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: ENST00000373295
Querying Taster for transcript #2: ENST00000373293
MT speed 0 s - this script 3.418842 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CFAP157polymorphism_automatic2.05371053496606e-10simple_aaeaffectedY483Ssingle base exchangers497632show file
CFAP157polymorphism_automatic1.16066542044102e-07without_aaeaffectedsingle base exchangers497632show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999794629 (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) chr9:130475442A>CN/A show variant in all transcripts   IGV
HGNC symbol CFAP157
Ensembl transcript ID ENST00000373295
Genbank transcript ID NM_001012502
UniProt peptide Q5JU67
alteration type single base exchange
alteration region CDS
DNA changes c.1448A>C
cDNA.1488A>C
g.6175A>C
AA changes Y483S Score: 144 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 483
frameshift no
known variant Reference ID: rs497632
databasehomozygous (C/C)heterozygousallele carriers
1000G78011281908
ExAC19537-630713230
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5320.004
0.0960.001
(flanking)-0.1320
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 increased6176wt: 0.4559 / mu: 0.5241 (marginal change - not scored)wt: GACCTCAGGCTGCTGTCATATATCACCCGTGTGGGGACCTT
mu: GACCTCAGGCTGCTGTCATCTATCACCCGTGTGGGGACCTT		 atat|ATCA
Acc increased6185wt: 0.48 / mu: 0.74wt: CTGCTGTCATATATCACCCGTGTGGGGACCTTCCGGGCACA
mu: CTGCTGTCATCTATCACCCGTGTGGGGACCTTCCGGGCACA		 ccgt|GTGG
Acc marginally increased6183wt: 0.9300 / mu: 0.9695 (marginal change - not scored)wt: GGCTGCTGTCATATATCACCCGTGTGGGGACCTTCCGGGCA
mu: GGCTGCTGTCATCTATCACCCGTGTGGGGACCTTCCGGGCA		 accc|GTGT
Donor marginally increased6180wt: 0.5044 / mu: 0.5261 (marginal change - not scored)wt: ATATCACCCGTGTGG
mu: CTATCACCCGTGTGG		 ATCA|cccg
Acc gained61800.50mu: TCAGGCTGCTGTCATCTATCACCCGTGTGGGGACCTTCCGG atca|CCCG
distance from splice site 44
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      483PPNPQDLRLLSYITRVGTFRAHSS
mutated  not conserved    483LSSITRVGTFRAHS
Ptroglodytes  all identical  ENSPTRG00000021393  483LSYITRVGTFRAHS
Mmulatta  all identical  ENSMMUG00000016423  484LLSYITRVGTFRAHS
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000038987  488QDLRPLSYITRMGI--CQN
Ggallus  no homologue    
Trubripes  no alignment  ENSTRUG00000015719  n/a
Drerio  no alignment  ENSDARG00000090068  n/a
Dmelanogaster  no alignment  FBgn0036962  n/a
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000004470  n/a
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1563 / 1563
position (AA) of stopcodon in wt / mu AA sequence 521 / 521
position of stopcodon in wt / mu cDNA 1603 / 1603
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 41 / 41
chromosome 9
strand 1
last intron/exon boundary 1532
theoretical NMD boundary in CDS 1441
length of CDS 1563
coding sequence (CDS) position 1448
cDNA position
(for ins/del: last normal base / first normal base)		 1488
gDNA position
(for ins/del: last normal base / first normal base)		 6175
chromosomal position
(for ins/del: last normal base / first normal base)		 130475442
original gDNA sequence snippet GGACCTCAGGCTGCTGTCATATATCACCCGTGTGGGGACCT
altered gDNA sequence snippet GGACCTCAGGCTGCTGTCATCTATCACCCGTGTGGGGACCT
original cDNA sequence snippet GGACCTCAGGCTGCTGTCATATATCACCCGTGTGGGGACCT
altered cDNA sequence snippet GGACCTCAGGCTGCTGTCATCTATCACCCGTGTGGGGACCT
wildtype AA sequence MAPKKSVSKA GKELEVKKKG GKKEPVVAVE PPLAKEMKEF YHIQIRDLED RLARYQRKWD
