chrX:153278829:G>A Detail (hg19) (IRAK1)

Information

Genome

Assembly Position
hg19 chrX:153,278,829-153,278,829
hg38 chrX:154,013,378-154,013,378 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001025243.1:c.1358C>T NP_001020414.1:p.Ser453Leu
NM_001025242.1:c.1595C>T NP_001020413.1:p.Ser532Leu
NM_001569.3:c.1595C>T NP_001560.2:p.Ser532Leu
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.218
ToMMo:0.237
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.232

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 300283 OMIM
HGNC 6112 HGNC
Ensembl ENSG00000184216 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv67028668 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-24 criteria provided, single submitter not specified germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.001 Septicemia We previously described that a commonly occurring IRAK-1 variant haplotype, cont... BeFree 17785851 Detail
0.006 Sepsis We previously described that a commonly occurring IRAK-1 variant haplotype, cont... BeFree 17785851 Detail
0.003 Cerebrovascular accident An initial chi(2) test (false discovery rate <0.05) and subsequent multivaria... BeFree 18566305 Detail
0.003 Cerebrovascular accident An initial chi(2) test (false discovery rate <0.05) and subsequent multivaria... BeFree 18566305 Detail
<0.001 Subarachnoid Hemorrhage An initial chi(2) test (false discovery rate &lt;0.05) and subsequent multivaria... BeFree 18566305 Detail
0.006 cerebral infarction An initial chi(2) test (false discovery rate &lt;0.05) and subsequent multivaria... BeFree 18566305 Detail
0.011 Cerebrovascular accident An initial chi(2) test (false discovery rate &lt;0.05) and subsequent multivaria... BeFree 18566305 Detail
<0.001 cerebral infarction An initial chi(2) test (false discovery rate &lt;0.05) and subsequent multivaria... BeFree 18566305 Detail
<0.001 Subarachnoid Hemorrhage An initial chi(2) test (false discovery rate &lt;0.05) and subsequent multivaria... BeFree 18566305 Detail
<0.001 cerebral infarction An initial chi(2) test (false discovery rate &lt;0.05) and subsequent multivaria... BeFree 18566305 Detail
<0.001 cerebral infarction An initial chi(2) test (false discovery rate &lt;0.05) and subsequent multivaria... BeFree 18566305 Detail
<0.001 Cerebrovascular accident An initial chi(2) test (false discovery rate &lt;0.05) and subsequent multivaria... BeFree 18566305 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001569.4(IRAK1):c.1595C>T (p.Ser532Leu) AND not specified ClinVar Detail
We previously described that a commonly occurring IRAK-1 variant haplotype, containing amino acid ch... DisGeNET Detail
We previously described that a commonly occurring IRAK-1 variant haplotype, containing amino acid ch... DisGeNET Detail
An initial chi(2) test (false discovery rate &lt;0.05) and subsequent multivariable logistic-regress... DisGeNET Detail
An initial chi(2) test (false discovery rate &lt;0.05) and subsequent multivariable logistic-regress... DisGeNET Detail
An initial chi(2) test (false discovery rate &lt;0.05) and subsequent multivariable logistic-regress... DisGeNET Detail
An initial chi(2) test (false discovery rate &lt;0.05) and subsequent multivariable logistic-regress... DisGeNET Detail
An initial chi(2) test (false discovery rate &lt;0.05) and subsequent multivariable logistic-regress... DisGeNET Detail
An initial chi(2) test (false discovery rate &lt;0.05) and subsequent multivariable logistic-regress... DisGeNET Detail
An initial chi(2) test (false discovery rate &lt;0.05) and subsequent multivariable logistic-regress... DisGeNET Detail
An initial chi(2) test (false discovery rate &lt;0.05) and subsequent multivariable logistic-regress... DisGeNET Detail
An initial chi(2) test (false discovery rate &lt;0.05) and subsequent multivariable logistic-regress... DisGeNET Detail
An initial chi(2) test (false discovery rate &lt;0.05) and subsequent multivariable logistic-regress... 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
chrX:153,278,829-153,278,829
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1183
Mean of sample read depth (HGVD)
77.77
Standard deviation of sample read depth (HGVD)
43.41
Number of reference allele (HGVD)
1850
Number of alternative allele (HGVD)
516
Allele Frequency (HGVD)
0.2180896027049873
Gene Symbol (HGVD)
IRAK1
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))
rs1059703
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2373
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3045
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
12833
East Asian Chromosome Counts (ExAC)
6336
East Asian Allele Counts (ExAC)
1468
East Asian Heterozygous Counts (ExAC)
802
East Asian Homozygous Counts (ExAC)
114
East Asian Allele Frequency (ExAC)
0.2316919191919192
Chromosome Counts in All Race (ExAC)
81558
Allele Counts in All Race (ExAC)
55883
Heterozygous Counts in All Race (ExAC)
8528
Homozygous Counts in All Race (ExAC)
12643
Allele Frequency in All Race (ExAC)
0.6851933593271047
East Asian Hemizygous Counts (ExAC)
438
Hemizygous Counts in All Race (ExAC)
22069
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