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: ENST00000319540
Querying Taster for transcript #2: ENST00000273908
MT speed 2.76 s - this script 7.195999 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
SCD5polymorphism_automatic3.47899486996539e-12simple_aaeaffectedE197Qsingle base exchangers3733227show file
SCD5polymorphism_automatic0.000690414286712016without_aaeaffectedsingle base exchangers3733227show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999996521 (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) chr4:83582211C>GN/A show variant in all transcripts   IGV
HGNC symbol SCD5
Ensembl transcript ID ENST00000273908
Genbank transcript ID NM_024906
UniProt peptide Q86SK9
alteration type single base exchange
alteration region CDS
DNA changes c.589G>C
cDNA.824G>C
g.137800G>C
AA changes E197Q Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS
197
frameshift no
known variant Reference ID: rs3733227
databasehomozygous (G/G)heterozygousallele carriers
1000G93311812114
ExAC26134-195016633
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.9860.077
1.1350.071
(flanking)0.3050.033
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 increased137801wt: 0.9808 / mu: 0.9871 (marginal change - not scored)wt: GAAAGAAGGAAGAGC
mu: GAAACAAGGAAGAGC
 AAGA|agga
Donor increased137802wt: 0.80 / mu: 0.92wt: AAAGAAGGAAGAGCT
mu: AAACAAGGAAGAGCT
 AGAA|ggaa
Donor marginally increased137795wt: 0.8937 / mu: 0.9382 (marginal change - not scored)wt: CATCCAGAAAGAAGG
mu: CATCCAGAAACAAGG
 TCCA|gaaa
Donor marginally increased137803wt: 0.9884 / mu: 0.9927 (marginal change - not scored)wt: AAGAAGGAAGAGCTC
mu: AACAAGGAAGAGCTC
 GAAG|gaag
Donor increased137798wt: 0.24 / mu: 0.47wt: CCAGAAAGAAGGAAG
mu: CCAGAAACAAGGAAG
 AGAA|agaa
distance from splice site 20
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      197RIQRNTQHIQKEGRALNQEAACEM
mutated  all conserved    197RIQRNTQHIQKQGRALNQEAACE
Ptroglodytes  no alignment  ENSPTRG00000016220  n/a
Mmulatta  no alignment  ENSMMUG00000000866  n/a
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no alignment  ENSGALG00000011173  n/a
Trubripes  no alignment  ENSTRUG00000012356  n/a
Drerio  no homologue    
Dmelanogaster  no alignment  FBgn0086687  n/a
Celegans  no alignment  W06D12.3  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
194214TRANSMEMHelical; (Potential).lost
216238TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
272276MOTIFHistidine box-3 (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 771 / 771
position (AA) of stopcodon in wt / mu AA sequence 257 / 257
position of stopcodon in wt / mu cDNA 1006 / 1006
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 236 / 236
chromosome 4
strand -1
last intron/exon boundary 805
theoretical NMD boundary in CDS 519
length of CDS 771
coding sequence (CDS) position 589
cDNA position
(for ins/del: last normal base / first normal base)
824
gDNA position
(for ins/del: last normal base / first normal base)
137800
chromosomal position
(for ins/del: last normal base / first normal base)
83582211
original gDNA sequence snippet GTACACAGCACATCCAGAAAGAAGGAAGAGCTCTCAATCAA
altered gDNA sequence snippet GTACACAGCACATCCAGAAACAAGGAAGAGCTCTCAATCAA
original cDNA sequence snippet ATACACAGCACATCCAGAAAGAAGGAAGAGCTCTCAATCAA
