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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000528170
Querying Taster for transcript #2: ENST00000337911
Querying Taster for transcript #3: ENST00000405633
MT speed 0 s - this script 4.855449 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
MS4A15polymorphism_automatic0.00104753702840699simple_aaeaffectedL47Rsingle base exchangers1032939show file
MS4A15polymorphism_automatic0.00171816248760104simple_aaeaffectedL47Rsingle base exchangers1032939show file
MS4A15polymorphism_automatic0.999928631052835without_aaeaffectedsingle base exchangers1032939show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.998952462971593 (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) chr11:60531346T>GN/A show variant in all transcripts   IGV
HGNC symbol MS4A15
Ensembl transcript ID ENST00000528170
Genbank transcript ID N/A
UniProt peptide Q8N5U1
alteration type single base exchange
alteration region CDS
DNA changes c.140T>G
cDNA.274T>G
g.6921T>G
AA changes L47R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 47
frameshift no
known variant Reference ID: rs1032939
databasehomozygous (G/G)heterozygousallele carriers
1000G5449451489
ExAC13392598319375
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
EBF, Transcription Factor, EBF Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.0570.466
1.3140.469
(flanking)-0.810.432
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased6918wt: 0.21 / mu: 0.49wt: GCCACCGCTGGGGGC
mu: GCCACCGCGGGGGGC		 CACC|gctg
Donor increased6912wt: 0.58 / mu: 0.82wt: TGAGGAGCCACCGCT
mu: TGAGGAGCCACCGCG		 AGGA|gcca
Donor gained69200.62mu: CACCGCGGGGGGCAC CCGC|gggg
distance from splice site 86
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      47PPGIMQFEEPPLGAQTPRATQPPD
mutated  not conserved    47PPGIMQFEEPPRGAQTPRATQPP
Ptroglodytes  all identical  ENSPTRG00000003719  47PPGIMQFEEPPLGAQTPRATQPP
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000067571  50PPGIMQFEESQLGAQAPRATQPP
Ggallus  no homologue    
Trubripes  no alignment  ENSTRUG00000009051  n/a
Drerio  no alignment  ENSDARG00000053561  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
7393TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
100120TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
144164TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
173193TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 600 / 600
position (AA) of stopcodon in wt / mu AA sequence 200 / 200
position of stopcodon in wt / mu cDNA 734 / 734
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 135 / 135
chromosome 11
strand 1
last intron/exon boundary 624
theoretical NMD boundary in CDS 439
length of CDS 600
coding sequence (CDS) position 140
cDNA position
(for ins/del: last normal base / first normal base)		 274
gDNA position
(for ins/del: last normal base / first normal base)		 6921
chromosomal position
(for ins/del: last normal base / first normal base)		 60531346
original gDNA sequence snippet GCAGTTTGAGGAGCCACCGCTGGGGGCACAGACACCAAGGG
altered gDNA sequence snippet GCAGTTTGAGGAGCCACCGCGGGGGGCACAGACACCAAGGG
original cDNA sequence snippet GCAGTTTGAGGAGCCACCGCTGGGGGCACAGACACCAAGGG
altered cDNA sequence snippet GCAGTTTGAGGAGCCACCGCGGGGGGCACAGACACCAAGGG
wildtype AA sequence MSAAPASNGV FVVIPPNNAS GLCPPPAILP TSMCQPPGIM QFEEPPLGAQ TPRATQPPDL
RPVETFLTGE PKVLGFIISG SLSVAAEKNH TSCLVRSSLG TNILSVMAAF AGTAILLMDF
GVTNRDVDRG YLAVLTIFTV LEFFTAVIAM HFGCQAIHAQ ASAPVIFLPN AFSADFNIPS
PAASAPPAYD NVAYAQGVV*
mutated AA sequence MSAAPASNGV FVVIPPNNAS GLCPPPAILP TSMCQPPGIM QFEEPPRGAQ TPRATQPPDL
RPVETFLTGE PKVLGFIISG SLSVAAEKNH TSCLVRSSLG TNILSVMAAF AGTAILLMDF
GVTNRDVDRG YLAVLTIFTV LEFFTAVIAM HFGCQAIHAQ ASAPVIFLPN AFSADFNIPS
PAASAPPAYD NVAYAQGVV*
speed 1.50 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: 0.998281837512399 (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) chr11:60531346T>GN/A show variant in all transcripts   IGV
HGNC symbol MS4A15
Ensembl transcript ID ENST00000405633
Genbank transcript ID NM_001098835
UniProt peptide Q8N5U1
alteration type single base exchange
alteration region CDS
DNA changes c.140T>G
cDNA.219T>G
g.6921T>G
AA changes L47R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 47
frameshift no
known variant Reference ID: rs1032939
databasehomozygous (G/G)heterozygousallele carriers
1000G5449451489
ExAC13392598319375
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
EBF, Transcription Factor, EBF Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.0570.466
1.3140.469
(flanking)-0.810.432
