chr6:31740551:C>T Detail (hg38) (MSH5, MSH5-SAPCD1)
Information
Genome
Assembly | Position |
---|---|
hg19 | chr6:31,708,328-31,708,328 View the variant detail on this assembly version. |
hg38 | chr6:31,740,551-31,740,551 |
HGVS
Type | Transcript | Protein |
---|---|---|
RefSeq | NM_172165.3:c.85C>T | NP_751897.1:p.Pro29Ser |
NM_025259.5:c.85C>T | NP_079535.4:p.Pro29Ser | |
NM_172166.3:c.85C>T | NP_751898.1:p.Pro29Ser |
Type | Transcript | Protein |
---|---|---|
RefSeq | NR_037846.1:c.85C>T | |
Ensemble | ENST00000493662.6:c.85C>T | ENST00000493662.6:p.Pro29Ser |
Summary
MGeND
Clinical significance | |
Variant entry | |
GWAS entry | |
Disease area statistics | Show details |
Frequency
JP | HGVD:0.243 |
ToMMo:0.277 | |
NCBN:[No Data.] | |
NCBN(Hondo):[No Data.] | |
NCBN(Ryukyu):[No Data.] | |
East asia | ExAC:0.242 |
Prediction
ClinVar
Clinical Significance |
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Review star | ![]() |
Show details |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
CIViC
[No Data.]
DisGeNET
Score | Disease name | Description | Source | Pubmed | Links |
---|---|---|---|---|---|
0.003 | male infertility | The role of MSH5 C85T and MLH3 C2531T polymorphisms in the risk of male infertil... | BeFree | 19808033 | Detail |
0.003 | oligospermia | The role of MSH5 C85T and MLH3 C2531T polymorphisms in the risk of male infertil... | BeFree | 19808033 | Detail |
0.003 | azoospermia | The role of MSH5 C85T and MLH3 C2531T polymorphisms in the risk of male infertil... | BeFree | 19808033 | Detail |
<0.001 | oligospermia | The role of MSH5 C85T and MLH3 C2531T polymorphisms in the risk of male infertil... | BeFree | 19808033 | Detail |
0.005 | azoospermia | The role of MSH5 C85T and MLH3 C2531T polymorphisms in the risk of male infertil... | BeFree | 19808033 | Detail |
0.003 | male infertility | The role of MSH5 C85T and MLH3 C2531T polymorphisms in the risk of male infertil... | BeFree | 19808033 | Detail |
<0.001 | oligospermia | One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059... | BeFree | 22594646 | Detail |
<0.001 | azoospermia | One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059... | BeFree | 22594646 | Detail |
0.005 | azoospermia | One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059... | BeFree | 22594646 | Detail |
0.003 | oligospermia | One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059... | BeFree | 22594646 | Detail |
<0.001 | azoospermia | One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059... | BeFree | 22594646 | Detail |
<0.001 | oligospermia | One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059... | BeFree | 22594646 | Detail |
Annotation
Annotations
Descrption | Source | Links |
---|---|---|
NM_172166.4(MSH5):c.85C>T (p.Pro29Ser) AND not specified | ClinVar | Detail |
NM_172166.4(MSH5):c.85C>T (p.Pro29Ser) AND MSH5-related disorder | ClinVar | Detail |
The role of MSH5 C85T and MLH3 C2531T polymorphisms in the risk of male infertility with azoospermia... | DisGeNET | Detail |
The role of MSH5 C85T and MLH3 C2531T polymorphisms in the risk of male infertility with azoospermia... | DisGeNET | Detail |
The role of MSH5 C85T and MLH3 C2531T polymorphisms in the risk of male infertility with azoospermia... | DisGeNET | Detail |
The role of MSH5 C85T and MLH3 C2531T polymorphisms in the risk of male infertility with azoospermia... | DisGeNET | Detail |
The role of MSH5 C85T and MLH3 C2531T polymorphisms in the risk of male infertility with azoospermia... | DisGeNET | Detail |
The role of MSH5 C85T and MLH3 C2531T polymorphisms in the risk of male infertility with azoospermia... | DisGeNET | Detail |
One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059060, Ser775Asn) and ... | DisGeNET | Detail |
One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059060, Ser775Asn) and ... | DisGeNET | Detail |
One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059060, Ser775Asn) and ... | DisGeNET | Detail |
One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059060, Ser775Asn) and ... | DisGeNET | Detail |
One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059060, Ser775Asn) and ... | DisGeNET | Detail |
One intronic SNP in MLH1 (rs4647269) and two non-synonymous SNPs in PMS2 (rs1059060, Ser775Asn) and ... | 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
- rs2075789 dbSNP
- Genome
- hg38
- Position
- chr6:31,740,551-31,740,551
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1014
- Mean of sample read depth (HGVD)
- 43.11
- Standard deviation of sample read depth (HGVD)
- 20.45
- Number of reference allele (HGVD)
- 1536
- Number of alternative allele (HGVD)
- 492
- Allele Frequency (HGVD)
- 0.24260355029585798
- Gene Symbol (HGVD)
- MSH5
- 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))
- rs2075789
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.2767
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 4638
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 596
- East Asian Allele Counts (ExAC)
- 144
- East Asian Heterozygous Counts (ExAC)
- 114
- East Asian Homozygous Counts (ExAC)
- 15
- East Asian Allele Frequency (ExAC)
- 0.24161073825503357
- Chromosome Counts in All Race (ExAC)
- 15122
- Allele Counts in All Race (ExAC)
- 2212
- Heterozygous Counts in All Race (ExAC)
- 1934
- Homozygous Counts in All Race (ExAC)
- 139
- Allele Frequency in All Race (ExAC)
- 0.14627694749371775
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