chr11:100933412:C>A Detail (hg19) (PGR)

Information

Genome

Assembly Position
hg19 chr11:100,933,412-100,933,412
hg38 chr11:101,062,681-101,062,681 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001271162.1:c.196G>T NP_001258091.1:p.Val66Leu
NM_001271161.2:c.1907-11113G>T
NM_000926.4:c.1978G>T NP_000917.3:p.Val660Leu
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.009
ToMMo:0.009
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.011

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 607311 OMIM
HGNC 8910 HGNC
Ensembl ENSG00000082175 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv43796176 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.033 breast carcinoma We did not observe an association between potential functional genetic polymorph... BeFree 23935996 Detail
0.114 Malignant neoplasm of breast We did not observe an association between potential functional genetic polymorph... BeFree 23935996 Detail
0.004 breast carcinoma We did not observe an association between potential functional genetic polymorph... BeFree 23935996 Detail
0.080 breast carcinoma We did not observe an association between potential functional genetic polymorph... BeFree 23935996 Detail
0.028 Malignant neoplasm of breast We did not observe an association between potential functional genetic polymorph... BeFree 23935996 Detail
0.132 Malignant neoplasm of breast We did not observe an association between potential functional genetic polymorph... BeFree 23935996 Detail
0.011 ovarian carcinoma No significant association between progesterone receptor exon 4 Val660Leu G/T po... BeFree 11323389 Detail
<0.001 Invasive breast carcinoma In conclusion, our data provide persuasive evidence against an overall associati... BeFree 19423537 Detail
0.080 breast carcinoma The increased risk of breast cancer associated with E+P use was greater among wo... BeFree 18628428 Detail
0.080 breast carcinoma The progesterone receptor exon 4 Val660Leu G/T polymorphism and risk of breast c... BeFree 12010857 Detail
0.001 breast carcinoma Previous studies have suggested that minor alleles for ERCC4 rs744154, TNF rs361... BeFree 19423537 Detail
<0.001 Tension Headache We aimed to explore the single-locus, haplotype and epistasis patterns and the c... BeFree 19673915 Detail
0.132 Malignant neoplasm of breast The increased risk of breast cancer associated with E+P use was greater among wo... BeFree 18628428 Detail
0.104 Malignant neoplasm of breast The increased risk of breast cancer associated with E+P use was greater among wo... BeFree 18628428 Detail
0.006 Malignant neoplasm of breast Previous studies have suggested that minor alleles for ERCC4 rs744154, TNF rs361... BeFree 19423537 Detail
0.028 Malignant neoplasm of ovary No significant association between progesterone receptor exon 4 Val660Leu G/T po... BeFree 11323389 Detail
0.024 breast carcinoma The increased risk of breast cancer associated with E+P use was greater among wo... BeFree 18628428 Detail
<0.001 Tension Headache We aimed to explore the single-locus, haplotype and epistasis patterns and the c... BeFree 19673915 Detail
0.132 Malignant neoplasm of breast The progesterone receptor exon 4 Val660Leu G/T polymorphism and risk of breast c... BeFree 12010857 Detail
Annotation

Annotations

DescrptionSourceLinks
We did not observe an association between potential functional genetic polymorphisms in the estrogen... DisGeNET Detail
We did not observe an association between potential functional genetic polymorphisms in the estrogen... DisGeNET Detail
We did not observe an association between potential functional genetic polymorphisms in the estrogen... DisGeNET Detail
We did not observe an association between potential functional genetic polymorphisms in the estrogen... DisGeNET Detail
We did not observe an association between potential functional genetic polymorphisms in the estrogen... DisGeNET Detail
We did not observe an association between potential functional genetic polymorphisms in the estrogen... DisGeNET Detail
No significant association between progesterone receptor exon 4 Val660Leu G/T polymorphism and risk ... DisGeNET Detail
In conclusion, our data provide persuasive evidence against an overall association between invasive ... DisGeNET Detail
The increased risk of breast cancer associated with E+P use was greater among women with at least on... DisGeNET Detail
The progesterone receptor exon 4 Val660Leu G/T polymorphism and risk of breast cancer in Australian ... DisGeNET Detail
Previous studies have suggested that minor alleles for ERCC4 rs744154, TNF rs361525, CASP10 rs130106... DisGeNET Detail
We aimed to explore the single-locus, haplotype and epistasis patterns and the contribution of oestr... DisGeNET Detail
The increased risk of breast cancer associated with E+P use was greater among women with at least on... DisGeNET Detail
The increased risk of breast cancer associated with E+P use was greater among women with at least on... DisGeNET Detail
Previous studies have suggested that minor alleles for ERCC4 rs744154, TNF rs361525, CASP10 rs130106... DisGeNET Detail
No significant association between progesterone receptor exon 4 Val660Leu G/T polymorphism and risk ... DisGeNET Detail
The increased risk of breast cancer associated with E+P use was greater among women with at least on... DisGeNET Detail
We aimed to explore the single-locus, haplotype and epistasis patterns and the contribution of oestr... DisGeNET Detail
The progesterone receptor exon 4 Val660Leu G/T polymorphism and risk of breast cancer in Australian ... 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
-
Genome
hg19
Position
chr11:100,933,412-100,933,412
Variant Type
snv
Reference Allele
C
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
87.41
Standard deviation of sample read depth (HGVD)
40.52
Number of reference allele (HGVD)
2399
Number of alternative allele (HGVD)
21
Allele Frequency (HGVD)
0.008677685950413223
Gene Symbol (HGVD)
PGR
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))
rs1042838
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.009
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
150
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8592
East Asian Allele Counts (ExAC)
97
East Asian Heterozygous Counts (ExAC)
97
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.011289571694599628
Chromosome Counts in All Race (ExAC)
120756
Allele Counts in All Race (ExAC)
15187
Heterozygous Counts in All Race (ExAC)
12851
Homozygous Counts in All Race (ExAC)
1168
Allele Frequency in All Race (ExAC)
0.12576600748617045
Genome browser