chr5:7897191:C>T Detail (hg19) (MTRR)

Information

Genome

Assembly Position
hg19 chr5:7,897,191-7,897,191
hg38 chr5:7,897,078-7,897,078 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_002454.2:c.1864C>T NP_002445.2:p.His622Tyr
NM_024010.2:c.1864C>T NP_076915.2:p.His622Tyr
NR_134480.1:c.1864C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.127
ToMMo:0.121
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.156

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 602568 OMIM
HGNC 7473 HGNC
Ensembl ENSG00000124275 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv20179003 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2013-05-29 criteria provided, single submitter not specified germline Detail
Uncertain significance no assertion criteria provided gastrointestinal stromal tumor germline Detail
Benign 2018-03-06 criteria provided, single submitter Disorders of Intracellular Cobalamin Metabolism germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts Methylcobalamin deficiency type cblE germline Detail
Benign 2023-11-29 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.020 spina bifida With respect to spina bifida, we observed ORs with 95% confidence intervals that... BeFree 19493349 Detail
0.010 spina bifida With respect to spina bifida, we observed ORs with 95% confidence intervals that... BeFree 19493349 Detail
0.008 spina bifida With respect to spina bifida, we observed ORs with 95% confidence intervals that... BeFree 19493349 Detail
0.005 spina bifida With respect to spina bifida, we observed ORs with 95% confidence intervals that... BeFree 19493349 Detail
<0.001 spina bifida With respect to spina bifida, we observed ORs with 95% confidence intervals that... BeFree 19493349 Detail
0.021 breast carcinoma We found three single-nucleotide polymorphisms in those genes associated with LI... BeFree 24130171 Detail
0.006 Malignant neoplasm of breast We found three single-nucleotide polymorphisms in those genes associated with LI... BeFree 24130171 Detail
0.101 Malignant neoplasm of breast We found three single-nucleotide polymorphisms in those genes associated with LI... BeFree 24130171 Detail
<0.001 liver carcinoma Results showed that six SNPs (MTHFR rs1801133, MTRR rs2287780, MTRR rs10380, FTH... BeFree 25318605 Detail
<0.001 pancreatic carcinoma His595Tyr polymorphism in the methionine synthase reductase (MTRR) gene is assoc... BeFree 18515090 Detail
<0.001 Malignant neoplasm of pancreas His595Tyr polymorphism in the methionine synthase reductase (MTRR) gene is assoc... BeFree 18515090 Detail
0.003 breast carcinoma We found three single-nucleotide polymorphisms in those genes associated with LI... BeFree 24130171 Detail
0.003 breast carcinoma We found three single-nucleotide polymorphisms in those genes associated with LI... BeFree 24130171 Detail
0.017 Malignant neoplasm of breast We found three single-nucleotide polymorphisms in those genes associated with LI... BeFree 24130171 Detail
<0.001 liver carcinoma Results showed that six SNPs (MTHFR rs1801133, MTRR rs2287780, MTRR rs10380, FTH... BeFree 25318605 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002454.3(MTRR):c.1783C>T (p.His595Tyr) AND not specified ClinVar Detail
NM_002454.3(MTRR):c.1783C>T (p.His595Tyr) AND Gastrointestinal stromal tumor ClinVar Detail
NM_002454.3(MTRR):c.1783C>T (p.His595Tyr) AND Disorders of Intracellular Cobalamin Metabolism ClinVar Detail
NM_002454.3(MTRR):c.1783C>T (p.His595Tyr) AND Methylcobalamin deficiency type cblE ClinVar Detail
NM_002454.3(MTRR):c.1783C>T (p.His595Tyr) AND not provided ClinVar Detail
With respect to spina bifida, we observed ORs with 95% confidence intervals that did not include 1.0... DisGeNET Detail
With respect to spina bifida, we observed ORs with 95% confidence intervals that did not include 1.0... DisGeNET Detail
With respect to spina bifida, we observed ORs with 95% confidence intervals that did not include 1.0... DisGeNET Detail
With respect to spina bifida, we observed ORs with 95% confidence intervals that did not include 1.0... DisGeNET Detail
With respect to spina bifida, we observed ORs with 95% confidence intervals that did not include 1.0... DisGeNET Detail
We found three single-nucleotide polymorphisms in those genes associated with LINE-1 methylation: SL... DisGeNET Detail
We found three single-nucleotide polymorphisms in those genes associated with LINE-1 methylation: SL... DisGeNET Detail
We found three single-nucleotide polymorphisms in those genes associated with LINE-1 methylation: SL... DisGeNET Detail
Results showed that six SNPs (MTHFR rs1801133, MTRR rs2287780, MTRR rs10380, FTHFD rs1127717, GART r... DisGeNET Detail
His595Tyr polymorphism in the methionine synthase reductase (MTRR) gene is associated with pancreati... DisGeNET Detail
His595Tyr polymorphism in the methionine synthase reductase (MTRR) gene is associated with pancreati... DisGeNET Detail
We found three single-nucleotide polymorphisms in those genes associated with LINE-1 methylation: SL... DisGeNET Detail
We found three single-nucleotide polymorphisms in those genes associated with LINE-1 methylation: SL... DisGeNET Detail
We found three single-nucleotide polymorphisms in those genes associated with LINE-1 methylation: SL... 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
rs10380 dbSNP
Genome
hg19
Position
chr5:7,897,191-7,897,191
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
109.01
Standard deviation of sample read depth (HGVD)
46.81
Number of reference allele (HGVD)
2113
Number of alternative allele (HGVD)
307
Allele Frequency (HGVD)
0.1268595041322314
Gene Symbol (HGVD)
MTRR
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))
rs10380
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1214
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2035
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8600
East Asian Allele Counts (ExAC)
1344
East Asian Heterozygous Counts (ExAC)
1142
East Asian Homozygous Counts (ExAC)
101
East Asian Allele Frequency (ExAC)
0.15627906976744185
Chromosome Counts in All Race (ExAC)
120950
Allele Counts in All Race (ExAC)
18251
Heterozygous Counts in All Race (ExAC)
14245
Homozygous Counts in All Race (ExAC)
2003
Allele Frequency in All Race (ExAC)
0.15089706490285243
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