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: ENST00000261448
Querying Taster for transcript #2: ENST00000456138
MT speed 2.51 s - this script 6.088471 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CASQ2polymorphism_automatic7.20534742981727e-14simple_aaeaffectedT66Asingle base exchangers4074536show file
CASQ2polymorphism_automatic4.93050045236032e-13simple_aaeaffectedT66Asingle base exchangers4074536show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999928 (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 CM108210)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:116310967T>CN/A show variant in all transcripts   IGV
HGNC symbol CASQ2
Ensembl transcript ID ENST00000261448
Genbank transcript ID NM_001232
UniProt peptide O14958
alteration type single base exchange
alteration region CDS
DNA changes c.196A>G
cDNA.436A>G
g.436A>G
AA changes T66A Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
66
frameshift no
known variant Reference ID: rs4074536
databasehomozygous (C/C)heterozygousallele carriers
1000G44411211565
ExAC69501886725817

known disease mutation at this position, please check HGMD for details (HGMD ID CM108210)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4310.007
0.9220.005
(flanking)-2.020
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 increased431wt: 0.4968 / mu: 0.5255 (marginal change - not scored)wt: TGAGCCGGTGTCTTCAGATAAGGTCACGCAAAAACAGTTCC
mu: TGAGCCGGTGTCTTCAGATAAGGTCGCGCAAAAACAGTTCC
 ataa|GGTC
Acc increased427wt: 0.23 / mu: 0.26wt: ACCATGAGCCGGTGTCTTCAGATAAGGTCACGCAAAAACAG
mu: ACCATGAGCCGGTGTCTTCAGATAAGGTCGCGCAAAAACAG
 tcag|ATAA
Donor marginally increased441wt: 0.8750 / mu: 0.8841 (marginal change - not scored)wt: ACGCAAAAACAGTTC
mu: GCGCAAAAACAGTTC
 GCAA|aaac
distance from splice site 39
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      66YYHEPVSSDKVTQKQFQLKEIVLE
mutated  not conserved    66SSDKVAQKQFQLKEIVL
Ptroglodytes  not conserved  ENSPTRG00000001148  66SSDKVAQKQFQLKEIVL
Mmulatta  not conserved  ENSMMUG00000008970  66SSDKVAQKQFQLKEIVL
Fcatus  no alignment  ENSFCAG00000010496  n/a
Mmusculus  all conserved  ENSMUSG00000027861  66SSDKVSQKQFQLKEIVL
Ggallus  all conserved  ENSGALG00000015018  66SSDRVSQKQFQMTEMVL
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000008982  67LQKQLHLTELVL
Dmelanogaster  no homologue    
Celegans  not conserved  F40E10.3  76VFFNDVEEDDSELDQY---ECFL
Xtropicalis  no alignment  ENSXETG00000023738  n/a
protein features
start (aa)end (aa)featuredetails 
4966STRANDlost
6767CONFLICTQ -> P (in Ref. 1; BAA23494).might get lost (downstream of altered splice site)
6784HELIXmight get lost (downstream of altered splice site)
8597STRANDmight get lost (downstream of altered splice site)
98103HELIXmight get lost (downstream of altered splice site)
104130STRANDmight get lost (downstream of altered splice site)
131141HELIXmight get lost (downstream of altered splice site)
142152STRANDmight get lost (downstream of altered splice site)
153158HELIXmight get lost (downstream of altered splice site)
159176STRANDmight get lost (downstream of altered splice site)
175175CONFLICTD -> G (in Ref. 2; BAG35873).might get lost (downstream of altered splice site)
177188HELIXmight get lost (downstream of altered splice site)
189200STRANDmight get lost (downstream of altered splice site)
201207HELIXmight get lost (downstream of altered splice site)
208217STRANDmight get lost (downstream of altered splice site)
219223STRANDmight get lost (downstream of altered splice site)
229233STRANDmight get lost (downstream of altered splice site)
234243HELIXmight get lost (downstream of altered splice site)
248252STRANDmight get lost (downstream of altered splice site)
256261HELIXmight get lost (downstream of altered splice site)
262278STRANDmight get lost (downstream of altered splice site)
279294HELIXmight get lost (downstream of altered splice site)
295298STRANDmight get lost (downstream of altered splice site)
300307STRANDmight get lost (downstream of altered splice site)
312320HELIXmight get lost (downstream of altered splice site)
