non-Hodgkin | A borderline significantly increased risk of NHL was also observed for CBS (rs18... | BeFree | 23913011 | Detail |
| <0.001 | Lymphoma, Large-Cell, Follicular | A borderline significantly increased risk of NHL was also observed for CBS (rs18... | BeFree | 23913011 | Detail |
| <0.001 | Lymphoma, Large-Cell, Follicular | A borderline significantly increased risk of NHL was also observed for CBS (rs18... | BeFree | 23913011 | Detail |
| <0.001 | Lymphoma, Non-Hodgkin | A borderline significantly increased risk of NHL was also observed for CBS (rs18... | BeFree | 23913011 | Detail |
| 0.003 | autistic disorder | MTHFR C677T is a risk factor, whereas MTRR A66G and SHMT C1420T polymorphisms re... | BeFree | 19440165 | Detail |
| 0.003 | autistic disorder | A total of 138 children diagnosed as autistic based on Diagnostic and Statistica... | BeFree | 19440165 | Detail |
| 0.003 | autistic disorder | MTHFR C677T is a risk factor, whereas MTRR A66G and SHMT C1420T polymorphisms re... | BeFree | 19440165 | Detail |
| 0.006 | Malignant neoplasm of prostate | Role of polymorphic variants of MTR gene A2756G and SHMT1 gene C1420T in the dev... | BeFree | 22803112 | Detail |
| 0.009 | Malignant neoplasm of prostate | Role of polymorphic variants of MTR gene A2756G and SHMT1 gene C1420T in the dev... | BeFree | 22803112 | Detail |
| <0.001 | adult acute lymphocytic leukemia | Polymorphisms in methionine synthase (MS A2756G), cytosolic serine hydroxymethyl... | BeFree | 11986237 | Detail |
| 0.008 | Malignant neoplasm of breast | However, we found evidence for association of SHMT1 C1420T polymorphism with sig... | BeFree | 24789272 | Detail |
| <0.001 | Giant Cell Arteritis | Association of MTHFR C677T and SHMT(1) C1420T with susceptibility to ESCC and GC... | BeFree | 17206530 | Detail |
| 0.001 | colorectal carcinoma | Otherwise, SHMT1 C1420T polymorphism may have a protective effect on colorectal ... | BeFree | 25194438 | Detail |
| 0.011 | colorectal cancer | Otherwise, SHMT1 C1420T polymorphism may have a protective effect on colorectal ... | BeFree | 25194438 | Detail |
| 0.010 | Precursor Cell Lymphoblastic Leukemia Lymphoma | [Polymorphisms in folate-related genes and risk of pediatric acute lymphoblastic... | GAD | 19020309 | Detail |
| <0.001 | Carcinogenesis | To assess the association between the C to T transition in the methylenetetrahyd... | BeFree | 17206530 | Detail |
| <0.001 | gastric cardia adenocarcinoma | To assess the association between the C to T transition in the methylenetetrahyd... | BeFree | 17206530 | Detail |
| <0.001 | Carcinogenesis | DNMT3B C46359T and SHMT1 C1420T polymorphisms in the folate pathway in carcinoge... | BeFree | 24362509 | Detail |
| <0.001 | gastric cardia adenocarcinoma | To assess the association between the C to T transition in the methylenetetrahyd... | BeFree | 17206530 | Detail |
| 0.014 | Carcinogenesis | To assess the association between the C to T transition in the methylenetetrahyd... | BeFree | 17206530 | Detail |
| 0.001 | breast carcinoma | However, we found evidence for association of SHMT1 C1420T polymorphism with sig... | BeFree | 24789272 | Detail |
| <0.001 | Adenoma of large intestine | In a case-control study, including 768 cases and 709 controls, we investigated t... | BeFree | 17113224 | Detail |
| <0.001 | adult acute lymphocytic leukemia | Polymorphisms in thymidylate synthase (TS) 28-bp tandem repeats in the promoter ... | BeFree | 12604405 | Detail |
| 0.011 | colorectal cancer | Results for other variants varied across individual studies; in our meta-analyse... | BeFree | 23401104 | Detail |
