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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000356840
Querying Taster for transcript #2: ENST00000349606
MT speed 0 s - this script 3.249846 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
MYLIPpolymorphism_automatic0simple_aaeaffectedN342Ssingle base exchangers9370867show file
MYLIPpolymorphism_automatic0simple_aaeaffectedN161Ssingle base exchangers9370867show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 1 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM116474)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:16145325A>GN/A show variant in all transcripts   IGV
HGNC symbol MYLIP
Ensembl transcript ID ENST00000356840
Genbank transcript ID NM_013262
UniProt peptide Q8WY64
alteration type single base exchange
alteration region CDS
DNA changes c.1025A>G
cDNA.1223A>G
g.15970A>G
AA changes N342S Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 342
frameshift no
known variant Reference ID: rs9370867
databasehomozygous (G/G)heterozygousallele carriers
1000G15836902273
ExAC24045-153238722

known disease mutation at this position, please check HGMD for details (HGMD ID CM116474)
regulatory features PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0870
1.5320.002
(flanking)-0.6050
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased15961wt: 0.74 / mu: 0.87wt: CCTCGTTTCAAGAAA
mu: CCTCGTTTCAAGAAG		 TCGT|ttca
Acc gained159660.38mu: GCGTTGTGGACCTCGTTTCAAGAAGCAACCAGAGCCCTTCA tcaa|GAAG
Donor gained159690.91mu: CAAGAAGCAACCAGA AGAA|gcaa
Donor gained159640.63mu: CGTTTCAAGAAGCAA TTTC|aaga
distance from splice site 198
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      342YNAGVVDLVSRNNQSPSHSPLKSS
mutated  all conserved    342YNAGVVDLVSRSNQSPSHSPLKS
Ptroglodytes  all conserved  ENSPTRG00000023743  342YNAGVVDLVSRSNQSPSHSPLKS
Mmulatta  all conserved  ENSMMUG00000015474  342YNAGVVDLVSRSNQSPSHSPLKS
Fcatus  all conserved  ENSFCAG00000010500  313SDPSPPNSPLKS
Mmusculus  all conserved  ENSMUSG00000038175  342YNAGVVDLVSRSDQSPPSSPLKS
Ggallus  all conserved  ENSGALG00000012704  314YNAGIVDLVSRSDQTPPSSPLKS
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000008859  342YNAGIVDMMSRPGERTPSNRSPSRE
Dmelanogaster  not conserved  FBgn0260866  481HERG-GDLVAEGAEGCSAVAGGLGASAVGEPGVSPWAM
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000015431  342YNAGIVDLVSGSGHSEPSSPLKT
protein features
start (aa)end (aa)featuredetails 
360360METALIron.might get lost (downstream of altered splice site)
363363METALIron.might get lost (downstream of altered splice site)
368368METALIron.might get lost (downstream of altered splice site)
374384HELIXmight get lost (downstream of altered splice site)
387387MUTAGENC->A: Abolishes autoubiquitination.might get lost (downstream of altered splice site)
387387MUTAGENC->A: Abolishes ubiquitin ligase activity.might get lost (downstream of altered splice site)
387422ZN_FINGRING-type.might get lost (downstream of altered splice site)
388390TURNmight get lost (downstream of altered splice site)
389389MUTAGENV->R: Inhibits LDLR degradation.might get lost (downstream of altered splice site)
391394STRANDmight get lost (downstream of altered splice site)
397400STRANDmight get lost (downstream of altered splice site)
409412HELIXmight get lost (downstream of altered splice site)
415415MUTAGENL->E: Inhibits LDLR degradation.might get lost (downstream of altered splice site)
419421TURNmight get lost (downstream of altered splice site)
427430STRANDmight get lost (downstream of altered splice site)
431433REGIONCritical for homodimerization.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1338 / 1338