321328STRANDmight get lost (downstream of altered splice site)
330351STRANDmight get lost (downstream of altered splice site)
335335CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
356361HELIXmight get lost (downstream of altered splice site)
356399COMPBIASAsp/Glu-rich (acidic).might get lost (downstream of altered splice site)
362369STRANDmight get lost (downstream of altered splice site)
385385MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
393393MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1200 / 1200
position (AA) of stopcodon in wt / mu AA sequence 400 / 400
position of stopcodon in wt / mu cDNA 1440 / 1440
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 241 / 241
chromosome 1
strand -1
last intron/exon boundary 1255
theoretical NMD boundary in CDS 964
length of CDS 1200
coding sequence (CDS) position 196
cDNA position
(for ins/del: last normal base / first normal base)
436
gDNA position
(for ins/del: last normal base / first normal base)
436
chromosomal position
(for ins/del: last normal base / first normal base)
116310967
original gDNA sequence snippet CGGTGTCTTCAGATAAGGTCACGCAAAAACAGTTCCAACTG
altered gDNA sequence snippet CGGTGTCTTCAGATAAGGTCGCGCAAAAACAGTTCCAACTG
original cDNA sequence snippet CGGTGTCTTCAGATAAGGTCACGCAAAAACAGTTCCAACTG
altered cDNA sequence snippet CGGTGTCTTCAGATAAGGTCGCGCAAAAACAGTTCCAACTG
wildtype AA sequence MKRTHLFIVG IYFLSSCRAE EGLNFPTYDG KDRVVSLSEK NFKQVLKKYD LLCLYYHEPV
SSDKVTQKQF QLKEIVLELV AQVLEHKAIG FVMVDAKKEA KLAKKLGFDE EGSLYILKGD
RTIEFDGEFA ADVLVEFLLD LIEDPVEIIS SKLEVQAFER IEDYIKLIGF FKSEDSEYYK
AFEEAAEHFQ PYIKFFATFD KGVAKKLSLK MNEVDFYEPF MDEPIAIPNK PYTEEELVEF
VKEHQRPTLR RLRPEEMFET WEDDLNGIHI VAFAEKSDPD GYEFLEILKQ VARDNTDNPD
LSILWIDPDD FPLLVAYWEK TFKIDLFRPQ IGVVNVTDAD SVWMEIPDDD DLPTAEELED
WIEDVLSGKI NTEDDDEDDD DDDNSDEEDN DDSDDDDDE*
mutated AA sequence MKRTHLFIVG IYFLSSCRAE EGLNFPTYDG KDRVVSLSEK NFKQVLKKYD LLCLYYHEPV
SSDKVAQKQF QLKEIVLELV AQVLEHKAIG FVMVDAKKEA KLAKKLGFDE EGSLYILKGD
RTIEFDGEFA ADVLVEFLLD LIEDPVEIIS SKLEVQAFER IEDYIKLIGF FKSEDSEYYK
AFEEAAEHFQ PYIKFFATFD KGVAKKLSLK MNEVDFYEPF MDEPIAIPNK PYTEEELVEF
VKEHQRPTLR RLRPEEMFET WEDDLNGIHI VAFAEKSDPD GYEFLEILKQ VARDNTDNPD
LSILWIDPDD FPLLVAYWEK TFKIDLFRPQ IGVVNVTDAD SVWMEIPDDD DLPTAEELED
WIEDVLSGKI NTEDDDEDDD DDDNSDEEDN DDSDDDDDE*
speed 1.18 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: 0.999999999999507 (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 CM108210)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:116310967T>CN/A show variant in all transcripts   IGV
HGNC symbol CASQ2
Ensembl transcript ID ENST00000456138
Genbank transcript ID N/A
UniProt peptide O14958
alteration type single base exchange
alteration region CDS
DNA changes c.196A>G
cDNA.369A>G
g.436A>G
AA changes T66A Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
66
frameshift no
known variant Reference ID: rs4074536
databasehomozygous (C/C)heterozygousallele carriers
1000G44411211565
ExAC69501886725817

known disease mutation at this position, please check HGMD for details (HGMD ID CM108210)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4310.007
0.9220.005
(flanking)-2.020
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 increased431wt: 0.4968 / mu: 0.5255 (marginal change - not scored)wt: TGAGCCGGTGTCTTCAGATAAGGTCACGCAAAAACAGTTCC
mu: TGAGCCGGTGTCTTCAGATAAGGTCGCGCAAAAACAGTTCC
 ataa|GGTC
Acc increased427wt: 0.23 / mu: 0.26wt: ACCATGAGCCGGTGTCTTCAGATAAGGTCACGCAAAAACAG
mu: ACCATGAGCCGGTGTCTTCAGATAAGGTCGCGCAAAAACAG
 tcag|ATAA
Donor marginally increased441wt: 0.8750 / mu: 0.8841 (marginal change - not scored)wt: ACGCAAAAACAGTTC
mu: GCGCAAAAACAGTTC
 GCAA|aaac
distance from splice site 39
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      66YYHEPVSSDKVTQKQFQLKEIVLE
mutated  not conserved    66SSDKVAQKQFQLKEIVL
Ptroglodytes  not conserved  ENSPTRG00000001148  66SSDKVAQKQFQLKEIVL
Mmulatta  not conserved  ENSMMUG00000008970  135AADVLVEFLLDLIEDPV
Fcatus  no alignment  ENSFCAG00000010496  n/a
Mmusculus  not conserved  ENSMUSG00000027861  135AADVLVEFLLDLIEDPV
Ggallus  not conserved  ENSGALG00000015018  135LATDVLVEFLLDLLEDPV
