Yum, tasty mutations...

MutationTaster - study a chromosomal position

MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 5 transcript(s)...
Querying Taster for transcript #1: ENST00000540418
Querying Taster for transcript #2: ENST00000303145
Querying Taster for transcript #3: ENST00000411698
Querying Taster for transcript #4: ENST00000393543
Querying Taster for transcript #5: ENST00000430606
MT speed 3.08 s - this script 5.367241 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
MDM1polymorphism_automatic1.59690038969984e-11simple_aaeT103Isingle base exchangers962976show file
MDM1polymorphism_automatic1.59690038969984e-11simple_aaeT103Isingle base exchangers962976show file
MDM1polymorphism_automatic2.89730461844329e-11simple_aaeT103Isingle base exchangers962976show file
MDM1polymorphism_automatic2.86099763002756e-06without_aaesingle base exchangers962976show file
MDM1polymorphism_automatic2.86099763002756e-06without_aaesingle base exchangers962976show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999984031 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:68720627G>AN/A show variant in all transcripts   IGV
HGNC symbol MDM1
Ensembl transcript ID ENST00000411698
Genbank transcript ID NM_001205028
UniProt peptide Q8TC05
alteration type single base exchange
alteration region CDS
DNA changes c.308C>T
cDNA.349C>T
g.5535C>T
AA changes T103I Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS
103
frameshift no
known variant Reference ID: rs962976
databasehomozygous (A/A)heterozygousallele carriers
1000G118810052193
ExAC29833-268992934
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0110.018
0.0150.012
(flanking)1.8190.014
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased5538wt: 0.9756 / mu: 0.9808 (marginal change - not scored)wt: TACTCAAGAAAGAGT
mu: TATTCAAGAAAGAGT
 CTCA|agaa
distance from splice site 175
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      103PKSQEAEQKDVTQERVHSLEASRV
mutated  not conserved    103PKSQEAEQKDVIQERVHSLEASR
Ptroglodytes  all identical  ENSPTRG00000005196  103PKSQEAEQKDVTQERVHSLEASR
Mmulatta  all identical  ENSMMUG00000018725  103PKSQEAEQKDVTQERVDSLEASR
Fcatus  no alignment  ENSFCAG00000018582  n/a
Mmusculus  not conserved  ENSMUSG00000020212  103PKPQEAEQGEDANQEAVLSLEASR
Ggallus  not conserved  ENSGALG00000009905  100AESLAEHSNDVNQENTETPEGPR
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000045675  100LRATSAERQ------VTPLAPRD
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000001452  101LRL-DLDRESLAEEKLHTPDAPR
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2040 / 2040
position (AA) of stopcodon in wt / mu AA sequence 680 / 680
position of stopcodon in wt / mu cDNA 2081 / 2081
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now
N/A
position of start ATG in wt / mu cDNA 42 / 42
chromosome 12
strand -1
last intron/exon boundary 1969
theoretical NMD boundary in CDS 1877
length of CDS 2040
coding sequence (CDS) position 308
cDNA position
(for ins/del: last normal base / first normal base)
349
gDNA position
(for ins/del: last normal base / first normal base)
5535
chromosomal position
(for ins/del: last normal base / first normal base)
68720627
original gDNA sequence snippet AGCAGAACAAAAGGATGTTACTCAAGAAAGAGTTCACTCAC
