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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: ENST00000423431
Querying Taster for transcript #2: ENST00000233025
MT speed 4.43 s - this script 8.919922 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
SPCS1polymorphism_automatic1.0991207943789e-14simple_aaeaffectedP41Asingle base exchangers6617show file
SPCS1polymorphism_automatic4.80911673295115e-06without_aaeaffectedsingle base exchangers6617show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999989 (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) chr3:52740182C>GN/A show variant in all transcripts   IGV
HGNC symbol SPCS1
Ensembl transcript ID ENST00000233025
Genbank transcript ID NM_014041
UniProt peptide Q9Y6A9
alteration type single base exchange
alteration region CDS
DNA changes c.121C>G
cDNA.531C>G
g.1212C>G
AA changes P41A Score: 27 explain score(s)
position(s) of altered AA
if AA alteration in CDS
41
frameshift no
known variant Reference ID: rs6617
databasehomozygous (G/G)heterozygousallele carriers
1000G53511601695
ExAC148351316614
regulatory features Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
ETS1, Transcription Factor, ETS1 Transcription Factor Binding
Gabp, Transcription Factor, Gabp TF binding
H2AZ, Histone, Histone 2A variant Z
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4ac, Histone, Histone 3 Lysine 4 Acetylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K5ac, Histone, Histone 4 Lysine 5 Acetylation
H4K8ac, Histone, Histone 4 Lysine 8 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
HDAC1, Transcription Factor, HDAC1 Transcription Factor Binding
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
SIX5, Transcription Factor, SIX5 Transcription Factor Binding
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
THAP1, Transcription Factor, THAP1 Transcription Factor Binding
Tcf12, Transcription Factor, Tcf12 Transcription Factor Binding
Tr4, Transcription Factor, Tr4 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)0.2160
-1.3220
(flanking)-1.0720
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained12060.52mu: GCCAGACCTTAGCCC CAGA|cctt
distance from splice site 117
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      41GPATDAQCQTLPLTVLKSRSPSPR
mutated  not conserved    41GPATDAQCQTLALTVLKSRSPSP
Ptroglodytes  not conserved  ENSPTRG00000015011  41GPAANAQCQTLALTVLKSRSPSP
Mmulatta  no alignment  ENSMMUG00000017370  n/a
Fcatus  no homologue    
Mmusculus  no alignment  ENSMUSG00000021917  n/a
Ggallus  no alignment  ENSGALG00000001655  n/a
Trubripes  no alignment  ENSTRUG00000005172  n/a
Drerio  no alignment  ENSDARG00000059298  n/a
Dmelanogaster  no alignment  FBgn0040623  n/a
Celegans  no alignment  C34B2.10  n/a
Xtropicalis  no alignment  ENSXETG00000013668  n/a
protein features
start (aa)end (aa)featuredetails 
193TOPO_DOMCytoplasmic (Potential).lost
4141CONFLICTP -> A (in Ref. 5; AAH00884 and 2; AAD40380).lost
94114TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
9595CONFLICTI -> Y (in Ref. 4; AAL31361).might get lost (downstream of altered splice site)
115115TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
116136TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
128128CONFLICTL -> LAQ (in Ref. 5; AAH00884).might get lost (downstream of altered splice site)
137169TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 510 / 510
position (AA) of stopcodon in wt / mu AA sequence 170 / 170
position of stopcodon in wt / mu cDNA 920 / 920
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 411 / 411
chromosome 3
strand 1
last intron/exon boundary 795
theoretical NMD boundary in CDS 334
length of CDS 510
coding sequence (CDS) position 121
cDNA position
(for ins/del: last normal base / first normal base)
531
gDNA position
(for ins/del: last normal base / first normal base)
1212
chromosomal position
