chr7:55229255:G>A Detail (hg19) (EGFR)

Information

Genome

Assembly Position
hg19 chr7:55,229,255-55,229,255
hg38 chr7:55,161,562-55,161,562 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_201284.1:c.1562G>A NP_958441.1:p.Arg521Lys
NM_001346897.1:c.1427G>A NP_001333826.1:p.Arg476Lys
NM_005228.3:c.1562G>A NP_005219.2:p.Arg521Lys
Summary

MGeND

Clinical significance Pathogenic
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.630
ToMMo:0.619
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.536

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 131550 OMIM
HGNC 3236 HGNC
Ensembl ENSG00000146648 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv29353876 TogoVar
COSMIC COSM3721608 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic Esophagus somatic MGS000038
(TMGS000091) 		Manabu Muto
Ichiro Kinoshita		 Kyoto University
Department of Medical Oncology Faculty of Medicine and Graduate School of Medicine Hokkaido University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign criteria provided, single submitter not specified germline Detail
Benign 2024-02-01 criteria provided, single submitter EGFR-related lung cancer germline Detail
Benign 2021-07-30 criteria provided, single submitter Inflammatory skin and bowel disease, neonatal, 2 germline Detail
Benign 2019-02-11 criteria provided, single submitter not provided germline Detail
other 2022-12-10 no assertion criteria provided cholangiocarcinoma germline Detail
Benign 2023-07-07 criteria provided, single submitter lung cancer germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.001 Squamous cell carcinoma, metastatic Fifty-one patients enrolled in a single-arm phase II multicenter study for secon... BeFree 20028750 Detail
0.026 Tumor Progression The common EGFR-R521K genotype (G/G) was significantly associated with increased... BeFree 20028750 Detail
0.004 Squamous cell carcinoma of esophagus EGFR:rs2227983 and 3 SNPs of PIK3CA also showed borderline significant correlati... BeFree 24945674 Detail
0.080 breast carcinoma Genetic polymorphisms in the EGFR (R521K) and estrogen receptor (T594T) genes, E... BeFree 19636371 Detail
0.001 Nodule These data suggest that the R521K might be a prognostic factor, because it corre... BeFree 19636371 Detail
0.108 colorectal cancer The EGFR R521K polymorphism influences the risk to develop colorectal cancer. BeFree 21896992 Detail
0.128 Squamous cell carcinoma of esophagus EGFR:rs2227983 and 3 SNPs of PIK3CA also showed borderline significant correlati... BeFree 24945674 Detail
<0.001 bronchitis A novel association between bronchitis and a non-synonymous functional ERBB1 SNP... BeFree 23551418 Detail
0.240 Malignant neoplasm of breast Genetic polymorphisms in the EGFR (R521K) and estrogen receptor (T594T) genes, E... BeFree 19636371 Detail
0.104 Malignant neoplasm of breast Genetic polymorphisms in the EGFR (R521K) and estrogen receptor (T594T) genes, E... BeFree 19636371 Detail
<0.001 bronchitis A novel association between bronchitis and a non-synonymous functional ERBB1 SNP... BeFree 23551418 Detail
0.240 Malignant neoplasm of breast Genetic polymorphisms in the EGFR (R521K) and estrogen receptor (T594T) genes, E... BeFree 19636371 Detail
0.080 colorectal carcinoma The EGFR R521K polymorphism influences the risk to develop colorectal cancer. BeFree 21896992 Detail
0.080 breast carcinoma Genetic polymorphisms in the EGFR (R521K) and estrogen receptor (T594T) genes, E... BeFree 19636371 Detail
0.004 Skin toxicity Our study revealed an influence of the EGFR-R521K genotype on skin toxicity and ... BeFree 20028750 Detail
<0.001 bronchitis A novel association between bronchitis and a non-synonymous functional ERBB1 SNP... BeFree 23551418 Detail
0.080 breast carcinoma Genetic polymorphisms in the EGFR (R521K) and estrogen receptor (T594T) genes, E... BeFree 19636371 Detail
0.022 stomach carcinoma Our data suggest that the EGFR-R521K and ERBB2-I655V polymorphisms are not suita... BeFree 23844533 Detail
