chr1:17336144:T>C Detail (hg38) (PADI4)

Information

Genome

Assembly Position
hg19 chr1:17,662,639-17,662,639 View the variant detail on this assembly version.
hg38 chr1:17,336,144-17,336,144

HGVS

Type Transcript Protein
RefSeq NM_012387.2:c.341-15T>C
Ensemble ENST00000375448.4:c.341-15T>C
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.591
ToMMo:0.605
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.582

Prediction

ClinVar

Clinical Significance association
Review star
Show details
Links
Type Database ID Link
Gene MIM 605347 OMIM
HGNC 18368 HGNC
Ensembl ENSG00000159339 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv552494 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
association no assertion criteria provided rheumatoid arthritis germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.332 rheumatoid arthritis These findings suggest that the functional single-nucleotide polymorphism PADI4 ... BeFree 22505706 Detail
0.129 rheumatoid arthritis Genetic factors regarded as putative risk factors were RA-susceptible polymorphi... BeFree 23577190 Detail
0.006 rheumatoid arthritis Genetic factors regarded as putative risk factors were RA-susceptible polymorphi... BeFree 23577190 Detail
0.248 rheumatoid arthritis Genetic factors regarded as putative risk factors were RA-susceptible polymorphi... BeFree 23577190 Detail
0.123 rheumatoid arthritis Genetic factors regarded as putative risk factors were RA-susceptible polymorphi... BeFree 23577190 Detail
<0.001 rheumatoid arthritis Genetic factors regarded as putative risk factors were RA-susceptible polymorphi... BeFree 23577190 Detail
0.168 rheumatoid arthritis Genetic factors regarded as putative risk factors were RA-susceptible polymorphi... BeFree 23577190 Detail
0.243 rheumatoid arthritis Genetic factors regarded as putative risk factors were RA-susceptible polymorphi... BeFree 23577190 Detail
0.243 rheumatoid arthritis Genetic factors regarded as putative risk factors were RA-susceptible polymorphi... BeFree 23577190 Detail
0.243 rheumatoid arthritis Genetic factors regarded as putative risk factors were RA-susceptible polymorphi... BeFree 23577190 Detail
0.123 rheumatoid arthritis Genetic factors regarded as putative risk factors were RA-susceptible polymorphi... BeFree 23577190 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_012387.3(PADI4):c.341-15T>C AND Rheumatoid arthritis ClinVar Detail
These findings suggest that the functional single-nucleotide polymorphism PADI4 rs2240340 G/A varian... DisGeNET Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th... DisGeNET Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th... DisGeNET Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th... DisGeNET Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th... DisGeNET Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th... DisGeNET Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th... DisGeNET Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th... DisGeNET Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th... DisGeNET Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th... DisGeNET Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2240340 dbSNP
Genome
hg38
Position
chr1:17,336,144-17,336,144
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
837
Mean of sample read depth (HGVD)
183.36
Standard deviation of sample read depth (HGVD)
82.17
Number of reference allele (HGVD)
685
Number of alternative allele (HGVD)
989
Allele Frequency (HGVD)
0.5908004778972521
Gene Symbol (HGVD)
PADI4
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))
rs2240340
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6054
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10147
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8504
East Asian Allele Counts (ExAC)
4953
East Asian Heterozygous Counts (ExAC)
2039
East Asian Homozygous Counts (ExAC)
1457
East Asian Allele Frequency (ExAC)
0.5824317968015051
Chromosome Counts in All Race (ExAC)
119334
Allele Counts in All Race (ExAC)
67056
Heterozygous Counts in All Race (ExAC)
29366
Homozygous Counts in All Race (ExAC)
18845
Allele Frequency in All Race (ExAC)
0.5619186484991704
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