altered cDNA sequence snippet ATACACAGCACATCCAGAAACAAGGAAGAGCTCTCAATCAA
wildtype AA sequence MPGPATDAGK IPFCDAKEEI RAGLESSEGG GGPERPGARG QRQNIVWRNV VLMSLLHLGA
VYSLVLIPKA KPLTLLWAYF CFLLAALGVT AGAHRLWSHR SYRAKLPLRI FLAVANSMAF
QNDIFEWSRD HRAHHKYSET DADPHNARRG FFFSHIGWLF VRKHRDVIEK GRKLDVTDLL
ADPVVRIQRN TQHIQKEGRA LNQEAACEML REWHQGHILK VTLPGLHILA LLHTHCNHSE
KCCLMLRALS VSLEVF*
mutated AA sequence MPGPATDAGK IPFCDAKEEI RAGLESSEGG GGPERPGARG QRQNIVWRNV VLMSLLHLGA
VYSLVLIPKA KPLTLLWAYF CFLLAALGVT AGAHRLWSHR SYRAKLPLRI FLAVANSMAF
QNDIFEWSRD HRAHHKYSET DADPHNARRG FFFSHIGWLF VRKHRDVIEK GRKLDVTDLL
ADPVVRIQRN TQHIQKQGRA LNQEAACEML REWHQGHILK VTLPGLHILA LLHTHCNHSE
KCCLMLRALS VSLEVF*
speed 1.79 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: 0.999309585713288 (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) chr4:83582211C>GN/A show variant in all transcripts   IGV
HGNC symbol SCD5
Ensembl transcript ID ENST00000319540
Genbank transcript ID NM_001037582
UniProt peptide Q86SK9
alteration type single base exchange
alteration region intron
DNA changes g.137800G>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs3733227
databasehomozygous (G/G)heterozygousallele carriers
1000G93311812114
ExAC26134-195016633
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.9860.077
1.1350.071
(flanking)0.3050.033
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 increased137801wt: 0.9808 / mu: 0.9871 (marginal change - not scored)wt: GAAAGAAGGAAGAGC
mu: GAAACAAGGAAGAGC
 AAGA|agga
Donor increased137802wt: 0.80 / mu: 0.92wt: AAAGAAGGAAGAGCT
mu: AAACAAGGAAGAGCT
 AGAA|ggaa
Donor marginally increased137795wt: 0.8937 / mu: 0.9382 (marginal change - not scored)wt: CATCCAGAAAGAAGG
mu: CATCCAGAAACAAGG
 TCCA|gaaa
Donor marginally increased137803wt: 0.9884 / mu: 0.9927 (marginal change - not scored)wt: AAGAAGGAAGAGCTC
mu: AACAAGGAAGAGCTC
 GAAG|gaag
Donor increased137798wt: 0.24 / mu: 0.47wt: CCAGAAAGAAGGAAG
mu: CCAGAAACAAGGAAG
 AGAA|agaa
distance from splice site 19649
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
N/A
protein features
start (aa)end (aa)featuredetails 
194214TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
216238TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
272276MOTIFHistidine box-3 (By similarity).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 321 / 321
chromosome 4
strand -1
last intron/exon boundary 1123
theoretical NMD boundary in CDS 752
length of CDS 993
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)
137800
chromosomal position
(for ins/del: last normal base / first normal base)
83582211
original gDNA sequence snippet GTACACAGCACATCCAGAAAGAAGGAAGAGCTCTCAATCAA
altered gDNA sequence snippet GTACACAGCACATCCAGAAACAAGGAAGAGCTCTCAATCAA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MPGPATDAGK IPFCDAKEEI RAGLESSEGG GGPERPGARG QRQNIVWRNV VLMSLLHLGA
VYSLVLIPKA KPLTLLWAYF CFLLAALGVT AGAHRLWSHR SYRAKLPLRI FLAVANSMAF
QNDIFEWSRD HRAHHKYSET DADPHNARRG FFFSHIGWLF VRKHRDVIEK GRKLDVTDLL
ADPVVRIQRK YYKISVVLMC FVVPTLVPWY IWGESLWNSY FLASILRYTI SLNISWLVNS
AAHMYGNRPY DKHISPRQNP LVALGAIGEG FHNYHHTFPF DYSASEFGLN FNPTTWFIDF
MCWLGLATDR KRATKPMIEA RKARTGDSSA *
mutated AA sequence N/A
speed 0.97 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