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: ENST00000370336
Querying Taster for transcript #2: ENST00000370318
MT speed 0 s - this script 3.38462 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
DDX43polymorphism_automatic1.87194704182048e-12simple_aaeaffectedQ629Rsingle base exchangers311685show file
CGASpolymorphism_automatic8.43084410062644e-08without_aaeaffectedsingle base exchangers311685show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999998128 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:74125888A>GN/A show variant in all transcripts   IGV
HGNC symbol DDX43
Ensembl transcript ID ENST00000370336
Genbank transcript ID NM_018665
UniProt peptide Q9NXZ2
alteration type single base exchange
alteration region CDS
DNA changes c.1886A>G
cDNA.2044A>G
g.21418A>G
AA changes Q629R Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 629
frameshift no
known variant Reference ID: rs311685
databasehomozygous (G/G)heterozygousallele carriers
1000G64611641810
ExAC16565-36316202
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.1470.021
0.0020.014
(flanking)0.0360.021
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained214120.78mu: GGCACATCAACGGAA CACA|tcaa
Donor gained214170.95mu: ATCAACGGAAAAGGG CAAC|ggaa
distance from splice site 53
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      629VSMAERFKAHQQKREMERKMERPQ
mutated  all conserved    629VSMAERFKAHQRKREMERKMERP
Ptroglodytes  all identical  ENSPTRG00000018344  629VSMAERFKAHQQKREMERKMERP
Mmulatta  all identical  ENSMMUG00000019599  629VSMAERFKAHQQKREMERKMERP
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000070291  627VLMAERYKANKLKREMEKKMGRP
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000022614  665VLMAERYEKHRREKEM
Dmelanogaster  not conserved  FBgn0037549  671HNMARRFKAMKDKR
Celegans  not conserved  Y54G11A.3  480RRDAEKYRL---KCQSGRDGPRP
Xtropicalis  not conserved  ENSXETG00000011767  647IKKDSERDLIPR
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1947 / 1947
position (AA) of stopcodon in wt / mu AA sequence 649 / 649
position of stopcodon in wt / mu cDNA 2105 / 2105
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 159 / 159
chromosome 6
strand 1
last intron/exon boundary 2131
theoretical NMD boundary in CDS 1922
length of CDS 1947
coding sequence (CDS) position 1886
cDNA position
(for ins/del: last normal base / first normal base)		 2044
gDNA position
(for ins/del: last normal base / first normal base)		 21418
chromosomal position
(for ins/del: last normal base / first normal base)		 74125888
original gDNA sequence snippet GAGGTTTAAGGCACATCAACAGAAAAGGGAAATGGAAAGAA
altered gDNA sequence snippet GAGGTTTAAGGCACATCAACGGAAAAGGGAAATGGAAAGAA
original cDNA sequence snippet GAGGTTTAAGGCACATCAACAGAAAAGGGAAATGGAAAGAA
altered cDNA sequence snippet GAGGTTTAAGGCACATCAACGGAAAAGGGAAATGGAAAGAA
wildtype AA sequence MSHHGGAPKA STWVVASRRS STVSRAPERR PAEELNRTGP EGYSVGRGGR WRGTSRPPEA
VAAGHEELPL CFALKSHFVG AVIGRGGSKI KNIQSTTNTT IQIIQEQPES LVKIFGSKAM
QTKAKAVIDN FVKKLEENYN SECGIDTAFQ PSVGKDGSTD NNVVAGDRPL IDWDQIREEG
LKWQKTKWAD LPPIKKNFYK ESTATSAMSK VEADSWRKEN FNITWDDLKD GEKRPIPNPT
CTFDDAFQCY PEVMENIKKA GFQKPTPIQS QAWPIVLQGI DLIGVAQTGT GKTLCYLMPG
FIHLVLQPSL KGQRNRPGML VLTPTRELAL QVEGECCKYS YKGLRSVCVY GGGNRDEQIE
ELKKGVDIII ATPGRLNDLQ MSNFVNLKNI TYLVLDEADK MLDMGFEPQI MKILLDVRPD
RQTVMTSATW PHSVHRLAQS YLKEPMIVYV GTLDLVAVSS VKQNIIVTTE EEKWSHMQTF
LQSMSSTDKV IVFVSRKAVA DHLSSDLILG NISVESLHGD REQRDREKAL ENFKTGKVRI
LIATDLASRG LDVHDVTHVY NFDFPRNIEE YVHRIGRTGR AGRTGVSITT LTRNDWRVAS
ELINILERAN QSIPEELVSM AERFKAHQQK REMERKMERP QGRPKKFH*
mutated AA sequence MSHHGGAPKA STWVVASRRS STVSRAPERR PAEELNRTGP EGYSVGRGGR WRGTSRPPEA
VAAGHEELPL CFALKSHFVG AVIGRGGSKI KNIQSTTNTT IQIIQEQPES LVKIFGSKAM
QTKAKAVIDN FVKKLEENYN SECGIDTAFQ PSVGKDGSTD NNVVAGDRPL IDWDQIREEG
LKWQKTKWAD LPPIKKNFYK ESTATSAMSK VEADSWRKEN FNITWDDLKD GEKRPIPNPT
CTFDDAFQCY PEVMENIKKA GFQKPTPIQS QAWPIVLQGI DLIGVAQTGT GKTLCYLMPG
FIHLVLQPSL KGQRNRPGML VLTPTRELAL QVEGECCKYS YKGLRSVCVY GGGNRDEQIE
