chr11:102713620:T>C Detail (hg19) (MMP3)

Information

Genome

Assembly Position
hg19 chr11:102,713,620-102,713,620
hg38 chr11:102,842,889-102,842,889 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_002422.4:c.133A>G NP_002413.1:p.Lys45Glu
Ensemble ENST00000299855.10:c.133A>G ENST00000299855.10:p.Lys45Glu
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.705
ToMMo:0.681
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.676

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 185250 OMIM
HGNC 7173 HGNC
Ensembl ENSG00000149968 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv43840321 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2016-03-28 criteria provided, single submitter not specified germline Detail
Benign 2018-11-12 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Chronic Kidney Diseases The Chi-square test, multivariable logistic regression analysis with adjustment ... BeFree 19424605 Detail
<0.001 Chronic Kidney Diseases The Chi-square test, multivariable logistic regression analysis with adjustment ... BeFree 19424605 Detail
<0.001 Chronic Kidney Diseases The Chi-square test, multivariable logistic regression analysis with adjustment ... BeFree 19424605 Detail
0.002 Chronic Kidney Diseases The Chi-square test, multivariable logistic regression analysis with adjustment ... BeFree 19424605 Detail
0.002 Chronic Kidney Diseases The Chi-square test, multivariable logistic regression analysis with adjustment ... BeFree 19424605 Detail
0.003 Tendinopathy Furthermore, the MMP3 gene variant rs679620 and the COL5A1 marker rs12722 intera... BeFree 19042922 Detail
<0.001 Tendinopathy Furthermore, the MMP3 gene variant rs679620 and the COL5A1 marker rs12722 intera... BeFree 19042922 Detail
0.143 coronary artery disease Although results thus far are inconsistent, meta-analysis has demonstrated that ... BeFree 24938016 Detail
0.030 coronary artery disease Although results thus far are inconsistent, meta-analysis has demonstrated that ... BeFree 24938016 Detail
0.018 Hypertensive disease [Surprisingly, MMP3_rs679620 had the opposite effect on women with low BMI, resu... GAD 19008710 Detail
0.002 Chronic Kidney Diseases The chi-square test and multivariable logistic regression analysis with adjustme... BeFree 19406964 Detail
<0.001 Chronic Kidney Diseases The chi-square test and multivariable logistic regression analysis with adjustme... BeFree 19406964 Detail
0.002 Chronic Kidney Diseases The chi-square test and multivariable logistic regression analysis with adjustme... BeFree 19406964 Detail
<0.001 Chronic Kidney Diseases The chi-square test and multivariable logistic regression analysis with adjustme... BeFree 19406964 Detail
<0.001 Chronic Kidney Diseases The chi-square test and multivariable logistic regression analysis with adjustme... BeFree 19406964 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002422.5(MMP3):c.133A>G (p.Lys45Glu) AND not specified ClinVar Detail
NM_002422.5(MMP3):c.133A>G (p.Lys45Glu) AND not provided ClinVar Detail
The Chi-square test, multivariable logistic regression analysis with adjustment for covariates, as w... DisGeNET Detail
The Chi-square test, multivariable logistic regression analysis with adjustment for covariates, as w... DisGeNET Detail
The Chi-square test, multivariable logistic regression analysis with adjustment for covariates, as w... DisGeNET Detail
The Chi-square test, multivariable logistic regression analysis with adjustment for covariates, as w... DisGeNET Detail
The Chi-square test, multivariable logistic regression analysis with adjustment for covariates, as w... DisGeNET Detail
Furthermore, the MMP3 gene variant rs679620 and the COL5A1 marker rs12722 interact to modify the ris... DisGeNET Detail
Furthermore, the MMP3 gene variant rs679620 and the COL5A1 marker rs12722 interact to modify the ris... DisGeNET Detail
Although results thus far are inconsistent, meta-analysis has demonstrated that MMP-3 Glu45Lys and M... DisGeNET Detail
Although results thus far are inconsistent, meta-analysis has demonstrated that MMP-3 Glu45Lys and M... DisGeNET Detail
[Surprisingly, MMP3_rs679620 had the opposite effect on women with low BMI, resulting in higher dias... DisGeNET Detail
The chi-square test and multivariable logistic regression analysis with adjustment for covariates re... DisGeNET Detail
The chi-square test and multivariable logistic regression analysis with adjustment for covariates re... DisGeNET Detail
The chi-square test and multivariable logistic regression analysis with adjustment for covariates re... DisGeNET Detail
The chi-square test and multivariable logistic regression analysis with adjustment for covariates re... DisGeNET Detail
The chi-square test and multivariable logistic regression analysis with adjustment for covariates re... 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
rs679620 dbSNP
Genome
hg19
Position
chr11:102,713,620-102,713,620
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1073
Mean of sample read depth (HGVD)
132.78
Standard deviation of sample read depth (HGVD)
65.57
Number of reference allele (HGVD)
631
Number of alternative allele (HGVD)
1511
Allele Frequency (HGVD)
0.7054154995331466
Gene Symbol (HGVD)
MMP3
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))
rs679620
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6807
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
11407
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8080
East Asian Allele Counts (ExAC)
5466
East Asian Heterozygous Counts (ExAC)
1826
East Asian Homozygous Counts (ExAC)
1820
East Asian Allele Frequency (ExAC)
0.6764851485148515
Chromosome Counts in All Race (ExAC)
113454
Allele Counts in All Race (ExAC)
66832
Heterozygous Counts in All Race (ExAC)
27864
Homozygous Counts in All Race (ExAC)
19484
Allele Frequency in All Race (ExAC)
0.5890669346166728
Genome browser