chrX:153284192:A>G Detail (hg19) (IRAK1)

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Summary
Information
Links
Disease area statistics
MGeND
ClinVar
CIViC
DisGeNET
Annotation
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Information

Genome

Assembly	Position
hg19	chrX:153,284,192-153,284,192
hg38	chrX:154,018,741-154,018,741 View the variant detail on this assembly version.

HGVS

IRAK1

Type	Transcript	Protein
RefSeq	NM_001025243.1:c.587T>C	NP_001020414.1:p.Phe196Ser
	NM_001025242.1:c.587T>C	NP_001020413.1:p.Phe196Ser
	NM_001569.3:c.587T>C	NP_001560.2:p.Phe196Ser
Ensemble	ENST00000369974.6:c.587T>C	ENST00000369974.6:p.Phe196Ser
	ENST00000369980.8:c.587T>C	ENST00000369980.8:p.Phe196Ser
	ENST00000393687.6:c.587T>C	ENST00000393687.6:p.Phe196Ser
	ENST00000429936.6:c.665T>C	ENST00000429936.6:p.Phe222Ser

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:0.219
	ToMMo:0.241
	NCBN:[No Data.]
	NCBN(Hondo):[No Data.]
	NCBN(Ryukyu):[No Data.]
East asia	ExAC:0.253

Prediction

ClinVar

Clinical Significance	Benign
Review star
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Links

IRAK1

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	tgv67028901	TogoVar
	COSMIC	COSM5038195	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	Giant Cell Arteritis	Our data suggest that IRAK1 rs1059702 and MECP2 rs17435 genetic variants do not ...	BeFree	24709033	Detail
0.001	Septicemia	We previously described that a commonly occurring IRAK-1 variant haplotype, cont...	BeFree	17785851	Detail
<0.001	systemic scleroderma	On the other hand, IRAK1 rs1059702 was consistently associated with presence of ...	BeFree	23444193	Detail
0.006	Sepsis	We previously described that a commonly occurring IRAK-1 variant haplotype, cont...	BeFree	17785851	Detail
0.011	Lupus Erythematosus, Systemic	Association of interleukin-1 receptor-associated kinase (IRAK1) gene polymorphis...	BeFree	23435933	Detail

Annotation

Annotations

Descrption	Source	Links
NM_001569.4(IRAK1):c.587T>C (p.Phe196Ser) AND not specified	ClinVar	Detail
Our data suggest that IRAK1 rs1059702 and MECP2 rs17435 genetic variants do not play a significant r...	DisGeNET	Detail
We previously described that a commonly occurring IRAK-1 variant haplotype, containing amino acid ch...	DisGeNET	Detail
On the other hand, IRAK1 rs1059702 was consistently associated with presence of pulmonary fibrosis (...	DisGeNET	Detail
We previously described that a commonly occurring IRAK-1 variant haplotype, containing amino acid ch...	DisGeNET	Detail
Association of interleukin-1 receptor-associated kinase (IRAK1) gene polymorphisms (rs3027898, rs105...	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:153,284,192-153,284,192
Variant Type: snv
Reference Allele: A
Alternative Allele: G
Filtering Status (HGVD): PASS
# of samples (HGVD): 1194
Mean of sample read depth (HGVD): 75.70
Standard deviation of sample read depth (HGVD): 41.77
Number of reference allele (HGVD): 1864
Number of alternative allele (HGVD): 524
Allele Frequency (HGVD): 0.21943048576214405
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)): rs1059702
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.2409
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 3093
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 12839
East Asian Chromosome Counts (ExAC): 6059
East Asian Allele Counts (ExAC): 1533
East Asian Heterozygous Counts (ExAC): 832
East Asian Homozygous Counts (ExAC): 132
East Asian Allele Frequency (ExAC): 0.25301204819277107
Chromosome Counts in All Race (ExAC): 84056
Allele Counts in All Race (ExAC): 63078
Heterozygous Counts in All Race (ExAC): 7709
Homozygous Counts in All Race (ExAC): 15910
Allele Frequency in All Race (ExAC): 0.750428285904635
East Asian Hemizygous Counts (ExAC): 437
Hemizygous Counts in All Race (ExAC): 23549

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