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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000376228
Querying Taster for transcript #2: ENST00000383329
Querying Taster for transcript #3: ENST00000396254
Querying Taster for transcript #4: ENST00000539307
MT speed 0 s - this script 4.237466 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
HLA-Cpolymorphism_automatic2.28039809258007e-13simple_aaeaffectedC387Ssingle base exchangers35708511show file
HLA-Cpolymorphism_automatic2.89990254032091e-13simple_aaeaffectedC350Ssingle base exchangers35708511show file
HLA-Cpolymorphism_automatic2.89990254032091e-13simple_aaeaffectedC356Ssingle base exchangers35708511show file
HLA-Cpolymorphism_automatic1.2544965066752e-11simple_aaeaffectedA349Psingle base exchangers35708511show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999772 (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) chr6:31237162C>GN/A show variant in all transcripts   IGV
HGNC symbol HLA-C
Ensembl transcript ID ENST00000539307
Genbank transcript ID N/A
UniProt peptide P30501
alteration type single base exchange
alteration region CDS
DNA changes c.1160G>C
cDNA.1160G>C
g.2746G>C
AA changes C387S Score: 112 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 387
frameshift no
known variant Reference ID: rs35708511
databasehomozygous (G/G)heterozygousallele carriers
1000G15628102372
ExAC32501-32235266
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.1360
-0.4780.002
(flanking)1.8070.03
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost2745.5sequence motif lost- wt: ccca|GGCA
 mu: ccca.GCCA
Acc marginally increased2740wt: 0.9823 / mu: 0.9832 (marginal change - not scored)wt: AGGTCTTTTTTTTTGTTCTACCCCAGGCAGCAACAGTGCCC
mu: AGGTCTTTTTTTTTGTTCTACCCCAGCCAGCAACAGTGCCC		 ctac|CCCA
Acc marginally increased2741wt: 0.8732 / mu: 0.9170 (marginal change - not scored)wt: GGTCTTTTTTTTTGTTCTACCCCAGGCAGCAACAGTGCCCA
mu: GGTCTTTTTTTTTGTTCTACCCCAGCCAGCAACAGTGCCCA		 tacc|CCAG
Acc marginally increased2744wt: 0.9911 / mu: 0.9912 (marginal change - not scored)wt: CTTTTTTTTTGTTCTACCCCAGGCAGCAACAGTGCCCAGGG
mu: CTTTTTTTTTGTTCTACCCCAGCCAGCAACAGTGCCCAGGG		 ccca|GGCA
Acc marginally increased2737wt: 0.9957 / mu: 0.9962 (marginal change - not scored)wt: ACCAGGTCTTTTTTTTTGTTCTACCCCAGGCAGCAACAGTG
mu: ACCAGGTCTTTTTTTTTGTTCTACCCCAGCCAGCAACAGTG		 gttc|TACC
Acc marginally increased2743wt: 0.9642 / mu: 0.9707 (marginal change - not scored)wt: TCTTTTTTTTTGTTCTACCCCAGGCAGCAACAGTGCCCAGG
mu: TCTTTTTTTTTGTTCTACCCCAGCCAGCAACAGTGCCCAGG		 cccc|AGGC
Donor increased2749wt: 0.54 / mu: 0.61wt: AGGCAGCAACAGTGC
mu: AGCCAGCAACAGTGC		 GCAG|caac
Donor marginally increased2748wt: 0.9143 / mu: 0.9188 (marginal change - not scored)wt: CAGGCAGCAACAGTG
mu: CAGCCAGCAACAGTG		 GGCA|gcaa
Acc gained27480.87mu: TTTTTTGTTCTACCCCAGCCAGCAACAGTGCCCAGGGCTCT gcca|GCAA
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      387GGKGGSCSQAACSNSAQGSDESLI
mutated  not conserved    387GGKGGSCSQAASSNSAQGSDESL