position (AA) of stopcodon in wt / mu AA sequence 446 / 446
position of stopcodon in wt / mu cDNA 1536 / 1536
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 199 / 199
chromosome 6
strand 1
last intron/exon boundary 1447
theoretical NMD boundary in CDS 1198
length of CDS 1338
coding sequence (CDS) position 1025
cDNA position
(for ins/del: last normal base / first normal base)		 1223
gDNA position
(for ins/del: last normal base / first normal base)		 15970
chromosomal position
(for ins/del: last normal base / first normal base)		 16145325
original gDNA sequence snippet TGTGGACCTCGTTTCAAGAAACAACCAGAGCCCTTCACACT
altered gDNA sequence snippet TGTGGACCTCGTTTCAAGAAGCAACCAGAGCCCTTCACACT
original cDNA sequence snippet TGTGGACCTCGTTTCAAGAAACAACCAGAGCCCTTCACACT
altered cDNA sequence snippet TGTGGACCTCGTTTCAAGAAGCAACCAGAGCCCTTCACACT
wildtype AA sequence MLCYVTRPDA VLMEVEVEAK ANGEDCLNQV CRRLGIIEVD YFGLQFTGSK GESLWLNLRN
RISQQMDGLA PYRLKLRVKF FVEPHLILQE QTRHIFFLHI KEALLAGHLL CSPEQAVELS
ALLAQTKFGD YNQNTAKYNY EELCAKELSS ATLNSIVAKH KELEGTSQAS AEYQVLQIVS
AMENYGIEWH SVRDSEGQKL LIGVGPEGIS ICKDDFSPIN RIAYPVVQMA TQSGKNVYLT
VTKESGNSIV LLFKMISTRA ASGLYRAITE THAFYRCDTV TSAVMMQYSR DLKGHLASLF
LNENINLGKK YVFDIKRTSK EVYDHARRAL YNAGVVDLVS RNNQSPSHSP LKSSESSMNC
SSCEGLSCQQ TRVLQEKLRK LKEAMLCMVC CEEEINSTFC PCGHTVCCES CAAQLQSCPV
CRSRVEHVQH VYLPTHTSLL NLTVI*
mutated AA sequence MLCYVTRPDA VLMEVEVEAK ANGEDCLNQV CRRLGIIEVD YFGLQFTGSK GESLWLNLRN
RISQQMDGLA PYRLKLRVKF FVEPHLILQE QTRHIFFLHI KEALLAGHLL CSPEQAVELS
ALLAQTKFGD YNQNTAKYNY EELCAKELSS ATLNSIVAKH KELEGTSQAS AEYQVLQIVS
AMENYGIEWH SVRDSEGQKL LIGVGPEGIS ICKDDFSPIN RIAYPVVQMA TQSGKNVYLT
VTKESGNSIV LLFKMISTRA ASGLYRAITE THAFYRCDTV TSAVMMQYSR DLKGHLASLF
LNENINLGKK YVFDIKRTSK EVYDHARRAL YNAGVVDLVS RSNQSPSHSP LKSSESSMNC
SSCEGLSCQQ TRVLQEKLRK LKEAMLCMVC CEEEINSTFC PCGHTVCCES CAAQLQSCPV
CRSRVEHVQH VYLPTHTSLL NLTVI*
speed 0.88 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: 1 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM116474)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:16145325A>GN/A show variant in all transcripts   IGV
HGNC symbol MYLIP
Ensembl transcript ID ENST00000349606
Genbank transcript ID N/A
UniProt peptide Q8WY64
alteration type single base exchange
alteration region CDS
DNA changes c.482A>G
cDNA.986A>G
g.15970A>G
AA changes N161S Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 161
frameshift no
known variant Reference ID: rs9370867
databasehomozygous (G/G)heterozygousallele carriers
1000G15836902273
ExAC24045-153238722

known disease mutation at this position, please check HGMD for details (HGMD ID CM116474)
regulatory features PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0870
1.5320.002
(flanking)-0.6050
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased15961wt: 0.74 / mu: 0.87wt: CCTCGTTTCAAGAAA
mu: CCTCGTTTCAAGAAG		 TCGT|ttca
Acc gained159660.38mu: GCGTTGTGGACCTCGTTTCAAGAAGCAACCAGAGCCCTTCA tcaa|GAAG
Donor gained159690.91mu: CAAGAAGCAACCAGA AGAA|gcaa
Donor gained159640.63mu: CGTTTCAAGAAGCAA TTTC|aaga
distance from splice site 198
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      161YNAGVVDLVSRNNQSPSHSPLKSS
mutated  all conserved    161YNAGVVDLVSRSNQSPSHSPLKS
Ptroglodytes  all conserved  ENSPTRG00000023743  342YNAGVVDLVSRSNQSPSHSPLKS
Mmulatta  all conserved  ENSMMUG00000015474  342YNAGVVDLVSRSNQSPSHSPLKS
Fcatus  all conserved  ENSFCAG00000010500  313SDPSPPNSPLKS
Mmusculus  all conserved  ENSMUSG00000038175  342YNAGVVDLVSRSDQSPPSSPLKS
Ggallus  all conserved  ENSGALG00000012704  314YNAGIVDLVSRSDQTPPSSPLKS