| <0.001 | Giant Cell Arteritis | Association of MTHFR C677T and SHMT(1) C1420T with susceptibility to ESCC and GC... | BeFree | 17206530 | Detail |
| 0.033 | colorectal carcinoma | Results for other variants varied across individual studies; in our meta-analyse... | BeFree | 23401104 | Detail |
| 0.011 | colorectal cancer | A meta-analysis of the C1420T polymorphism in cytosolic serine hydroxymethyltran... | BeFree | 23322534 | Detail |
| 0.004 | Squamous cell carcinoma of esophagus | The association between the MTHFR C677T and SHMT ( 1 ) C1420T polymorphisms and ... | BeFree | 17206530 | Detail |
| 0.006 | Carcinogenesis | DNMT3B C46359T and SHMT1 C1420T polymorphisms in the folate pathway in carcinoge... | BeFree | 24362509 | Detail |
| 0.001 | colorectal carcinoma | Results for other variants varied across individual studies; in our meta-analyse... | BeFree | 23401104 | Detail |
| 0.001 | colorectal carcinoma | A meta-analysis of the C1420T polymorphism in cytosolic serine hydroxymethyltran... | BeFree | 23322534 | Detail |
| <0.001 | adult acute lymphocytic leukemia | Polymorphisms in thymidylate synthase (TS) 28-bp tandem repeats in the promoter ... | BeFree | 12604405 | Detail |
| <0.001 | Squamous cell carcinoma of esophagus | The association between the MTHFR C677T and SHMT ( 1 ) C1420T polymorphisms and ... | BeFree | 17206530 | Detail |
| 0.112 | colorectal cancer | Results for other variants varied across individual studies; in our meta-analyse... | BeFree | 23401104 | Detail |
| 0.028 | Malignant neoplasm of breast | In this case-control study, we investigated the association between MTHFR C677T ... | BeFree | 22134752 | Detail |
| 0.003 | Acute lymphocytic leukemia | Children with ALL (n = 96) were screened for GCPII C1561T, RFC1 G80A, cSHMT C142... | BeFree | 22838948 | Detail |
| 0.001 | breast carcinoma | Conversely, for women over 50, the risk of breast cancer development was statist... | BeFree | 22134752 | Detail |
| <0.001 | Precursor Cell Lymphoblastic Leukemia Lymphoma | Children with ALL (n = 96) were screened for GCPII C1561T, RFC1 G80A, cSHMT C142... | BeFree | 22838948 | Detail |
| 0.021 | breast carcinoma | Conversely, for women over 50, the risk of breast cancer development was statist... | BeFree | 22134752 | Detail |
| 0.005 | Lymphoma, Non-Hodgkin | The polymorphisms examined and haplotypes generated included thymidylate synthas... | BeFree | 15198953 | Detail |
| 0.007 | breast carcinoma | In this case-control study, we investigated the association between MTHFR C677T ... | BeFree | 22134752 | Detail |
| 0.010 | Precursor Cell Lymphoblastic Leukemia Lymphoma | Children with ALL (n = 96) were screened for GCPII C1561T, RFC1 G80A, cSHMT C142... | BeFree | 22838948 | Detail |
| 0.006 | Malignant neoplasm of breast | Conversely, for women over 50, the risk of breast cancer development was statist... | BeFree | 22134752 | Detail |
| 0.232 | Precursor Cell Lymphoblastic Leukemia Lymphoma | Children with ALL (n = 96) were screened for GCPII C1561T, RFC1 G80A, cSHMT C142... | BeFree | 22838948 | Detail |
| 0.004 | Acute lymphocytic leukemia | Children with ALL (n = 96) were screened for GCPII C1561T, RFC1 G80A, cSHMT C142... | BeFree | 22838948 | Detail |
| 0.128 | Lymphoma, Non-Hodgkin | The polymorphisms examined and haplotypes generated included thymidylate synthas... | BeFree | 15198953 | Detail |
| <0.001 | Acute lymphocytic leukemia | Children with ALL (n = 96) were screened for GCPII C1561T, RFC1 G80A, cSHMT C142... | BeFree | 22838948 | Detail |
| <0.001 | Lymphoma, Large-Cell, Follicular | The polymorphisms examined and haplotypes generated included thymidylate synthas... | BeFree | 15198953 | Detail |
