chr17:18232096:G>A Detail (hg19) (SHMT1)

Information

Genome

Assembly Position
hg19 chr17:18,232,096-18,232,096
hg38 chr17:18,328,782-18,328,782 View the variant detail on this assembly version.

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
Links
Type Database ID Link
Gene MIM 182144 OMIM
HGNC 10850 HGNC
Ensembl ENSG00000176974 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv57271344 TogoVar
COSMIC
MONDO
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

DescrptionSourceLinks
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&gt;T... DisGeNET Detail
A borderline significantly increased risk of NHL was also observed for CBS (rs1801181, Ex13+41C&gt;T... DisGeNET Detail
A borderline significantly increased risk of NHL was also observed for CBS (rs1801181, Ex13+41C&gt;T... DisGeNET Detail
A borderline significantly increased risk of NHL was also observed for CBS (rs1801181, Ex13+41C&gt;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
hg19
Position
chr17:18,232,096-18,232,096
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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