chr4:55593464:A>C Detail (hg19) (KIT)

Information

Genome

Assembly Position
hg19 chr4:55,593,464-55,593,464
hg38 chr4:54,727,298-54,727,298 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000222.2:c.1621A>C NP_000213.1:p.Met541Leu
NM_001093772.1:c.1612A>C NP_001087241.1:p.Met538Leu
Ensemble ENST00000288135.6:c.1621A>C ENST00000288135.6:p.Met541Leu
Summary

MGeND

Clinical significance Benign Uncertain significance not provided
Variant entry 845
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.038
ToMMo:0.046
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.045

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 164920 OMIM
HGNC 6342 HGNC
Ensembl ENSG00000157404 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv17039060 TogoVar
COSMIC COSM28026 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
not provided cervical part of oesophagus not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided upper third of oesophagus not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided middle third of oesophagus not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided lower third of oesophagus not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided oesophagus, unspecified not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided fundus of stomach not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided body of stomach not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided pyloric antrum not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided stomach, unspecified not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided duodenum not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided jejunum not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided ileum not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided caecum not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided appendix not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided transverse colon not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided descending colon not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided sigmoid colon not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided colon, unspecified not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided malignant neoplasm of rectosigmoid junction not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided malignant neoplasm of rectum not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided liver cell carcinoma not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided intrahepatic bile duct carcinoma not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided malignant neoplasm of gallbladder not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided extrahepatic bile duct not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided ampulla of vater not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided head of pancreas not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided body of pancreas not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided ill-defined sites within the digestive system not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided bronchus or lung, unspecified not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
not provided Non-small cell lung cancer somatic MGS000026
(TMGS000046) 		Manabu Muto Kyoto University
Uncertain significance Others somatic MGS000038
(TMGS000091) 		Manabu Muto
Ichiro Kinoshita		 Kyoto University
Department of Medical Oncology Faculty of Medicine and Graduate School of Medicine Hokkaido University
Benign Centenarian germline MGS000068
(TMGS000140) 		Kenjiro Kosaki Keio University
not provided other somatic MGS000039
(TMGS000092) 		Hitoshi Nakagama National Cancer Center Japan 29659903
not provided breast cancer somatic MGS000039
(TMGS000092) 		Hitoshi Nakagama National Cancer Center Japan 29659903
not provided lung cancer somatic MGS000039
(TMGS000092) 		Hitoshi Nakagama National Cancer Center Japan 29659903
not provided other somatic MGS000039
(TMGS000092) 		Hitoshi Nakagama National Cancer Center Japan 29659903
not provided stomach cancer somatic MGS000039
(TMGS000092) 		Hitoshi Nakagama National Cancer Center Japan 29659903
not provided upper third of oesophagus not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided middle third of oesophagus not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided lower third of oesophagus not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided oesophagus, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided fundus of stomach not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided body of stomach not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided pyloric antrum not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided stomach, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided duodenum not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided jejunum not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided small intestine, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided caecum not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided appendix not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided ascending colon not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided transverse colon not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided descending colon not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided sigmoid colon not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided colon, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided malignant neoplasm of rectosigmoid junction not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided malignant neoplasm of rectum not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided intrahepatic bile duct carcinoma not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided malignant neoplasm of gallbladder not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided extrahepatic bile duct not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided ampulla of vater not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided head of pancreas not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided body of pancreas not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided tail of pancreas not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided ill-defined sites within the digestive system not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided bronchus or lung, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-06-22 criteria provided, single submitter not provided germline Detail
Benign criteria provided, single submitter not specified germline Detail
Likely benign 2017-04-27 criteria provided, single submitter mastocytosis germline Detail
Likely benign 2017-04-27 criteria provided, single submitter piebaldism germline Detail
Benign Likely benign 2024-02-01 criteria provided, multiple submitters, no conflicts gastrointestinal stromal tumor germline Detail
not provided 2016-03-10 no assertion provided chronic myelogenous leukemia, BCR-ABL1 positive somatic Detail
Benign 2019-05-08 criteria provided, single submitter Hereditary cancer-predisposing syndrome germline Detail
Pathogenic 2019-04-30 no assertion criteria provided Lip and oral cavity carcinoma somatic Detail
CIViC
Disease Drug EL ET ED CS VO TR Pubmed Links
chronic leukemia Imatinib C Predictive Supports Sensitivity/Response Somatic 2 25015329 Detail
chronic myeloid leukemia B Diagnostic Does Not Support Positive Somatic 4 16307017 Detail
DisGeNET
Score Disease name Description Source Pubmed Links
0.019 urticaria pigmentosa Association of paediatric mastocytosis with a polymorphism resulting in an amino... BeFree 18795925 Detail
0.118 mastocytosis Association of paediatric mastocytosis with a polymorphism resulting in an amino... BeFree 18795925 Detail
0.001 chronic eosinophilic leukemia We investigated the presence of KIT(M541L) in five males with chronic eosinophil... BeFree 25015329 Detail
0.118 mastocytosis The M541L KIT substitution (KIT(M541L)) has been described to be associated with... BeFree 25015329 Detail
<0.001 Fibromatosis, Aggressive Impact of KIT exon 10 M541L allelic variant on the response to imatinib in aggre... BeFree 25174682 Detail
0.019 urticaria pigmentosa The M541L KIT substitution (KIT(M541L)) has been described to be associated with... BeFree 25015329 Detail
0.007 Merkel cell carcinoma Identification of the M541L sequence variation of the transmembrane KIT domain i... BeFree 21498700 Detail
Annotation