altered gDNA sequence snippet AGCAGAACAAAAGGATGTTATTCAAGAAAGAGTTCACTCAC
original cDNA sequence snippet AGCAGAACAAAAGGATGTTACTCAAGAAAGAGTTCACTCAC
altered cDNA sequence snippet AGCAGAACAAAAGGATGTTATTCAAGAAAGAGTTCACTCAC
wildtype AA sequence MPVRFKGLSE YQRNFLWKKS YLSESCNSSV GRKYPWAGLR SDQLGITKEP SFISKRRVPY
HDPQISKSLE WNGAISESNV VASPEPEAPE TPKSQEAEQK DVTQERVHSL EASRVPKRTR
SHSADSRAEG ASDVENNEGV TNHTPVNENV ELEHSTKVLS ENVDNGVFHN KSQFVPPFKG
NSVIHETEYK RNFKGLSPVK EPKLRNDLRE NRNLETVSPE RKSNKIDDRL KLEAEMELKD
LHQPKRKLTP WKHQRLGKVN SEYRAKFLSP AQYLYKAGAW THVKGNMPNQ GSLNAMWYAE
VKELREKAEF YRKRVQGTHF SRDHLNQILS DSNCCWDVSS TTSSEGTVSS NIRALDLAGD
PTSHKTLQKC PSTEPEEKGN IVEEQPQKNT TEKLGVSAPT IPVRRRLAWD TENTSEDVQK
QPGEKEEEDD NEEEGDRKTG KQAFMGEQEK LDVREKSKAD KMKEGSDSSV SSEKGGRLPT
PKLRELGGIQ RTHHDLTTPA VGGAVLVSPS KMKPPAPEQR KRMTSQDCLE TSKNDFTKKE
SRAVSLLTSP AAGIKTVDPL PLREDSEDNI HKFAEATLPV SKIPKYPTNP PGQLPSPPHV
PSYWHPSRRI QGSLRDPEFQ HNVGKARMNN LQLPQHEAFN DEDEDRLSEI SARSAASSLR
AFQTLARAKK RKENFWGKT*
mutated AA sequence MPVRFKGLSE YQRNFLWKKS YLSESCNSSV GRKYPWAGLR SDQLGITKEP SFISKRRVPY
HDPQISKSLE WNGAISESNV VASPEPEAPE TPKSQEAEQK DVIQERVHSL EASRVPKRTR
SHSADSRAEG ASDVENNEGV TNHTPVNENV ELEHSTKVLS ENVDNGVFHN KSQFVPPFKG
NSVIHETEYK RNFKGLSPVK EPKLRNDLRE NRNLETVSPE RKSNKIDDRL KLEAEMELKD
LHQPKRKLTP WKHQRLGKVN SEYRAKFLSP AQYLYKAGAW THVKGNMPNQ GSLNAMWYAE
VKELREKAEF YRKRVQGTHF SRDHLNQILS DSNCCWDVSS TTSSEGTVSS NIRALDLAGD
PTSHKTLQKC PSTEPEEKGN IVEEQPQKNT TEKLGVSAPT IPVRRRLAWD TENTSEDVQK
QPGEKEEEDD NEEEGDRKTG KQAFMGEQEK LDVREKSKAD KMKEGSDSSV SSEKGGRLPT
PKLRELGGIQ RTHHDLTTPA VGGAVLVSPS KMKPPAPEQR KRMTSQDCLE TSKNDFTKKE
SRAVSLLTSP AAGIKTVDPL PLREDSEDNI HKFAEATLPV SKIPKYPTNP PGQLPSPPHV
PSYWHPSRRI QGSLRDPEFQ HNVGKARMNN LQLPQHEAFN DEDEDRLSEI SARSAASSLR
AFQTLARAKK RKENFWGKT*
speed 0.93 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999984031 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:68720627G>AN/A show variant in all transcripts   IGV
HGNC symbol MDM1
Ensembl transcript ID ENST00000430606
Genbank transcript ID NM_020128
UniProt peptide Q8TC05
alteration type single base exchange
alteration region CDS
DNA changes c.308C>T
cDNA.444C>T
g.5535C>T
AA changes T103I Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS
103
frameshift no
known variant Reference ID: rs962976
databasehomozygous (A/A)heterozygousallele carriers
1000G118810052193
ExAC29833-268992934
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0110.018
0.0150.012
(flanking)1.8190.014
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased5538wt: 0.9756 / mu: 0.9808 (marginal change - not scored)wt: TACTCAAGAAAGAGT
mu: TATTCAAGAAAGAGT
 CTCA|agaa
distance from splice site 175
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      103PKSQEAEQKDVTQERVHSLEASRV
mutated  not conserved    103PKSQEAEQKDVIQERVHSLEASR
Ptroglodytes  all identical  ENSPTRG00000005196  103PKSQEAEQKDVTQERVHSLEASR
Mmulatta  all identical  ENSMMUG00000018725  103PKSQEAEQKDVTQERVDSLEASR
Fcatus  no alignment  ENSFCAG00000018582  n/a
Mmusculus  not conserved  ENSMUSG00000020212  103PKPQEAEQGEDANQEAVLSLEASR
Ggallus  not conserved  ENSGALG00000009905  100AESLAEHSNDVNQENTETPEGPR
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000045675  100LRATSAER------QVTPLAPRD