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased6918wt: 0.21 / mu: 0.49wt: GCCACCGCTGGGGGC
mu: GCCACCGCGGGGGGC		 CACC|gctg
Donor increased6912wt: 0.58 / mu: 0.82wt: TGAGGAGCCACCGCT
mu: TGAGGAGCCACCGCG		 AGGA|gcca
Donor gained69200.62mu: CACCGCGGGGGGCAC CCGC|gggg
distance from splice site 86
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      47PPGIMQFEEPPLGAQTPRATQPPD
mutated  not conserved    47PPGIMQFEEPPRGAQTPRATQPP
Ptroglodytes  all identical  ENSPTRG00000003719  47PPGIMQFEEPPLGAQTPRATQPP
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000067571  50PPGIMQFEESQLGAQAPRATQPP
Ggallus  no homologue    
Trubripes  no alignment  ENSTRUG00000009051  n/a
Drerio  all conserved  ENSDARG00000053561  47SSSV------PVYIQHVAGVSP-
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
7393TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
100120TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
144164TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
173193TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 723 / 723
position (AA) of stopcodon in wt / mu AA sequence 241 / 241
position of stopcodon in wt / mu cDNA 802 / 802
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 80 / 80
chromosome 11
strand 1
last intron/exon boundary 692
theoretical NMD boundary in CDS 562
length of CDS 723
coding sequence (CDS) position 140
cDNA position
(for ins/del: last normal base / first normal base)		 219
gDNA position
(for ins/del: last normal base / first normal base)		 6921
chromosomal position
(for ins/del: last normal base / first normal base)		 60531346
original gDNA sequence snippet GCAGTTTGAGGAGCCACCGCTGGGGGCACAGACACCAAGGG
altered gDNA sequence snippet GCAGTTTGAGGAGCCACCGCGGGGGGCACAGACACCAAGGG
original cDNA sequence snippet GCAGTTTGAGGAGCCACCGCTGGGGGCACAGACACCAAGGG
altered cDNA sequence snippet GCAGTTTGAGGAGCCACCGCGGGGGGCACAGACACCAAGGG
wildtype AA sequence MSAAPASNGV FVVIPPNNAS GLCPPPAILP TSMCQPPGIM QFEEPPLGAQ TPRATQPPDL
RPVETFLTGE PKVLGTVQIL IGLIHLGFGS VLLMVRRGHV GIFFIEGGVP FWGGACFIIS
GSLSVAAEKN HTSCLVRSSL GTNILSVMAA FAGTAILLMD FGVTNRDVDR GYLAVLTIFT
VLEFFTAVIA MHFGCQAIHA QASAPVIFLP NAFSADFNIP SPAASAPPAY DNVAYAQGVV
*
mutated AA sequence MSAAPASNGV FVVIPPNNAS GLCPPPAILP TSMCQPPGIM QFEEPPRGAQ TPRATQPPDL
RPVETFLTGE PKVLGTVQIL IGLIHLGFGS VLLMVRRGHV GIFFIEGGVP FWGGACFIIS
GSLSVAAEKN HTSCLVRSSL GTNILSVMAA FAGTAILLMD FGVTNRDVDR GYLAVLTIFT
VLEFFTAVIA MHFGCQAIHA QASAPVIFLP NAFSADFNIP SPAASAPPAY DNVAYAQGVV
*
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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 7.13689471653069e-05 (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) chr11:60531346T>GN/A show variant in all transcripts   IGV
HGNC symbol MS4A15
Ensembl transcript ID ENST00000337911
Genbank transcript ID NM_152717
UniProt peptide Q8N5U1
alteration type single base exchange
alteration region intron
DNA changes g.6921T>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs1032939
databasehomozygous (G/G)heterozygousallele carriers
1000G5449451489
ExAC13392598319375
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
EBF, Transcription Factor, EBF Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.0570.466
1.3140.469
(flanking)-0.810.432
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -6) |
effectgDNA positionscoredetection sequence  exon-intron border
Donor increased6918wt: 0.21 / mu: 0.49wt: GCCACCGCTGGGGGC
mu: GCCACCGCGGGGGGC		 CACC|gctg
Donor increased6912wt: 0.58 / mu: 0.82wt: TGAGGAGCCACCGCT
mu: TGAGGAGCCACCGCG		 AGGA|gcca
Donor gained69200.62mu: CACCGCGGGGGGCAC CCGC|gggg
distance from splice site 3694
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
7393TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
100120TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
144164TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
173193TRANSMEMHelical; (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 77 / 77
chromosome 11
strand 1
last intron/exon boundary 410
theoretical NMD boundary in CDS 283
length of CDS 444
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)		 6921
chromosomal position
(for ins/del: last normal base / first normal base)		 60531346
original gDNA sequence snippet GCAGTTTGAGGAGCCACCGCTGGGGGCACAGACACCAAGGG
altered gDNA sequence snippet GCAGTTTGAGGAGCCACCGCGGGGGGCACAGACACCAAGGG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MVRRGHVGIF FIEGGVPFWG GACFIISGSL SVAAEKNHTS CLVRSSLGTN ILSVMAAFAG
TAILLMDFGV TNRDVDRGYL AVLTIFTVLE FFTAVIAMHF GCQAIHAQAS APVIFLPNAF
SADFNIPSPA ASAPPAYDNV AYAQGVV*
mutated AA sequence N/A
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

Problems