chr16:55477894:C>T Detail (hg38) (MMP2)

Information

Genome

Assembly Position
hg19 chr16:55,511,806-55,511,806 View the variant detail on this assembly version.
hg38 chr16:55,477,894-55,477,894

HGVS

Type Transcript Protein
RefSeq
Ensemble ENST00000570308.5:c.-75-5015C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.069
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance association
Review star
Show details
Links
Type Database ID Link
Gene MIM 120360 OMIM
HGNC 7166 HGNC
Ensembl ENSG00000087245 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv55581055 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
association 2016-01-01 criteria provided, single submitter Lip and oral cavity carcinoma germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Glaucoma, Open-Angle Functional gene polymorphisms of these MMPs such as MMP1 -1607 1G/2G (rs1799750)... BeFree 20808730 Detail
0.006 Malignant neoplasm of urinary bladder To elucidate genetic polymorphisms of the matrix metalloproteinases (MMPs) MMP1 ... BeFree 23819551 Detail
<0.001 Carcinoma of bladder To elucidate genetic polymorphisms of the matrix metalloproteinases (MMPs) MMP1 ... BeFree 23819551 Detail
<0.001 Malignant neoplasm of urinary bladder To elucidate genetic polymorphisms of the matrix metalloproteinases (MMPs) MMP1 ... BeFree 23819551 Detail
<0.001 Carcinoma of bladder To elucidate genetic polymorphisms of the matrix metalloproteinases (MMPs) MMP1 ... BeFree 23819551 Detail
<0.001 Malignant neoplasm of urinary bladder To elucidate genetic polymorphisms of the matrix metalloproteinases (MMPs) MMP1 ... BeFree 23819551 Detail
<0.001 Carcinoma of bladder To elucidate genetic polymorphisms of the matrix metalloproteinases (MMPs) MMP1 ... BeFree 23819551 Detail
0.133 rheumatoid arthritis The MMP2 rs243865-T allele is not a major genetic factor for rheumatoid arthriti... BeFree 18205826 Detail
0.008 Malignant neoplasm of urinary bladder The combined genotype MMP2 -1306C/T (rs243865) allele T with MMP9 -1562C/T (rs39... BeFree 23819551 Detail
0.004 Carcinoma of bladder The combined genotype MMP2 -1306C/T (rs243865) allele T with MMP9 -1562C/T (rs39... BeFree 23819551 Detail
0.005 Carcinoma of bladder The combined genotype MMP2 -1306C/T (rs243865) allele T with MMP9 -1562C/T (rs39... BeFree 23819551 Detail
0.012 Malignant neoplasm of urinary bladder The combined genotype MMP2 -1306C/T (rs243865) allele T with MMP9 -1562C/T (rs39... BeFree 23819551 Detail
0.005 Secondary malignant neoplasm of lymph node Epistasis between PARP1 rs1136410 and MMP2 rs243865 increased the risk of LNM of... BeFree 21612407 Detail
0.009 stomach carcinoma Epistasis between PARP1 rs1136410 and MMP2 rs243865 increased the risk of LNM of... BeFree 21612407 Detail
0.013 Malignant neoplasm of stomach Epistasis between PARP1 rs1136410 and MMP2 rs243865 increased the risk of LNM of... BeFree 21612407 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_004530.5(MMP2):c.-1586C>T AND Lip and oral cavity carcinoma ClinVar Detail
Functional gene polymorphisms of these MMPs such as MMP1 -1607 1G/2G (rs1799750), MMP2 -1306 C/T (rs... DisGeNET Detail
To elucidate genetic polymorphisms of the matrix metalloproteinases (MMPs) MMP1 (rs1799750), MMP2 (r... DisGeNET Detail
To elucidate genetic polymorphisms of the matrix metalloproteinases (MMPs) MMP1 (rs1799750), MMP2 (r... DisGeNET Detail
To elucidate genetic polymorphisms of the matrix metalloproteinases (MMPs) MMP1 (rs1799750), MMP2 (r... DisGeNET Detail
To elucidate genetic polymorphisms of the matrix metalloproteinases (MMPs) MMP1 (rs1799750), MMP2 (r... DisGeNET Detail
To elucidate genetic polymorphisms of the matrix metalloproteinases (MMPs) MMP1 (rs1799750), MMP2 (r... DisGeNET Detail
To elucidate genetic polymorphisms of the matrix metalloproteinases (MMPs) MMP1 (rs1799750), MMP2 (r... DisGeNET Detail
The MMP2 rs243865-T allele is not a major genetic factor for rheumatoid arthritis in the French Cauc... DisGeNET Detail
The combined genotype MMP2 -1306C/T (rs243865) allele T with MMP9 -1562C/T (rs3918242) allele T was ... DisGeNET Detail
The combined genotype MMP2 -1306C/T (rs243865) allele T with MMP9 -1562C/T (rs3918242) allele T was ... DisGeNET Detail
The combined genotype MMP2 -1306C/T (rs243865) allele T with MMP9 -1562C/T (rs3918242) allele T was ... DisGeNET Detail
The combined genotype MMP2 -1306C/T (rs243865) allele T with MMP9 -1562C/T (rs3918242) allele T was ... DisGeNET Detail
Epistasis between PARP1 rs1136410 and MMP2 rs243865 increased the risk of LNM of GC. DisGeNET Detail
Epistasis between PARP1 rs1136410 and MMP2 rs243865 increased the risk of LNM of GC. DisGeNET Detail
Epistasis between PARP1 rs1136410 and MMP2 rs243865 increased the risk of LNM of GC. DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs243865 dbSNP
Genome
hg38
Position
chr16:55,477,894-55,477,894
Variant Type
snv
Reference Allele
C
Alternative Allele
T
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))
rs243865
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0693
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1161
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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