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000008982  136SADTLVEFLLDLLEDPV
Dmelanogaster  no homologue    
Celegans  not conserved  F40E10.3  76VFFNDVEEDDSELDQY---ECFL
Xtropicalis  all identical  ENSXETG00000023738  48FYEPFMEEPVTIPDKPYSEE--
protein features
start (aa)end (aa)featuredetails 
4966STRANDlost
6767CONFLICTQ -> P (in Ref. 1; BAA23494).might get lost (downstream of altered splice site)
6784HELIXmight get lost (downstream of altered splice site)
8597STRANDmight get lost (downstream of altered splice site)
98103HELIXmight get lost (downstream of altered splice site)
104130STRANDmight get lost (downstream of altered splice site)
131141HELIXmight get lost (downstream of altered splice site)
142152STRANDmight get lost (downstream of altered splice site)
153158HELIXmight get lost (downstream of altered splice site)
159176STRANDmight get lost (downstream of altered splice site)
175175CONFLICTD -> G (in Ref. 2; BAG35873).might get lost (downstream of altered splice site)
177188HELIXmight get lost (downstream of altered splice site)
189200STRANDmight get lost (downstream of altered splice site)
201207HELIXmight get lost (downstream of altered splice site)
208217STRANDmight get lost (downstream of altered splice site)
219223STRANDmight get lost (downstream of altered splice site)
229233STRANDmight get lost (downstream of altered splice site)
234243HELIXmight get lost (downstream of altered splice site)
248252STRANDmight get lost (downstream of altered splice site)
256261HELIXmight get lost (downstream of altered splice site)
262278STRANDmight get lost (downstream of altered splice site)
279294HELIXmight get lost (downstream of altered splice site)
295298STRANDmight get lost (downstream of altered splice site)
300307STRANDmight get lost (downstream of altered splice site)
312320HELIXmight get lost (downstream of altered splice site)
321328STRANDmight get lost (downstream of altered splice site)
330351STRANDmight get lost (downstream of altered splice site)
335335CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
356361HELIXmight get lost (downstream of altered splice site)
356399COMPBIASAsp/Glu-rich (acidic).might get lost (downstream of altered splice site)
362369STRANDmight get lost (downstream of altered splice site)
385385MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
393393MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 987 / 987
position (AA) of stopcodon in wt / mu AA sequence 329 / 329
position of stopcodon in wt / mu cDNA 1160 / 1160
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 174 / 174
chromosome 1
strand -1
last intron/exon boundary 975
theoretical NMD boundary in CDS 751
length of CDS 987
coding sequence (CDS) position 196
cDNA position
(for ins/del: last normal base / first normal base)
369
gDNA position
(for ins/del: last normal base / first normal base)
436
chromosomal position
(for ins/del: last normal base / first normal base)
116310967
original gDNA sequence snippet CGGTGTCTTCAGATAAGGTCACGCAAAAACAGTTCCAACTG
altered gDNA sequence snippet CGGTGTCTTCAGATAAGGTCGCGCAAAAACAGTTCCAACTG
original cDNA sequence snippet CGGTGTCTTCAGATAAGGTCACGCAAAAACAGTTCCAACTG
altered cDNA sequence snippet CGGTGTCTTCAGATAAGGTCGCGCAAAAACAGTTCCAACTG
wildtype AA sequence MKRTHLFIVG IYFLSSCRAE EGLNFPTYDG KDRVVSLSEK NFKQVLKKYD LLCLYYHEPV
SSDKVTQKQF QLKEIVLELV AQVLEHKAIG FVMVDAKKEA KLAKKLDYKA FEEAAEHFQP
YIKFFATFDK GVAKKLSLKM NEVDFYEPFM DEPIAIPNKP YTEEELVEFV KEHQRPTLRR
LRPEEMFETW EDDLNGIHIV AFAEKSDPDG YEFLEILKQV ARDNTDNPDL SILWIDPDDF
PLLVAYWEKT FKIDLFRPQI GVVNVTDADS VWMEIPDDDD LPTAEELEDW IEDVLSGKIN
TEDDDEDDDD DDNSDEEDND DSDDDDDE*
mutated AA sequence MKRTHLFIVG IYFLSSCRAE EGLNFPTYDG KDRVVSLSEK NFKQVLKKYD LLCLYYHEPV
SSDKVAQKQF QLKEIVLELV AQVLEHKAIG FVMVDAKKEA KLAKKLDYKA FEEAAEHFQP
YIKFFATFDK GVAKKLSLKM NEVDFYEPFM DEPIAIPNKP YTEEELVEFV KEHQRPTLRR
LRPEEMFETW EDDLNGIHIV AFAEKSDPDG YEFLEILKQV ARDNTDNPDL SILWIDPDDF
PLLVAYWEKT FKIDLFRPQI GVVNVTDADS VWMEIPDDDD LPTAEELEDW IEDVLSGKIN
TEDDDEDDDD DDNSDEEDND DSDDDDDE*
speed 1.33 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