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000001452  101QLRLDLDRESLAEEKLHTPDAPR
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 669 / 669
position (AA) of stopcodon in wt / mu AA sequence 223 / 223
position of stopcodon in wt / mu cDNA 805 / 805
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now
N/A
position of start ATG in wt / mu cDNA 137 / 137
chromosome 12
strand -1
last intron/exon boundary 270
theoretical NMD boundary in CDS 83
length of CDS 669
coding sequence (CDS) position 308
cDNA position
(for ins/del: last normal base / first normal base)
444
gDNA position
(for ins/del: last normal base / first normal base)
5535
chromosomal position
(for ins/del: last normal base / first normal base)
68720627
original gDNA sequence snippet AGCAGAACAAAAGGATGTTACTCAAGAAAGAGTTCACTCAC
altered gDNA sequence snippet AGCAGAACAAAAGGATGTTATTCAAGAAAGAGTTCACTCAC
original cDNA sequence snippet AGCAGAACAAAAGGATGTTACTCAAGAAAGAGTTCACTCAC
altered cDNA sequence snippet AGCAGAACAAAAGGATGTTATTCAAGAAAGAGTTCACTCAC
wildtype AA sequence MPVRFKGLSE YQRNFLWKKS YLSESCNSSV GRKYPWAGLR SDQLGITKEP SFISKRRVPY
HDPQISKSLE WNGAISESNV VASPEPEAPE TPKSQEAEQK DVTQERVHSL EASRVPKRTR
SHSADSRAEG ASDVENNEGV TNHTPVNENV ELEHSTKVLS ENVDNGVGIF TAFLFKSIEF
FIGFIVISVI LHFVFQNFPL LFSCLMSIRI VDNRLLTLVI VN*
mutated AA sequence MPVRFKGLSE YQRNFLWKKS YLSESCNSSV GRKYPWAGLR SDQLGITKEP SFISKRRVPY
HDPQISKSLE WNGAISESNV VASPEPEAPE TPKSQEAEQK DVIQERVHSL EASRVPKRTR
SHSADSRAEG ASDVENNEGV TNHTPVNENV ELEHSTKVLS ENVDNGVGIF TAFLFKSIEF
FIGFIVISVI LHFVFQNFPL LFSCLMSIRI VDNRLLTLVI VN*
speed 0.85 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999971027 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:68720627G>AN/A show variant in all transcripts   IGV
HGNC symbol MDM1
Ensembl transcript ID ENST00000303145
Genbank transcript ID NM_017440
UniProt peptide Q8TC05
alteration type single base exchange
alteration region CDS
DNA changes c.308C>T
cDNA.395C>T
g.5535C>T
AA changes T103I Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS
103
frameshift no
known variant Reference ID: rs962976
databasehomozygous (A/A)heterozygousallele carriers
1000G118810052193
ExAC29833-268992934
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0110.018
0.0150.012
(flanking)1.8190.014
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased5538wt: 0.9756 / mu: 0.9808 (marginal change - not scored)wt: TACTCAAGAAAGAGT
mu: TATTCAAGAAAGAGT
 CTCA|agaa
distance from splice site 175
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      103PKSQEAEQKDVTQERVHSLEASRV
mutated  not conserved    103PKSQEAEQKDVIQERVHSLEASR
Ptroglodytes  all identical  ENSPTRG00000005196  103PKSQEAEQKDVTQERVHSLEASR
Mmulatta  all identical  ENSMMUG00000018725  103PKSQEAEQKDVTQERVDSLEASR
Fcatus  no alignment  ENSFCAG00000018582  n/a
Mmusculus  not conserved  ENSMUSG00000020212  103PKPQEAEQGEDANQEAVLSLEASR
Ggallus  not conserved  ENSGALG00000009905  100AESLAEHSNDVNQENTETPEGPR
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000045675  100--------RDHSQQQLEKSRSPA
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000001452  101LRL-DLDRESLAEEKLHTPDAPR
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2145 / 2145
position (AA) of stopcodon in wt / mu AA sequence 715 / 715