0.030 Malignant neoplasm of stomach Our data suggest that the EGFR-R521K and ERBB2-I655V polymorphisms are not suita... BeFree 23844533 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_005228.5(EGFR):c.1562G>A (p.Arg521Lys) AND not specified ClinVar Detail
NM_005228.5(EGFR):c.1562G>A (p.Arg521Lys) AND EGFR-related lung cancer ClinVar Detail
NM_005228.5(EGFR):c.1562G>A (p.Arg521Lys) AND Inflammatory skin and bowel disease, neonatal, 2 ClinVar Detail
NM_005228.5(EGFR):c.1562G>A (p.Arg521Lys) AND not provided ClinVar Detail
NM_005228.5(EGFR):c.1562G>A (p.Arg521Lys) AND Cholangiocarcinoma ClinVar Detail
NM_005228.5(EGFR):c.1562G>A (p.Arg521Lys) AND Lung cancer ClinVar Detail
Fifty-one patients enrolled in a single-arm phase II multicenter study for second-line treatment of ... DisGeNET Detail
The common EGFR-R521K genotype (G/G) was significantly associated with increased skin toxicity (P = ... DisGeNET Detail
EGFR:rs2227983 and 3 SNPs of PIK3CA also showed borderline significant correlation with OS of advanc... DisGeNET Detail
Genetic polymorphisms in the EGFR (R521K) and estrogen receptor (T594T) genes, EGFR and ErbB-2 prote... DisGeNET Detail
These data suggest that the R521K might be a prognostic factor, because it correlates with both tumo... DisGeNET Detail
The EGFR R521K polymorphism influences the risk to develop colorectal cancer. DisGeNET Detail
EGFR:rs2227983 and 3 SNPs of PIK3CA also showed borderline significant correlation with OS of advanc... DisGeNET Detail
A novel association between bronchitis and a non-synonymous functional ERBB1 SNP, rs2227983 (aka epi... DisGeNET Detail
Genetic polymorphisms in the EGFR (R521K) and estrogen receptor (T594T) genes, EGFR and ErbB-2 prote... DisGeNET Detail
Genetic polymorphisms in the EGFR (R521K) and estrogen receptor (T594T) genes, EGFR and ErbB-2 prote... DisGeNET Detail
A novel association between bronchitis and a non-synonymous functional ERBB1 SNP, rs2227983 (aka epi... DisGeNET Detail
Genetic polymorphisms in the EGFR (R521K) and estrogen receptor (T594T) genes, EGFR and ErbB-2 prote... DisGeNET Detail
The EGFR R521K polymorphism influences the risk to develop colorectal cancer. DisGeNET Detail
Genetic polymorphisms in the EGFR (R521K) and estrogen receptor (T594T) genes, EGFR and ErbB-2 prote... DisGeNET Detail
Our study revealed an influence of the EGFR-R521K genotype on skin toxicity and suggested its relati... DisGeNET Detail
A novel association between bronchitis and a non-synonymous functional ERBB1 SNP, rs2227983 (aka epi... DisGeNET Detail
Genetic polymorphisms in the EGFR (R521K) and estrogen receptor (T594T) genes, EGFR and ErbB-2 prote... DisGeNET Detail
Our data suggest that the EGFR-R521K and ERBB2-I655V polymorphisms are not suitable as markers for i... DisGeNET Detail
Our data suggest that the EGFR-R521K and ERBB2-I655V polymorphisms are not suitable as markers for i... 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
rs2227983 dbSNP
Genome
hg19
Position
chr7:55,229,255-55,229,255
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1090
Mean of sample read depth (HGVD)
42.17
Standard deviation of sample read depth (HGVD)
21.55
Number of reference allele (HGVD)
807
Number of alternative allele (HGVD)
1373
Allele Frequency (HGVD)
0.6298165137614679
Gene Symbol (HGVD)
EGFR
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))
rs2227983
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6191
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10375
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8638
East Asian Allele Counts (ExAC)
4629
East Asian Heterozygous Counts (ExAC)
2173
East Asian Homozygous Counts (ExAC)
1228
East Asian Allele Frequency (ExAC)
0.5358879370224588
Chromosome Counts in All Race (ExAC)
121364
Allele Counts in All Race (ExAC)
34827
Heterozygous Counts in All Race (ExAC)
23613
Homozygous Counts in All Race (ExAC)
5607
Allele Frequency in All Race (ExAC)
0.2869631851290333
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