| 0.016 | Acute lymphocytic leukemia | Children with ALL (n = 96) were screened for GCPII C1561T, RFC1 G80A, cSHMT C142... | BeFree | 22838948 | Detail |
| 0.022 | Precursor Cell Lymphoblastic Leukemia Lymphoma | Children with ALL (n = 96) were screened for GCPII C1561T, RFC1 G80A, cSHMT C142... | BeFree | 22838948 | Detail |
| 0.008 | Malignant neoplasm of breast | Conversely, for women over 50, the risk of breast cancer development was statist... | BeFree | 22134752 | Detail |
| 0.005 | breast carcinoma | In this case-control study, we investigated the association between MTHFR C677T ... | BeFree | 22134752 | Detail |
| 0.132 | Precursor Cell Lymphoblastic Leukemia Lymphoma | Children with ALL (n = 96) were screened for GCPII C1561T, RFC1 G80A, cSHMT C142... | BeFree | 22838948 | Detail |
| 0.003 | breast carcinoma | Conversely, for women over 50, the risk of breast cancer development was statist... | BeFree | 22134752 | Detail |
| <0.001 | Lymphoma, Large-Cell, Follicular | The polymorphisms examined and haplotypes generated included thymidylate synthas... | BeFree | 15198953 | Detail |
| 0.035 | Malignant neoplasm of breast | In this case-control study, we investigated the association between MTHFR C677T ... | BeFree | 22134752 | Detail |
| 0.101 | Malignant neoplasm of breast | Conversely, for women over 50, the risk of breast cancer development was statist... | BeFree | 22134752 | Detail |
| <0.001 | Acute lymphocytic leukemia | Children with ALL (n = 96) were screened for GCPII C1561T, RFC1 G80A, cSHMT C142... | BeFree | 22838948 | Detail |
| <0.001 | liver carcinoma | Results showed that six SNPs (MTHFR rs1801133, MTRR rs2287780, MTRR rs10380, FTH... | BeFree | 25318605 | Detail |
| <0.001 | liver carcinoma | Results showed that six SNPs (MTHFR rs1801133, MTRR rs2287780, MTRR rs10380, FTH... | BeFree | 25318605 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_004169.5(SHMT1):c.1420C>T (p.Leu474Phe) AND Gastrointestinal stromal tumor | ClinVar | Detail |
| We conducted a case-control study (265 HNSCC cases and 466 non-cancer controls) to investigate assoc... | DisGeNET | Detail |
| We conducted a case-control study (265 HNSCC cases and 466 non-cancer controls) to investigate assoc... | DisGeNET | Detail |
| A borderline significantly increased risk of NHL was also observed for CBS (rs1801181, Ex13+41C>T... | DisGeNET | Detail |
| A borderline significantly increased risk of NHL was also observed for CBS (rs1801181, Ex13+41C>T... | DisGeNET | Detail |
| A borderline significantly increased risk of NHL was also observed for CBS (rs1801181, Ex13+41C>T... | DisGeNET | Detail |
| A borderline significantly increased risk of NHL was also observed for CBS (rs1801181, Ex13+41C>T... | DisGeNET | Detail |
| MTHFR C677T is a risk factor, whereas MTRR A66G and SHMT C1420T polymorphisms reduce risk for autism... | DisGeNET | Detail |
| A total of 138 children diagnosed as autistic based on Diagnostic and Statistical Manual of Mental D... | DisGeNET | Detail |
| MTHFR C677T is a risk factor, whereas MTRR A66G and SHMT C1420T polymorphisms reduce risk for autism... | DisGeNET | Detail |
| Role of polymorphic variants of MTR gene A2756G and SHMT1 gene C1420T in the development of prostati... | DisGeNET | Detail |
| Role of polymorphic variants of MTR gene A2756G and SHMT1 gene C1420T in the development of prostati... | DisGeNET | Detail |
| Polymorphisms in methionine synthase (MS A2756G), cytosolic serine hydroxymethyltransferase (SHMT1 C... | DisGeNET | Detail |
| However, we found evidence for association of SHMT1 C1420T polymorphism with significantly reduced r... | DisGeNET | Detail |