Annotations

DescrptionSourceLinks
In 5 patients with KIT M541L mutation-positive chronic eosinophilic leukemia (4 somatic and 1 germli... CIViC Evidence Detail
M541L mutation was not associated with CML in caucasian patients, and was common among healthy contr... CIViC Evidence Detail
NM_000222.3(KIT):c.1621A>C (p.Met541Leu) AND not provided ClinVar Detail
NM_000222.3(KIT):c.1621A>C (p.Met541Leu) AND not specified ClinVar Detail
NM_000222.3(KIT):c.1621A>C (p.Met541Leu) AND Mastocytosis ClinVar Detail
NM_000222.3(KIT):c.1621A>C (p.Met541Leu) AND Piebaldism ClinVar Detail
NM_000222.3(KIT):c.1621A>C (p.Met541Leu) AND Gastrointestinal stromal tumor ClinVar Detail
NM_000222.3(KIT):c.1621A>C (p.Met541Leu) AND Chronic myelogenous leukemia, BCR-ABL1 positive ClinVar Detail
NM_000222.3(KIT):c.1621A>C (p.Met541Leu) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000222.3(KIT):c.1621A>C (p.Met541Leu) AND Lip and oral cavity carcinoma ClinVar Detail
Association of paediatric mastocytosis with a polymorphism resulting in an amino acid substitution (... DisGeNET Detail
Association of paediatric mastocytosis with a polymorphism resulting in an amino acid substitution (... DisGeNET Detail
We investigated the presence of KIT(M541L) in five males with chronic eosinophilic leukemia, not oth... DisGeNET Detail
The M541L KIT substitution (KIT(M541L)) has been described to be associated with pediatric mastocyto... DisGeNET Detail
Impact of KIT exon 10 M541L allelic variant on the response to imatinib in aggressive fibromatosis: ... DisGeNET Detail
The M541L KIT substitution (KIT(M541L)) has been described to be associated with pediatric mastocyto... DisGeNET Detail
Identification of the M541L sequence variation of the transmembrane KIT domain in Merkel cell carcin... 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
rs3822214 dbSNP
Genome
hg19
Position
chr4:55,593,464-55,593,464
Variant Type
snv
Reference Allele
A
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
210.18
Standard deviation of sample read depth (HGVD)
90.59
Number of reference allele (HGVD)
2328
Number of alternative allele (HGVD)
92
Allele Frequency (HGVD)
0.03801652892561983
Gene Symbol (HGVD)
KIT
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))
rs3822214
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0462
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
774
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8646
East Asian Allele Counts (ExAC)
386
East Asian Heterozygous Counts (ExAC)
370
East Asian Homozygous Counts (ExAC)
8
East Asian Allele Frequency (ExAC)
0.04464492250751793
Chromosome Counts in All Race (ExAC)
121372
Allele Counts in All Race (ExAC)
9575
Heterozygous Counts in All Race (ExAC)
8725
Homozygous Counts in All Race (ExAC)
425
Allele Frequency in All Race (ExAC)
0.07888969449296378
Variant (CIViC) (CIViC Variant)
M541L
Transcript 1 (CIViC Variant)
ENST00000288135.5
Variant URL (CIViC Variant)
https://civic.genome.wustl.edu/links/variants/201
Genome browser