ELAVQEKMFR QEFEQLANNK KEIVAFLKRT LNQQVDEITD LNEQLQNLQL AKEMEKDAFE
AQLAQVRHEF QETKDQLTTE NIILGGKLAA LEEFRLQKEE VTDKFTLLEE QVRKQENEFR
DYAYNLEKKS VLDKDRLRKE IIQRVNLVAN EFHKVTTNRM WETTKRAIKE NNGITLQMAR
VSQQGMKLLQ ENEQLKGRQN NLCKQLELLE NTQKVMARHK RGHQKIILML TKKCQEQQQD
TKEAEELRLL LSQLEQRSLQ LQVDNQALKS QRDQLSLQLE QQQVDLQRLQ QELANEQKVR
ASLEAALVQA TSFLQNILQM HRDEEDSDVD VTFQPWHKEM LQQLLVMLSS TVATRPQKAA
CPHQESQSHG PPKESRPSIQ LPRTGSLLPQ LSDITPYQPG DLGLVPRQVH IPPNPQDLRL
LSYITRVGTF RAHSSPEMRA PGSLKRLEKF SLPEVPLRPK *
mutated AA sequence MAPKKSVSKA GKELEVKKKG GKKEPVVAVE PPLAKEMKEF YHIQIRDLED RLARYQRKWD
ELAVQEKMFR QEFEQLANNK KEIVAFLKRT LNQQVDEITD LNEQLQNLQL AKEMEKDAFE
AQLAQVRHEF QETKDQLTTE NIILGGKLAA LEEFRLQKEE VTDKFTLLEE QVRKQENEFR
DYAYNLEKKS VLDKDRLRKE IIQRVNLVAN EFHKVTTNRM WETTKRAIKE NNGITLQMAR
VSQQGMKLLQ ENEQLKGRQN NLCKQLELLE NTQKVMARHK RGHQKIILML TKKCQEQQQD
TKEAEELRLL LSQLEQRSLQ LQVDNQALKS QRDQLSLQLE QQQVDLQRLQ QELANEQKVR
ASLEAALVQA TSFLQNILQM HRDEEDSDVD VTFQPWHKEM LQQLLVMLSS TVATRPQKAA
CPHQESQSHG PPKESRPSIQ LPRTGSLLPQ LSDITPYQPG DLGLVPRQVH IPPNPQDLRL
LSSITRVGTF RAHSSPEMRA PGSLKRLEKF SLPEVPLRPK *
speed 0.95 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: 0.999999883933458 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • 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) chr9:130475442A>CN/A show variant in all transcripts   IGV
HGNC symbol CFAP157
Ensembl transcript ID ENST00000373293
Genbank transcript ID N/A
UniProt peptide Q5JU67
alteration type single base exchange
alteration region intron
DNA changes g.6175A>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs497632
databasehomozygous (C/C)heterozygousallele carriers
1000G78011281908
ExAC19537-630713230
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5320.004
0.0960.001
(flanking)-0.1320
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 increased6176wt: 0.4559 / mu: 0.5241 (marginal change - not scored)wt: GACCTCAGGCTGCTGTCATATATCACCCGTGTGGGGACCTT
mu: GACCTCAGGCTGCTGTCATCTATCACCCGTGTGGGGACCTT		 atat|ATCA
Acc increased6185wt: 0.48 / mu: 0.74wt: CTGCTGTCATATATCACCCGTGTGGGGACCTTCCGGGCACA
mu: CTGCTGTCATCTATCACCCGTGTGGGGACCTTCCGGGCACA		 ccgt|GTGG
Acc marginally increased6183wt: 0.9300 / mu: 0.9695 (marginal change - not scored)wt: GGCTGCTGTCATATATCACCCGTGTGGGGACCTTCCGGGCA
mu: GGCTGCTGTCATCTATCACCCGTGTGGGGACCTTCCGGGCA		 accc|GTGT
Donor marginally increased6180wt: 0.5044 / mu: 0.5261 (marginal change - not scored)wt: ATATCACCCGTGTGG
mu: CTATCACCCGTGTGG		 ATCA|cccg
Acc gained61800.50mu: TCAGGCTGCTGTCATCTATCACCCGTGTGGGGACCTTCCGG atca|CCCG
distance from splice site 288
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
33189COILEDPotential.might get lost (downstream of altered splice site)
236372COILEDPotential.might get lost (downstream of altered splice site)
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 736 / 736
chromosome 9
strand 1
last intron/exon boundary 987
theoretical NMD boundary in CDS 201
length of CDS 381
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)		 6175
chromosomal position
(for ins/del: last normal base / first normal base)		 130475442
original gDNA sequence snippet GGACCTCAGGCTGCTGTCATATATCACCCGTGTGGGGACCT
altered gDNA sequence snippet GGACCTCAGGCTGCTGTCATCTATCACCCGTGTGGGGACCT
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MGTEVGISWT RVGTGATVGL LPPHPHQQMH RDEEDSDVDV TFQPWHKEML QQLLVMLSST
VATRPQKAAC PHQESQSHGP PKESVPWAPT QRSGNAEQRC SGEGARRRGP ETRPLRTPEG
WAGRAP*
mutated AA sequence N/A
speed 0.52 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