(for ins/del: last normal base / first normal base)
52740182
original gDNA sequence snippet ACGCGCAGTGCCAGACCTTACCCCTCACGGTCCTTAAGTCT
altered gDNA sequence snippet ACGCGCAGTGCCAGACCTTAGCCCTCACGGTCCTTAAGTCT
original cDNA sequence snippet ACGCGCAGTGCCAGACCTTACCCCTCACGGTCCTTAAGTCT
altered cDNA sequence snippet ACGCGCAGTGCCAGACCTTAGCCCTCACGGTCCTTAAGTCT
wildtype AA sequence MARGGDTGCT GPSETSASGA AAIALPGLEG PATDAQCQTL PLTVLKSRSP SPRSLPPALS
CPPPQPAMLE HLSSLPTQMD YKGQKLAEQM FQGIILFSAI VGFIYGYVAE QFGWTVYIVM
AGFAFSCLLT LPPWPIYRRH PLKWLPVQES STDDKKPGER KIKRHAKNN*
mutated AA sequence MARGGDTGCT GPSETSASGA AAIALPGLEG PATDAQCQTL ALTVLKSRSP SPRSLPPALS
CPPPQPAMLE HLSSLPTQMD YKGQKLAEQM FQGIILFSAI VGFIYGYVAE QFGWTVYIVM
AGFAFSCLLT LPPWPIYRRH PLKWLPVQES STDDKKPGER KIKRHAKNN*
speed 2.18 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: without_aae, prob: 0.999995190883267 (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) chr3:52740182C>GN/A show variant in all transcripts   IGV
HGNC symbol SPCS1
Ensembl transcript ID ENST00000423431
Genbank transcript ID N/A
UniProt peptide Q9Y6A9
alteration type single base exchange
alteration region intron
DNA changes g.1212C>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs6617
databasehomozygous (G/G)heterozygousallele carriers
1000G53511601695
ExAC148351316614
regulatory features Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
ETS1, Transcription Factor, ETS1 Transcription Factor Binding
Gabp, Transcription Factor, Gabp TF binding
H2AZ, Histone, Histone 2A variant Z
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4ac, Histone, Histone 3 Lysine 4 Acetylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K5ac, Histone, Histone 4 Lysine 5 Acetylation
H4K8ac, Histone, Histone 4 Lysine 8 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
HDAC1, Transcription Factor, HDAC1 Transcription Factor Binding
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
SIX5, Transcription Factor, SIX5 Transcription Factor Binding
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
THAP1, Transcription Factor, THAP1 Transcription Factor Binding
Tcf12, Transcription Factor, Tcf12 Transcription Factor Binding
Tr4, Transcription Factor, Tr4 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)0.2160
-1.3220
(flanking)-1.0720
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -9) |
effectgDNA positionscoredetection sequence  exon-intron border
Donor gained12060.52mu: GCCAGACCTTAGCCC CAGA|cctt
distance from splice site 478
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
N/A
protein features
start (aa)end (aa)featuredetails 
193TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
4141CONFLICTP -> A (in Ref. 5; AAH00884 and 2; AAD40380).might get lost (downstream of altered splice site)
94114TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
9595CONFLICTI -> Y (in Ref. 4; AAL31361).might get lost (downstream of altered splice site)
115115TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
116136TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
128128CONFLICTL -> LAQ (in Ref. 5; AAH00884).might get lost (downstream of altered splice site)
137169TOPO_DOMCytoplasmic (Potential).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 235 / 235
chromosome 3
strand 1
last intron/exon boundary 352
theoretical NMD boundary in CDS 67
length of CDS 243
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)
1212
chromosomal position
(for ins/del: last normal base / first normal base)
52740182
original gDNA sequence snippet ACGCGCAGTGCCAGACCTTACCCCTCACGGTCCTTAAGTCT
altered gDNA sequence snippet ACGCGCAGTGCCAGACCTTAGCCCTCACGGTCCTTAAGTCT
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MFQGIILFSA IVGFIYGYVA EQFGWTVYIV MAGFAFSCLL TLPPWPIYRR HPLKWLPVQE
SSTDDKKPGE RKIKRHAKNN *
mutated AA sequence N/A
speed 2.25 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