Yum, tasty mutations...

MutationTaster - study a chromosomal position

MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000394427
Querying Taster for transcript #2: ENST00000334383
MT speed 2.34 s - this script 7.09389 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
QRFPRpolymorphism_automatic0.978497849106061simple_aaeaffectedL344Ssingle base exchangers2302310show file
QRFPRpolymorphism_automatic1without_aaeaffectedsingle base exchangers2302310show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.0215021508939395 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:122250734A>GN/A show variant in all transcripts   IGV
HGNC symbol QRFPR
Ensembl transcript ID ENST00000394427
Genbank transcript ID NM_198179
UniProt peptide Q96P65
alteration type single base exchange
alteration region CDS
DNA changes c.1031T>C
cDNA.1443T>C
g.51481T>C
AA changes L344S Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS
344
frameshift no
known variant Reference ID: rs2302310
databasehomozygous (G/G)heterozygousallele carriers
1000G3399271266
ExAC49902008925079
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1630.997
4.4811
(flanking)0.0480.976
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased51476wt: 0.62 / mu: 0.88wt: AAAAATGTTTTGTCT
mu: AAAAATGTTTCGTCT
 AAAT|gttt
distance from splice site 136
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      344AFMNENFKKNVLSAVCYCIVNKTF
mutated  not conserved    344AFMNENFKKNVSSAVCYCIVNKT
Ptroglodytes  all identical  ENSPTRG00000016406  344AFMNENFKKNVLSAVCYCIVKKT
Mmulatta  all identical  ENSMMUG00000007974  343AFMNENFKKNVLSAVCYCIVNKT
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000029917  343ALMNENFKKNFVSAVCYCIVKET
Ggallus  all identical  ENSGALG00000011890  298AFMNENFKKNFLSA
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  not conserved  FBgn0035610  330KFKREFNKRFAACFC
Celegans  no alignment  AC7.1  n/a
Xtropicalis  all identical  ENSXETG00000002104  344AFMNENFKKNFLSALCFCFLRDP
protein features
start (aa)end (aa)featuredetails 
333431TOPO_DOMCytoplasmic (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1296 / 1296
position (AA) of stopcodon in wt / mu AA sequence 432 / 432
position of stopcodon in wt / mu cDNA 1708 / 1708
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 413 / 413
chromosome 4
strand -1
last intron/exon boundary 1308
theoretical NMD boundary in CDS 845
length of CDS 1296
coding sequence (CDS) position 1031
cDNA position
(for ins/del: last normal base / first normal base)
1443
gDNA position
(for ins/del: last normal base / first normal base)
51481
chromosomal position
(for ins/del: last normal base / first normal base)
122250734
original gDNA sequence snippet AAACTTCAAAAAAAATGTTTTGTCTGCAGTTTGTTATTGCA
altered gDNA sequence snippet AAACTTCAAAAAAAATGTTTCGTCTGCAGTTTGTTATTGCA
original cDNA sequence snippet AAACTTCAAAAAAAATGTTTTGTCTGCAGTTTGTTATTGCA
altered cDNA sequence snippet AAACTTCAAAAAAAATGTTTCGTCTGCAGTTTGTTATTGCA
wildtype AA sequence MQALNITPEQ FSRLLRDHNL TREQFIALYR LRPLVYTPEL PGRAKLALVL TGVLIFALAL
FGNALVFYVV TRSKAMRTVT NIFICSLALS DLLITFFCIP VTMLQNISDN WLGGAFICKM
VPFVQSTAVV TEILTMTCIA VERHQGLVHP FKMKWQYTNR RAFTMLGVVW LVAVIVGSPM
WHVQQLEIKY DFLYEKEHIC CLEEWTSPVH QKIYTTFILV ILFLLPLMVM LILYSKIGYE
LWIKKRVGDG SVLRTIHGKE MSKIARKKKR AVIMMVTVVA LFAVCWAPFH VVHMMIEYSN
FEKEYDDVTI KMIFAIVQII GFSNSICNPI VYAFMNENFK KNVLSAVCYC IVNKTFSPAQ
RHGNSGITMM RKKAKFSLRE NPVEETKGEA FSDGNIEVKL CEQTEEKKKL KRHLALFRSE
LAENSPLDSG H*
mutated AA sequence MQALNITPEQ FSRLLRDHNL TREQFIALYR LRPLVYTPEL PGRAKLALVL TGVLIFALAL
FGNALVFYVV TRSKAMRTVT NIFICSLALS DLLITFFCIP VTMLQNISDN WLGGAFICKM
VPFVQSTAVV TEILTMTCIA VERHQGLVHP FKMKWQYTNR RAFTMLGVVW LVAVIVGSPM
WHVQQLEIKY DFLYEKEHIC CLEEWTSPVH QKIYTTFILV ILFLLPLMVM LILYSKIGYE
LWIKKRVGDG SVLRTIHGKE MSKIARKKKR AVIMMVTVVA LFAVCWAPFH VVHMMIEYSN
FEKEYDDVTI KMIFAIVQII GFSNSICNPI VYAFMNENFK KNVSSAVCYC IVNKTFSPAQ
RHGNSGITMM RKKAKFSLRE NPVEETKGEA FSDGNIEVKL CEQTEEKKKL KRHLALFRSE
LAENSPLDSG H*
speed 1.22 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: 1.30681713975326e-37 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:122250734A>GN/A show variant in all transcripts   IGV
HGNC symbol QRFPR
Ensembl transcript ID ENST00000334383
Genbank transcript ID N/A
UniProt peptide N/A
alteration type single base exchange
alteration region 3'UTR
DNA changes cDNA.950T>C
g.51481T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs2302310
databasehomozygous (G/G)heterozygousallele carriers
1000G3399271266
ExAC49902008925079
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1630.997
4.4811
(flanking)0.0480.976
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change occurs after stopcodon (at aa 305)
effectgDNA positionscoredetection sequence  exon-intron border
Donor increased51476wt: 0.62 / mu: 0.88wt: AAAAATGTTTTGTCT
mu: AAAAATGTTTCGTCT
 AAAT|gttt
distance from splice site 136
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 33 / 33
chromosome 4
strand -1
last intron/exon boundary 815
theoretical NMD boundary in CDS 732
length of CDS 777
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)
950
gDNA position
(for ins/del: last normal base / first normal base)
51481
chromosomal position
(for ins/del: last normal base / first normal base)
122250734
original gDNA sequence snippet AAACTTCAAAAAAAATGTTTTGTCTGCAGTTTGTTATTGCA
altered gDNA sequence snippet AAACTTCAAAAAAAATGTTTCGTCTGCAGTTTGTTATTGCA
original cDNA sequence snippet AAACTTCAAAAAAAATGTTTTGTCTGCAGTTTGTTATTGCA
altered cDNA sequence snippet AAACTTCAAAAAAAATGTTTCGTCTGCAGTTTGTTATTGCA
wildtype AA sequence MQALNITPEQ FSRLLRDHNL TREQFIALYR LRPLVYTPEL PGRAKLALVL TGVLIFALAL
FGNALVFYVV TRSKAMRTVT NIFICSLALS DLLITFFCIP VTMLQNISDN WLGGAFICKM
VPFVQSTAVV TEILTMTCIA VERHQGLVHP FKMKWQYTNR RAFTMLGVVW LVAVIVGSPM
WHVQQLEIKY DFLYEKEHIC CLEEWTSPVH QKIYTTFILV ILFLLPLMEE ETSCHYDGDS
GGSLCCVLGT IPCCPYDD*
mutated AA sequence N/A
speed 1.12 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