position of stopcodon in wt / mu cDNA 2232 / 2232
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now
N/A
position of start ATG in wt / mu cDNA 88 / 88
chromosome 12
strand -1
last intron/exon boundary 2120
theoretical NMD boundary in CDS 1982
length of CDS 2145
coding sequence (CDS) position 308
cDNA position
(for ins/del: last normal base / first normal base)
395
gDNA position
(for ins/del: last normal base / first normal base)
5535
chromosomal position
(for ins/del: last normal base / first normal base)
68720627
original gDNA sequence snippet AGCAGAACAAAAGGATGTTACTCAAGAAAGAGTTCACTCAC
altered gDNA sequence snippet AGCAGAACAAAAGGATGTTATTCAAGAAAGAGTTCACTCAC
original cDNA sequence snippet AGCAGAACAAAAGGATGTTACTCAAGAAAGAGTTCACTCAC
altered cDNA sequence snippet AGCAGAACAAAAGGATGTTATTCAAGAAAGAGTTCACTCAC
wildtype AA sequence MPVRFKGLSE YQRNFLWKKS YLSESCNSSV GRKYPWAGLR SDQLGITKEP SFISKRRVPY
HDPQISKSLE WNGAISESNV VASPEPEAPE TPKSQEAEQK DVTQERVHSL EASRVPKRTR
SHSADSRAEG ASDVENNEGV TNHTPVNENV ELEHSTKVLS ENVDNGLDRL LRKKAGLTVV
PSYNALRNSE YQRQFVWKTS KETAPAFAAN QVFHNKSQFV PPFKGNSVIH ETEYKRNFKG
LSPVKEPKLR NDLRENRNLE TVSPERKSNK IDDRLKLEAE MELKDLHQPK RKLTPWKHQR
LGKVNSEYRA KFLSPAQYLY KAGAWTHVKG NMPNQVKELR EKAEFYRKRV QGTHFSRDHL
NQILSDSNCC WDVSSTTSSE GTVSSNIRAL DLAGDPTSHK TLQKCPSTEP EEKGNIVEEQ
PQKNTTEKLG VSAPTIPVRR RLAWDTENTS EDVQKQPGEK EEEDDNEEEG DRKTGKQAFM
GEQEKLDVRE KSKADKMKEG SDSSVSSEKG GRLPTPKLRE LGGIQRTHHD LTTPAVGGAV
LVSPSKMKPP APEQRKRMTS QDCLETSKND FTKKESRAVS LLTSPAAGIK TVDPLPLRED
SEDNIHKFAE ATLPVSKIPK YPTNPPGQLP SPPHVPSYWH PSRRIQGSLR DPEFQHNVGK
ARMNNLQLPQ HEAFNDEDED RLSEISARSA ASSLRAFQTL ARAKKRKENF WGKT*
mutated AA sequence MPVRFKGLSE YQRNFLWKKS YLSESCNSSV GRKYPWAGLR SDQLGITKEP SFISKRRVPY
HDPQISKSLE WNGAISESNV VASPEPEAPE TPKSQEAEQK DVIQERVHSL EASRVPKRTR
SHSADSRAEG ASDVENNEGV TNHTPVNENV ELEHSTKVLS ENVDNGLDRL LRKKAGLTVV
PSYNALRNSE YQRQFVWKTS KETAPAFAAN QVFHNKSQFV PPFKGNSVIH ETEYKRNFKG
LSPVKEPKLR NDLRENRNLE TVSPERKSNK IDDRLKLEAE MELKDLHQPK RKLTPWKHQR
LGKVNSEYRA KFLSPAQYLY KAGAWTHVKG NMPNQVKELR EKAEFYRKRV QGTHFSRDHL
NQILSDSNCC WDVSSTTSSE GTVSSNIRAL DLAGDPTSHK TLQKCPSTEP EEKGNIVEEQ
PQKNTTEKLG VSAPTIPVRR RLAWDTENTS EDVQKQPGEK EEEDDNEEEG DRKTGKQAFM
GEQEKLDVRE KSKADKMKEG SDSSVSSEKG GRLPTPKLRE LGGIQRTHHD LTTPAVGGAV
LVSPSKMKPP APEQRKRMTS QDCLETSKND FTKKESRAVS LLTSPAAGIK TVDPLPLRED
SEDNIHKFAE ATLPVSKIPK YPTNPPGQLP SPPHVPSYWH PSRRIQGSLR DPEFQHNVGK
ARMNNLQLPQ HEAFNDEDED RLSEISARSA ASSLRAFQTL ARAKKRKENF WGKT*
speed 0.16 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.99999713900237 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:68720627G>AN/A show variant in all transcripts   IGV
HGNC symbol MDM1
Ensembl transcript ID ENST00000393543
Genbank transcript ID NM_001205029
UniProt peptide N/A
alteration type single base exchange
alteration region 3'UTR
DNA changes cDNA.876C>T
g.5535C>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs962976
databasehomozygous (A/A)heterozygousallele carriers
1000G118810052193
ExAC29833-268992934
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0110.018
0.0150.012
(flanking)1.8190.014
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased5538wt: 0.9756 / mu: 0.9808 (marginal change - not scored)wt: TACTCAAGAAAGAGT
