chr20:44640225:A>G Detail (hg19) (MMP9)

Information

Genome

Assembly Position
hg19 chr20:44,640,225-44,640,225
hg38 chr20:46,011,586-46,011,586 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_004994.2:c.836A>G NP_004985.2:p.Gln279Arg
Ensemble ENST00000372330.3:c.836A>G ENST00000372330.3:p.Gln279Arg
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.640
ToMMo:0.644
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.738

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 120361 OMIM
HGNC 7176 HGNC
Ensembl ENSG00000100985 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv63869174 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2021-09-05 criteria provided, multiple submitters, no conflicts Metaphyseal anadysplasia 2 germline Detail
Benign 2024-01-31 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.011 coronary artery disease We explored the association of MMP2 (C-735T, rs2285053), MMP7 (A-181G, rs1156881... BeFree 22664146 Detail
0.001 primary angle-closure glaucoma In contrast, the SNP rs17576 in MMP-9 might not be related to PACG in the same p... BeFree 19633731 Detail
0.005 colorectal carcinoma The aim of this study was to investigate the association of single-nucleotide po... BeFree 20662554 Detail
0.001 primary angle-closure glaucoma Our data suggest that the MMP1 rs1799750 (-1607 1G/2G) and MMP9 rs17576 polymorp... BeFree 23441116 Detail
0.021 colorectal cancer The MMP-9 279R/Q alleles and genotypes may be associated with the risk of CRC in... BeFree 20662554 Detail
0.001 Glaucoma, Primary Open Angle Our data suggest that the MMP1 -1607 1G/2G, MMP2 -1306 C/T, MMP2 -1575 G/A, and ... BeFree 20808730 Detail
0.009 colorectal carcinoma The MMP-9 279R/Q alleles and genotypes may be associated with the risk of CRC in... BeFree 20662554 Detail
0.027 colorectal cancer The aim of this study was to investigate the association of single-nucleotide po... BeFree 20662554 Detail
<0.001 Glaucoma, Primary Open Angle Our data suggest that the MMP1 rs1799750 (-1607 1G/2G) and MMP9 rs17576 polymorp... BeFree 23441116 Detail
0.001 Glaucoma, Primary Open Angle Our data suggest that the MMP1 rs1799750 (-1607 1G/2G) and MMP9 rs17576 polymorp... BeFree 23441116 Detail
0.030 coronary artery disease These findings suggest that MMP-9 R279Q, P574R and R668Q may have combined effec... BeFree 19283512 Detail
0.101 Hypertensive disease The investigated MMP-9 polymorphisms influenced gene- and protein expression dif... BeFree 21963461 Detail
<0.001 Glaucoma, Open-Angle Functional gene polymorphisms of these MMPs such as MMP1 -1607 1G/2G (rs1799750)... BeFree 20808730 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_004994.3(MMP9):c.836A>G (p.Gln279Arg) AND Metaphyseal anadysplasia 2 ClinVar Detail
NM_004994.3(MMP9):c.836A>G (p.Gln279Arg) AND not provided ClinVar Detail
We explored the association of MMP2 (C-735T, rs2285053), MMP7 (A-181G, rs11568818) and MMP9 (R279Q, ... DisGeNET Detail
In contrast, the SNP rs17576 in MMP-9 might not be related to PACG in the same population. DisGeNET Detail
The aim of this study was to investigate the association of single-nucleotide polymorphism (SNP) at ... DisGeNET Detail
Our data suggest that the MMP1 rs1799750 (-1607 1G/2G) and MMP9 rs17576 polymorphisms might be of va... DisGeNET Detail
The MMP-9 279R/Q alleles and genotypes may be associated with the risk of CRC in Han Chinese. DisGeNET Detail
Our data suggest that the MMP1 -1607 1G/2G, MMP2 -1306 C/T, MMP2 -1575 G/A, and MMP9 Q279R polymorph... DisGeNET Detail
The MMP-9 279R/Q alleles and genotypes may be associated with the risk of CRC in Han Chinese. DisGeNET Detail
The aim of this study was to investigate the association of single-nucleotide polymorphism (SNP) at ... DisGeNET Detail
Our data suggest that the MMP1 rs1799750 (-1607 1G/2G) and MMP9 rs17576 polymorphisms might be of va... DisGeNET Detail
Our data suggest that the MMP1 rs1799750 (-1607 1G/2G) and MMP9 rs17576 polymorphisms might be of va... DisGeNET Detail
These findings suggest that MMP-9 R279Q, P574R and R668Q may have combined effect in the occurrence ... DisGeNET Detail
The investigated MMP-9 polymorphisms influenced gene- and protein expression differently and the R27... DisGeNET Detail
Functional gene polymorphisms of these MMPs such as MMP1 -1607 1G/2G (rs1799750), MMP2 -1306 C/T (rs... 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
rs17576 dbSNP
Genome
hg19
Position
chr20:44,640,225-44,640,225
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1189
Mean of sample read depth (HGVD)
84.26
Standard deviation of sample read depth (HGVD)
43.80
Number of reference allele (HGVD)
856
Number of alternative allele (HGVD)
1521
Allele Frequency (HGVD)
0.6398822044594026
Gene Symbol (HGVD)
MMP9
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))
rs17576
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6444
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10797
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16756
East Asian Chromosome Counts (ExAC)
8646
East Asian Allele Counts (ExAC)
6379
East Asian Heterozygous Counts (ExAC)
1665
East Asian Homozygous Counts (ExAC)
2357
East Asian Allele Frequency (ExAC)
0.7377978255840851
Chromosome Counts in All Race (ExAC)
121284
Allele Counts in All Race (ExAC)
47546
Heterozygous Counts in All Race (ExAC)
27128
Homozygous Counts in All Race (ExAC)
10209
Allele Frequency in All Race (ExAC)
0.39202203093565513
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