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000008859  342YNAGIVDMMSRPGERTPSNRSPSRE
Dmelanogaster  not conserved  FBgn0260866  482HERG-GDLVAEGAEGCSAVAGGLGASAVG
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000015431  342YNAGIVDLVSGSGHSEPSSPLKT
protein features
start (aa)end (aa)featuredetails 
1279DOMAINFERM.lost
199199CONFLICTK -> R (in Ref. 1; AAF18974).might get lost (downstream of altered splice site)
262263CONFLICTSG -> TR (in Ref. 3; AAF87323).might get lost (downstream of altered splice site)
265265MUTAGENY->A: Unable to clear LDLR from the plasma membrane.might get lost (downstream of altered splice site)
269269MUTAGENT->R: Unable to clear LDLR from the plasma membrane.might get lost (downstream of altered splice site)
309310CONFLICTKK -> PRN (in Ref. 3; AAF87323).might get lost (downstream of altered splice site)
360360METALIron.might get lost (downstream of altered splice site)
363363METALIron.might get lost (downstream of altered splice site)
368368METALIron.might get lost (downstream of altered splice site)
374384HELIXmight get lost (downstream of altered splice site)
387387MUTAGENC->A: Abolishes ubiquitin ligase activity.might get lost (downstream of altered splice site)
387387MUTAGENC->A: Abolishes autoubiquitination.might get lost (downstream of altered splice site)
387422ZN_FINGRING-type.might get lost (downstream of altered splice site)
388390TURNmight get lost (downstream of altered splice site)
389389MUTAGENV->R: Inhibits LDLR degradation.might get lost (downstream of altered splice site)
391394STRANDmight get lost (downstream of altered splice site)
397400STRANDmight get lost (downstream of altered splice site)
409412HELIXmight get lost (downstream of altered splice site)
415415MUTAGENL->E: Inhibits LDLR degradation.might get lost (downstream of altered splice site)
419421TURNmight get lost (downstream of altered splice site)
427430STRANDmight get lost (downstream of altered splice site)
431433REGIONCritical for homodimerization.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 795 / 795
position (AA) of stopcodon in wt / mu AA sequence 265 / 265
position of stopcodon in wt / mu cDNA 1299 / 1299
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 505 / 505
chromosome 6
strand 1
last intron/exon boundary 1210
theoretical NMD boundary in CDS 655
length of CDS 795
coding sequence (CDS) position 482
cDNA position
(for ins/del: last normal base / first normal base)		 986
gDNA position
(for ins/del: last normal base / first normal base)		 15970
chromosomal position
(for ins/del: last normal base / first normal base)		 16145325
original gDNA sequence snippet TGTGGACCTCGTTTCAAGAAACAACCAGAGCCCTTCACACT
altered gDNA sequence snippet TGTGGACCTCGTTTCAAGAAGCAACCAGAGCCCTTCACACT
original cDNA sequence snippet TGTGGACCTCGTTTCAAGAAACAACCAGAGCCCTTCACACT
altered cDNA sequence snippet TGTGGACCTCGTTTCAAGAAGCAACCAGAGCCCTTCACACT
wildtype AA sequence MENYGIEWHS VRDSEGQKLL IGVGPEGISI CKDDFSPINR IAYPVVQMAT QSGKNVYLTV
TKESGNSIVL LFKMISTRAA SGLYRAITET HAFYRCDTVT SAVMMQYSRD LKGHLASLFL
NENINLGKKY VFDIKRTSKE VYDHARRALY NAGVVDLVSR NNQSPSHSPL KSSESSMNCS
SCEGLSCQQT RVLQEKLRKL KEAMLCMVCC EEEINSTFCP CGHTVCCESC AAQLQSCPVC
RSRVEHVQHV YLPTHTSLLN LTVI*
mutated AA sequence MENYGIEWHS VRDSEGQKLL IGVGPEGISI CKDDFSPINR IAYPVVQMAT QSGKNVYLTV
TKESGNSIVL LFKMISTRAA SGLYRAITET HAFYRCDTVT SAVMMQYSRD LKGHLASLFL
NENINLGKKY VFDIKRTSKE VYDHARRALY NAGVVDLVSR SNQSPSHSPL KSSESSMNCS
SCEGLSCQQT RVLQEKLRKL KEAMLCMVCC EEEINSTFCP CGHTVCCESC AAQLQSCPVC
RSRVEHVQHV YLPTHTSLLN LTVI*
speed 0.43 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

Problems