mu: TATTCAAGAAAGAGT
 CTCA|agaa
distance from splice site 664
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
N/A
protein features N/A
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
poly(A) signal signal is predicted to be ok
conservation
nucleotide level for all changes - no scoring up to now
N/A
position of start ATG in wt / mu cDNA 80 / 80
chromosome 12
strand -1
last intron/exon boundary 213
theoretical NMD boundary in CDS 83
length of CDS 210
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)
876
gDNA position
(for ins/del: last normal base / first normal base)
5535
chromosomal position
(for ins/del: last normal base / first normal base)
68720627
original gDNA sequence snippet AGCAGAACAAAAGGATGTTACTCAAGAAAGAGTTCACTCAC
altered gDNA sequence snippet AGCAGAACAAAAGGATGTTATTCAAGAAAGAGTTCACTCAC
original cDNA sequence snippet AGCAGAACAAAAGGATGTTACTCAAGAAAGAGTTCACTCAC
altered cDNA sequence snippet AGCAGAACAAAAGGATGTTATTCAAGAAAGAGTTCACTCAC
wildtype AA sequence MPVRFKGLSE YQRNFLWKKS YLSESCNSSV GRKYPWAGLR SDQLGNQGRC RTKIQHSDIS
SLLILVCST*
mutated AA sequence N/A
speed 0.38 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.99999713900237 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:68720627G>AN/A show variant in all transcripts   IGV
HGNC symbol MDM1
Ensembl transcript ID ENST00000540418
Genbank transcript ID N/A
UniProt peptide N/A
alteration type single base exchange
alteration region intron
DNA changes g.5535C>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs962976
databasehomozygous (A/A)heterozygousallele carriers
1000G118810052193
ExAC29833-268992934
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0110.018
0.0150.012
(flanking)1.8190.014
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased5538wt: 0.9756 / mu: 0.9808 (marginal change - not scored)wt: TACTCAAGAAAGAGT
mu: TATTCAAGAAAGAGT
 CTCA|agaa
distance from splice site 1272
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
N/A
protein features N/A
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now
N/A
position of start ATG in wt / mu cDNA 517 / 517
chromosome 12
strand -1
last intron/exon boundary 1709
theoretical NMD boundary in CDS 1142
length of CDS 1305
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)
N/A
gDNA position
(for ins/del: last normal base / first normal base)
5535
chromosomal position
(for ins/del: last normal base / first normal base)
68720627
original gDNA sequence snippet AGCAGAACAAAAGGATGTTACTCAAGAAAGAGTTCACTCAC
altered gDNA sequence snippet AGCAGAACAAAAGGATGTTATTCAAGAAAGAGTTCACTCAC
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MELKDLHQPK RKLTPWKHQR LGKVNSEYRA KFLSPAQYLY KAGAWTHVKG NMPNQVKELR
EKAEFYRKRV QGTHFSRDHL NQILSDSNCC WDVSSTTSSE GTVSSNIRAL DLAGDPTSHK
TLQKCPSTEP EEKGNIVEEQ PQKNTTEKLG VSAPTIPVRR RLAWDTENTS EDVQKQPGEK
EEEDDNEEEG DRKTGKQAFM GEQEKLDVRE KSKADKMKEG SDSSVSSEKG GRLPTPKLRE
LGGIQRTHHD LTTPAVGGAV LVSPSKMKPP APEQRKRMTS QDCLETSKND FTKKESRAVS
LLTSPAAGIK TVDPLPLRED SEDNIHKFAE ATLPVSKIPK YPTNPPGQLP SPPHVPSYWH
PSRRIQGSLR DPEFQHNVGK ARMNNLQLPQ HEAFNDEDED RLSEISARSA ASSLRAFQTL
ARAKKRKENF WGKT*
mutated AA sequence N/A
speed 0.76 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
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Problems