chr21:44524456:G>A Detail (hg19) (U2AF1)

Information

Genome

Assembly Position
hg19 chr21:44,524,456-44,524,456
hg38 chr21:43,104,346-43,104,346 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_006758.2:c.101C>T NP_006749.1:p.Ser34Phe
NM_001025203.1:c.101C>T NP_001020374.1:p.Ser34Phe
Ensemble ENST00000291552.9:c.101C>T ENST00000291552.9:p.Ser34Phe
Summary

MGeND

Clinical significance not provided
Variant entry 97
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:[No Data.]
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Likely pathogenic
Review star
Show details
Links
Type Database ID Link
Gene MIM 191317 OMIM
HGNC 12453 HGNC
Ensembl ENSG00000160201 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar
COSMIC COSM1142948 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
not provided malignant neoplasm of rectum 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 Acute myeloblastic leukaemia somatic MGS000005
(TMGS000006) 		Keizo Horibe National Hospital Organization Nagoya Medical Center
not provided Myelodysplastic syndromes somatic MGS000005
(TMGS000006) 		Keizo Horibe National Hospital Organization Nagoya Medical Center
not provided colon, unspecified 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 body 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
Likely pathogenic 2016-05-31 no assertion criteria provided somatic Detail
Likely pathogenic 2016-05-31 no assertion criteria provided pancreatic adenocarcinoma somatic Detail
Likely pathogenic 2016-05-31 no assertion criteria provided Squamous cell carcinoma of the head and neck somatic Detail
Likely pathogenic 2016-05-31 no assertion criteria provided acute myeloid leukemia somatic Detail
Likely pathogenic 2016-05-31 no assertion criteria provided lung adenocarcinoma somatic Detail
Likely pathogenic 2016-05-31 no assertion criteria provided Neoplasm of uterine cervix somatic Detail
Likely pathogenic 2016-05-31 no assertion criteria provided myelodysplastic syndrome somatic Detail
Likely pathogenic 2016-05-31 no assertion criteria provided Malignant neoplasm of body of uterus somatic Detail
Likely pathogenic 2016-05-31 no assertion criteria provided uterine carcinosarcoma somatic Detail
CIViC
Disease Drug EL ET ED CS VO TR Pubmed Links
acute myeloid leukemia B Diagnostic Does Not Support Positive Somatic 3 23029227 Detail
acute myeloid leukemia B Prognostic Does Not Support N/A Somatic 2 23029227 Detail
myelodysplastic syndrome B Prognostic Supports Poor Outcome Somatic 3 23861105 Detail
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 de novo myelodysplastic syndromes We previously identified missense mutations in the U2AF1 splicing factor affecti... BeFree 25311244 Detail
<0.001 Miller Dieker syndrome We previously identified missense mutations in the U2AF1 splicing factor affecti... BeFree 25311244 Detail
<0.001 de novo myelodysplastic syndromes We previously identified missense mutations in the U2AF1 splicing factor affecti... BeFree 25311244 Detail
<0.001 Miller Dieker syndrome These data suggest that the S34F mutation alters U2AF1 function in the context o... BeFree 25311244 Detail
Annotation

Annotations

DescrptionSourceLinks
Age, sex, FAB subtype and karyotypes were not statistically significant between AML patients with U2... CIViC Evidence Detail
In patients with AML, complete remission rates are not different between patients who harbor the U2A... CIViC Evidence Detail
After adjusting for age and cancer stage, the presence of U2AF mutations such as S34Y/F are prognost... CIViC Evidence Detail
NM_006758.3(U2AF1):c.101C>T (p.Ser34Phe) AND Transitional cell carcinoma of the bladder ClinVar Detail
NM_006758.3(U2AF1):c.101C>T (p.Ser34Phe) AND Pancreatic adenocarcinoma ClinVar Detail
NM_006758.3(U2AF1):c.101C>T (p.Ser34Phe) AND Squamous cell carcinoma of the head and neck ClinVar Detail
NM_006758.3(U2AF1):c.101C>T (p.Ser34Phe) AND Acute myeloid leukemia ClinVar Detail
NM_006758.3(U2AF1):c.101C>T (p.Ser34Phe) AND Lung adenocarcinoma ClinVar Detail
NM_006758.3(U2AF1):c.101C>T (p.Ser34Phe) AND Neoplasm of uterine cervix ClinVar Detail
NM_006758.3(U2AF1):c.101C>T (p.Ser34Phe) AND Myelodysplastic syndrome ClinVar Detail
NM_006758.3(U2AF1):c.101C>T (p.Ser34Phe) AND Malignant neoplasm of body of uterus ClinVar Detail
NM_006758.3(U2AF1):c.101C>T (p.Ser34Phe) AND Uterine carcinosarcoma ClinVar Detail
We previously identified missense mutations in the U2AF1 splicing factor affecting codons S34 (S34F ... DisGeNET Detail
We previously identified missense mutations in the U2AF1 splicing factor affecting codons S34 (S34F ... DisGeNET Detail
We previously identified missense mutations in the U2AF1 splicing factor affecting codons S34 (S34F ... DisGeNET Detail
These data suggest that the S34F mutation alters U2AF1 function in the context of specific RNA seque... 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
rs371769427 dbSNP
Genome
hg19
Position
chr21:44,524,456-44,524,456
Variant Type
snv
Reference Allele
G
Alternative Allele
A
East Asian Chromosome Counts (ExAC)
8582
East Asian Allele Counts (ExAC)
1
East Asian Heterozygous Counts (ExAC)
1
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
1.1652295502213937E-4
Chromosome Counts in All Race (ExAC)
118678
Allele Counts in All Race (ExAC)
5
Heterozygous Counts in All Race (ExAC)
5
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
4.213080773184584E-5
Variant (CIViC) (CIViC Variant)
S34Y/F
Transcript 1 (CIViC Variant)
ENST00000291552.4
Variant URL (CIViC Variant)
https://civic.genome.wustl.edu/links/variants/128
Summary (CIViC Variant)
U2AF1 S34Y/F has been shown to be a recurrent mutation in acute myeloid leukemia (AML), myelodysplastic syndromes (MDS) and lung adenocarcinomas. This mutation is the most commonly identified variant in MDS, occurs in the first zinc finger domain of U2AF1 and has been demonstrated to alter splicing. The impact of U2AF1 mutations on overall survival in MDS has been debated, however, patients with U2AF1 mutations were shown to be at an increased risk of transformation to secondary AML. The presence of this mutation was not associated with a specific prognostic outcome in AML when compared to U2AF1 wildtype patients.
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