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 Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 603382 OMIM
HGNC 7328 HGNC
Ensembl ENSG00000204410 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv24793140 TogoVar
COSMIC
MONDO
Type Database ID Link
Gene MIM
HGNC 41994 HGNC
Ensembl ENSG00000255152 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv24793140 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2016-03-29 criteria provided, single submitter not specified germline Detail
Benign 2019-07-24 criteria provided, single submitter MSH5-related disorder germline Detail
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

DescrptionSourceLinks
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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