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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 1 transcript(s)...
Querying Taster for transcript #1: ENST00000378026
MT speed 1.41 s - this script 4.955174 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CKAP4polymorphism_automatic4.55718649483572e-08simple_aaeA348Tsingle base exchangers3088113show file

Taster files

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documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999954428135 (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
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:106633569C>TN/A show variant in all transcripts   IGV
HGNC symbol CKAP4
Ensembl transcript ID ENST00000378026
Genbank transcript ID NM_006825
UniProt peptide Q07065
alteration type single base exchange
alteration region CDS
DNA changes c.1042G>A
cDNA.1179G>A
g.64489G>A
AA changes A348T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
348
frameshift no
known variant Reference ID: rs3088113
databasehomozygous (T/T)heterozygousallele carriers
1000G191716907
ExAC25211521417735
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.8180.105
1.3680.094
(flanking)-0.4340.001
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 increased64481wt: 0.2493 / mu: 0.2541 (marginal change - not scored)wt: CACGGAGCGGCTCGC
mu: CACGGAGCGGCTCAC
 CGGA|gcgg
distance from splice site 559
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      348AFKEAADTERLALQALTEKLLRSE
mutated  not conserved    348AFKEAADTERLTLQALTEKLLRS
Ptroglodytes  all identical  ENSPTRG00000005387  268AFKEAADTERLALQALTEKLLRS
Mmulatta  all identical  ENSMMUG00000006438  244ERLALQALTEKLLRS
Fcatus  not conserved  ENSFCAG00000012084  187ANSEHLTLQALTEKVLQS
Mmusculus  all identical  ENSMUSG00000046841  328AFKQAADSERLALQALTEKLLRS
Ggallus  all conserved  ENSGALG00000012659  294KFKEAADTEHLSLKALQEKVLRT
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000032405  280AMR--------TLIQSTVGSLRK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000010716  288DLKSNVDAQLAAVEELKAKLSD
protein features
start (aa)end (aa)featuredetails 
128602TOPO_DOMExtracellular (Potential).lost
256460COILEDPotential.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1809 / 1809
position (AA) of stopcodon in wt / mu AA sequence 603 / 603
position of stopcodon in wt / mu cDNA 1946 / 1946
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 138 / 138
chromosome 12
strand -1
last intron/exon boundary 621
theoretical NMD boundary in CDS 433
length of CDS 1809
coding sequence (CDS) position 1042
cDNA position
(for ins/del: last normal base / first normal base)
1179
gDNA position
(for ins/del: last normal base / first normal base)
64489
chromosomal position
(for ins/del: last normal base / first normal base)
106633569
original gDNA sequence snippet CGGCCGACACGGAGCGGCTCGCCCTGCAGGCCCTCACGGAG
altered gDNA sequence snippet CGGCCGACACGGAGCGGCTCACCCTGCAGGCCCTCACGGAG
original cDNA sequence snippet CGGCCGACACGGAGCGGCTCGCCCTGCAGGCCCTCACGGAG
altered cDNA sequence snippet CGGCCGACACGGAGCGGCTCACCCTGCAGGCCCTCACGGAG
wildtype AA sequence MPSAKQRGSK GGHGAASPSE KGAHPSGGAD DVAKKPPPAP QQPPPPPAPH PQQHPQQHPQ
NQAHGKGGHR GGGGGGGKSS SSSSASAAAA AAAASSSASC SRRLGRALNF LFYLALVAAA
AFSGWCVHHV LEEVQQVRRS HQDFSRQREE LGQGLQGVEQ KVQSLQATFG TFESILRSSQ
HKQDLTEKAV KQGESEVSRI SEVLQKLQNE ILKDLSDGIH VVKDARERDF TSLENTVEER
LTELTKSIND NIAIFTEVQK RSQKEINDMK AKVASLEESE GNKQDLKALK EAVKEIQTSA
KSREWDMEAL RSTLQTMESD IYTEVRELVS LKQEQQAFKE AADTERLALQ ALTEKLLRSE
ESVSRLPEEI RRLEEELRQL KSDSHGPKED GGFRHSEAFE ALQQKSQGLD SRLQHVEDGV
LSMQVASARQ TESLESLLSK SQEHEQRLAA LQGRLEGLGS SEADQDGLAS TVRSLGETQL
VLYGDVEELK RSVGELPSTV ESLQKVQEQV HTLLSQDQAQ AARLPPQDFL DRLSSLDNLK
ASVSQVEADL KMLRTAVDSL VAYSVKIETN ENNLESAKGL LDDLRNDLDR LFVKVEKIHE
KV*
mutated AA sequence MPSAKQRGSK GGHGAASPSE KGAHPSGGAD DVAKKPPPAP QQPPPPPAPH PQQHPQQHPQ
NQAHGKGGHR GGGGGGGKSS SSSSASAAAA AAAASSSASC SRRLGRALNF LFYLALVAAA
AFSGWCVHHV LEEVQQVRRS HQDFSRQREE LGQGLQGVEQ KVQSLQATFG TFESILRSSQ
HKQDLTEKAV KQGESEVSRI SEVLQKLQNE ILKDLSDGIH VVKDARERDF TSLENTVEER
LTELTKSIND NIAIFTEVQK RSQKEINDMK AKVASLEESE GNKQDLKALK EAVKEIQTSA
KSREWDMEAL RSTLQTMESD IYTEVRELVS LKQEQQAFKE AADTERLTLQ ALTEKLLRSE
ESVSRLPEEI RRLEEELRQL KSDSHGPKED GGFRHSEAFE ALQQKSQGLD SRLQHVEDGV
LSMQVASARQ TESLESLLSK SQEHEQRLAA LQGRLEGLGS SEADQDGLAS TVRSLGETQL
VLYGDVEELK RSVGELPSTV ESLQKVQEQV HTLLSQDQAQ AARLPPQDFL DRLSSLDNLK
ASVSQVEADL KMLRTAVDSL VAYSVKIETN ENNLESAKGL LDDLRNDLDR LFVKVEKIHE
KV*
speed 1.41 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