| Association of MTHFR C677T and SHMT(1) C1420T with susceptibility to ESCC and GCA in a high incident... | DisGeNET | Detail |
| Otherwise, SHMT1 C1420T polymorphism may have a protective effect on colorectal cancer and Asian pop... | DisGeNET | Detail |
| Otherwise, SHMT1 C1420T polymorphism may have a protective effect on colorectal cancer and Asian pop... | DisGeNET | Detail |
| [Polymorphisms in folate-related genes and risk of pediatric acute lymphoblastic leukemia.] | DisGeNET | Detail |
| To assess the association between the C to T transition in the methylenetetrahydro folate reductase ... | DisGeNET | Detail |
| To assess the association between the C to T transition in the methylenetetrahydro folate reductase ... | DisGeNET | Detail |
| DNMT3B C46359T and SHMT1 C1420T polymorphisms in the folate pathway in carcinogenesis of head and ne... | DisGeNET | Detail |
| To assess the association between the C to T transition in the methylenetetrahydro folate reductase ... | DisGeNET | Detail |
| To assess the association between the C to T transition in the methylenetetrahydro folate reductase ... | DisGeNET | Detail |
| However, we found evidence for association of SHMT1 C1420T polymorphism with significantly reduced r... | DisGeNET | Detail |
| In a case-control study, including 768 cases and 709 controls, we investigated the associations betw... | DisGeNET | Detail |
| Polymorphisms in thymidylate synthase (TS) 28-bp tandem repeats in the promoter region and in cytoso... | DisGeNET | Detail |
| Results for other variants varied across individual studies; in our meta-analyses we observed some e... | DisGeNET | Detail |
| Association of MTHFR C677T and SHMT(1) C1420T with susceptibility to ESCC and GCA in a high incident... | DisGeNET | Detail |
| Results for other variants varied across individual studies; in our meta-analyses we observed some e... | DisGeNET | Detail |
| A meta-analysis of the C1420T polymorphism in cytosolic serine hydroxymethyltransferase (SHMT1) amon... | DisGeNET | Detail |
| The association between the MTHFR C677T and SHMT ( 1 ) C1420T polymorphisms and the risk of ESCC and... | DisGeNET | Detail |
| DNMT3B C46359T and SHMT1 C1420T polymorphisms in the folate pathway in carcinogenesis of head and ne... | DisGeNET | Detail |
| Results for other variants varied across individual studies; in our meta-analyses we observed some e... | DisGeNET | Detail |
| A meta-analysis of the C1420T polymorphism in cytosolic serine hydroxymethyltransferase (SHMT1) amon... | DisGeNET | Detail |
| Polymorphisms in thymidylate synthase (TS) 28-bp tandem repeats in the promoter region and in cytoso... | DisGeNET | Detail |
| The association between the MTHFR C677T and SHMT ( 1 ) C1420T polymorphisms and the risk of ESCC and... | DisGeNET | Detail |
| Results for other variants varied across individual studies; in our meta-analyses we observed some e... | DisGeNET | Detail |
| In this case-control study, we investigated the association between MTHFR C677T and A1298C, TYMS 5'-... | DisGeNET | Detail |
| Children with ALL (n = 96) were screened for GCPII C1561T, RFC1 G80A, cSHMT C1420T, TYMS 5´-UTR 2R3R... | DisGeNET | Detail |
| Conversely, for women over 50, the risk of breast cancer development was statistically associated wi... | DisGeNET | Detail |
| Children with ALL (n = 96) were screened for GCPII C1561T, RFC1 G80A, cSHMT C1420T, TYMS 5´-UTR 2R3R... | DisGeNET | Detail |
| Conversely, for women over 50, the risk of breast cancer development was statistically associated wi... | DisGeNET | Detail |
| The polymorphisms examined and haplotypes generated included thymidylate synthase (TYMS 28-bp triple... | DisGeNET | Detail |