ELKKGVDIII ATPGRLNDLQ MSNFVNLKNI TYLVLDEADK MLDMGFEPQI MKILLDVRPD
RQTVMTSATW PHSVHRLAQS YLKEPMIVYV GTLDLVAVSS VKQNIIVTTE EEKWSHMQTF
LQSMSSTDKV IVFVSRKAVA DHLSSDLILG NISVESLHGD REQRDREKAL ENFKTGKVRI
LIATDLASRG LDVHDVTHVY NFDFPRNIEE YVHRIGRTGR AGRTGVSITT LTRNDWRVAS
ELINILERAN QSIPEELVSM AERFKAHQRK REMERKMERP QGRPKKFH*
speed 0.69 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: 0.999999915691559 (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) chr6:74125888A>GN/A show variant in all transcripts   IGV
HGNC symbol CGAS
Ensembl transcript ID ENST00000370318
Genbank transcript ID N/A
UniProt peptide Q8N884
alteration type single base exchange
alteration region intron
DNA changes g.36112T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs311685
databasehomozygous (G/G)heterozygousallele carriers
1000G64611641810
ExAC16565-36316202
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.1470.021
0.0020.014
(flanking)0.0360.021
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased36106wt: 0.9969 / mu: 0.9975 (marginal change - not scored)wt: CCATTTTTCTTTCCATTTCCCTTTTCTGTTGATGTGCCTTA
mu: CCATTTTTCTTTCCATTTCCCTTTTCCGTTGATGTGCCTTA		 tccc|TTTT
Acc marginally increased36116wt: 0.9834 / mu: 0.9853 (marginal change - not scored)wt: TTCCATTTCCCTTTTCTGTTGATGTGCCTTAAACCTCTCAG
mu: TTCCATTTCCCTTTTCCGTTGATGTGCCTTAAACCTCTCAG		 gttg|ATGT
Acc marginally increased36105wt: 0.9819 / mu: 0.9825 (marginal change - not scored)wt: TCCATTTTTCTTTCCATTTCCCTTTTCTGTTGATGTGCCTT
mu: TCCATTTTTCTTTCCATTTCCCTTTTCCGTTGATGTGCCTT		 ttcc|CTTT
Acc marginally increased36103wt: 0.9761 / mu: 0.9822 (marginal change - not scored)wt: TTTCCATTTTTCTTTCCATTTCCCTTTTCTGTTGATGTGCC
mu: TTTCCATTTTTCTTTCCATTTCCCTTTTCCGTTGATGTGCC		 attt|CCCT
Acc marginally increased36109wt: 0.9274 / mu: 0.9437 (marginal change - not scored)wt: TTTTTCTTTCCATTTCCCTTTTCTGTTGATGTGCCTTAAAC
mu: TTTTTCTTTCCATTTCCCTTTTCCGTTGATGTGCCTTAAAC		 cttt|TCTG
Acc marginally increased36112wt: 0.9984 / mu: 0.9985 (marginal change - not scored)wt: TTCTTTCCATTTCCCTTTTCTGTTGATGTGCCTTAAACCTC
mu: TTCTTTCCATTTCCCTTTTCCGTTGATGTGCCTTAAACCTC		 ttct|GTTG
Acc marginally increased36107wt: 0.9799 / mu: 0.9871 (marginal change - not scored)wt: CATTTTTCTTTCCATTTCCCTTTTCTGTTGATGTGCCTTAA
mu: CATTTTTCTTTCCATTTCCCTTTTCCGTTGATGTGCCTTAA		 ccct|TTTC
Acc marginally increased36104wt: 0.8524 / mu: 0.9256 (marginal change - not scored)wt: TTCCATTTTTCTTTCCATTTCCCTTTTCTGTTGATGTGCCT
mu: TTCCATTTTTCTTTCCATTTCCCTTTTCCGTTGATGTGCCT		 tttc|CCTT
Acc marginally increased36113wt: 0.9857 / mu: 0.9864 (marginal change - not scored)wt: TCTTTCCATTTCCCTTTTCTGTTGATGTGCCTTAAACCTCT
mu: TCTTTCCATTTCCCTTTTCCGTTGATGTGCCTTAAACCTCT		 tctg|TTGA
Donor increased36113wt: 0.67 / mu: 0.82wt: TTTCTGTTGATGTGC
mu: TTTCCGTTGATGTGC		 TCTG|ttga
distance from splice site 2144
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features no protein features affected
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 79 / 79
chromosome 6
strand -1
last intron/exon boundary 1411
theoretical NMD boundary in CDS 1282
length of CDS 1344
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)		 36112
chromosomal position
(for ins/del: last normal base / first normal base)		 74125888
original gDNA sequence snippet TTCTTTCCATTTCCCTTTTCTGTTGATGTGCCTTAAACCTC
altered gDNA sequence snippet TTCTTTCCATTTCCCTTTTCCGTTGATGTGCCTTAAACCTC
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MQPWHGKAMQ RASEAGATAP KASARNARGA PMDPTESPAA PEAALPKAGK FGPARKSGSR
QKKSAPDTQE RPPVRATGAR AKKAPQRAQD TQPSDATSAP GAEGLEPPAA REPALSRAGS
CRQRGARCST KPRPPPGPWD VPSPGLPVSA PILVRRDAAP GASKLRAVLE KLKLSRDDIS
TAAGMVKGVV DHLLLRLKCD SAFRGVGLLN TGSYYEHVKI SAPNEFDVMF KLEVPRIQLE
EYSNTRAYYF VKFKRNPKEN PLSQFLEGEI LSASKMLSKF RKIIKEEIND IKDTDVIMKR
KRGGSPAVTL LISEKISVDI TLALESKSSW PASTQEGLRI QNWLSAKVRK QLRLKPFYLV
PKHAKEGNGF QEETWRLSFS HIEKEILNNH GKSKTCCENK EEKCCRKDCL KLMKYLLEQL
KERFKDKKHL DKFSSYHVKT AFFHRLY*
mutated AA sequence N/A
speed 0.75 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