| In this case-control study, we investigated the association between MTHFR C677T and A1298C, TYMS 5'-... | DisGeNET | Detail |
| Children with ALL (n = 96) were screened for GCPII C1561T, RFC1 G80A, cSHMT C1420T, TYMS 5´-UTR 2R3R... | DisGeNET | Detail |
| Conversely, for women over 50, the risk of breast cancer development was statistically associated wi... | DisGeNET | Detail |
| Children with ALL (n = 96) were screened for GCPII C1561T, RFC1 G80A, cSHMT C1420T, TYMS 5´-UTR 2R3R... | DisGeNET | Detail |
| Children with ALL (n = 96) were screened for GCPII C1561T, RFC1 G80A, cSHMT C1420T, TYMS 5´-UTR 2R3R... | DisGeNET | Detail |
| The polymorphisms examined and haplotypes generated included thymidylate synthase (TYMS 28-bp triple... | DisGeNET | Detail |
| Children with ALL (n = 96) were screened for GCPII C1561T, RFC1 G80A, cSHMT C1420T, TYMS 5´-UTR 2R3R... | DisGeNET | Detail |
| The polymorphisms examined and haplotypes generated included thymidylate synthase (TYMS 28-bp triple... | DisGeNET | Detail |
| Children with ALL (n = 96) were screened for GCPII C1561T, RFC1 G80A, cSHMT C1420T, TYMS 5´-UTR 2R3R... | DisGeNET | Detail |
| Children with ALL (n = 96) were screened for GCPII C1561T, RFC1 G80A, cSHMT C1420T, TYMS 5´-UTR 2R3R... | DisGeNET | Detail |
| Conversely, for women over 50, the risk of breast cancer development was statistically associated wi... | DisGeNET | Detail |
| In this case-control study, we investigated the association between MTHFR C677T and A1298C, TYMS 5'-... | DisGeNET | Detail |
| Children with ALL (n = 96) were screened for GCPII C1561T, RFC1 G80A, cSHMT C1420T, TYMS 5´-UTR 2R3R... | DisGeNET | Detail |
| Conversely, for women over 50, the risk of breast cancer development was statistically associated wi... | DisGeNET | Detail |
| The polymorphisms examined and haplotypes generated included thymidylate synthase (TYMS 28-bp triple... | DisGeNET | Detail |
| In this case-control study, we investigated the association between MTHFR C677T and A1298C, TYMS 5'-... | DisGeNET | Detail |
| Conversely, for women over 50, the risk of breast cancer development was statistically associated wi... | DisGeNET | Detail |
| Children with ALL (n = 96) were screened for GCPII C1561T, RFC1 G80A, cSHMT C1420T, TYMS 5´-UTR 2R3R... | DisGeNET | Detail |
| Results showed that six SNPs (MTHFR rs1801133, MTRR rs2287780, MTRR rs10380, FTHFD rs1127717, GART r... | DisGeNET | Detail |
| Results showed that six SNPs (MTHFR rs1801133, MTRR rs2287780, MTRR rs10380, FTHFD rs1127717, GART r... | 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
- rs1979277 dbSNP
- Genome
- hg38
- Position
- chr17:18,328,782-18,328,782
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1184
- Mean of sample read depth (HGVD)
- 30.89
- Standard deviation of sample read depth (HGVD)
- 14.18
- Number of reference allele (HGVD)
- 2177
- Number of alternative allele (HGVD)
- 191
- Allele Frequency (HGVD)
- 0.08065878378378379
- Gene Symbol (HGVD)
- SHMT1
- 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))
- rs1979277
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0883
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 1480
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 3178
- East Asian Allele Counts (ExAC)
- 537
- East Asian Heterozygous Counts (ExAC)
- 491
- East Asian Homozygous Counts (ExAC)
- 23
- East Asian Allele Frequency (ExAC)
- 0.16897419760855883
- Chromosome Counts in All Race (ExAC)
- 62518
- Allele Counts in All Race (ExAC)
- 23302
- Heterozygous Counts in All Race (ExAC)
- 16854
- Homozygous Counts in All Race (ExAC)
- 3224
- Allele Frequency in All Race (ExAC)
- 0.3727246552992738
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