Ptroglodytes  not conserved  ENSPTRG00000041261  350GGKGGSCSQAASSNSAQGSDESL
Mmulatta  not conserved  ENSMMUG00000029841  339GGKGGSYSQAAWSNGAQGSDVSR
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1212 / 1212
position (AA) of stopcodon in wt / mu AA sequence 404 / 404
position of stopcodon in wt / mu cDNA 1212 / 1212
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 1 / 1
chromosome 6
strand -1
last intron/exon boundary 1208
theoretical NMD boundary in CDS 1157
length of CDS 1212
coding sequence (CDS) position 1160
cDNA position
(for ins/del: last normal base / first normal base)		 1160
gDNA position
(for ins/del: last normal base / first normal base)		 2746
chromosomal position
(for ins/del: last normal base / first normal base)		 31237162
original gDNA sequence snippet TTTTTTTTGTTCTACCCCAGGCAGCAACAGTGCCCAGGGCT
altered gDNA sequence snippet TTTTTTTTGTTCTACCCCAGCCAGCAACAGTGCCCAGGGCT
original cDNA sequence snippet GAGCTGCTCTCAGGCTGCGTGCAGCAACAGTGCCCAGGGCT
altered cDNA sequence snippet GAGCTGCTCTCAGGCTGCGTCCAGCAACAGTGCCCAGGGCT
wildtype AA sequence MRVMAPRALL LLLSGGLALT ETWACECGVG REAASAERSE GPPGEPRREV GRAGLSPSSP
PGSHSMRYFD TAVSRPGRGE PRFISVGYVD DTQFVRFDSD AASPRGEPRA PWVEQEGPEY
WDRETQKYKR QAQADRVSLR NLRGYYNQSE DGSHTLQRMS GCDLGPDGRL LRGYDQSAYD
GKDYIALNED LRSWTAADTA AQITQRKLEA ARAAEQLRAY LEGTCVEWLR RYLENGKETL
QRAEPPKTHV THHPLSDHEA TLRCWALGFY PAEITLTWQR DGEDQTQDTE LVETRPAGDG
TFQKWAAVVV PSGQEQRYTC HMQHEGLQEP LTLSWEPSSQ PTIPIMGIVA GLAVLVVLAV
LGAVVTAMMC RRKSSGGKGG SCSQAACSNS AQGSDESLIT CKA*
mutated AA sequence MRVMAPRALL LLLSGGLALT ETWACECGVG REAASAERSE GPPGEPRREV GRAGLSPSSP
PGSHSMRYFD TAVSRPGRGE PRFISVGYVD DTQFVRFDSD AASPRGEPRA PWVEQEGPEY
WDRETQKYKR QAQADRVSLR NLRGYYNQSE DGSHTLQRMS GCDLGPDGRL LRGYDQSAYD
GKDYIALNED LRSWTAADTA AQITQRKLEA ARAAEQLRAY LEGTCVEWLR RYLENGKETL
QRAEPPKTHV THHPLSDHEA TLRCWALGFY PAEITLTWQR DGEDQTQDTE LVETRPAGDG
TFQKWAAVVV PSGQEQRYTC HMQHEGLQEP LTLSWEPSSQ PTIPIMGIVA GLAVLVVLAV
LGAVVTAMMC RRKSSGGKGG SCSQAASSNS AQGSDESLIT CKA*
speed 0.64 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: 0.99999999999971 (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) chr6:31237162C>GN/A show variant in all transcripts   IGV
HGNC symbol HLA-C
Ensembl transcript ID ENST00000376228
Genbank transcript ID NM_002117
UniProt peptide P30501
alteration type single base exchange
alteration region CDS
DNA changes c.1049G>C
cDNA.1064G>C
g.2746G>C
AA changes C350S Score: 112 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 350
frameshift no
known variant Reference ID: rs35708511
databasehomozygous (G/G)heterozygousallele carriers
1000G15628102372
ExAC32501-32235266
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.1360
-0.4780.002
(flanking)1.8070.03
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost2745.5sequence motif lost- wt: ccca|GGCA
 mu: ccca.GCCA
Acc marginally increased2740wt: 0.9823 / mu: 0.9832 (marginal change - not scored)wt: AGGTCTTTTTTTTTGTTCTACCCCAGGCAGCAACAGTGCCC
mu: AGGTCTTTTTTTTTGTTCTACCCCAGCCAGCAACAGTGCCC		 ctac|CCCA
Acc marginally increased2741wt: 0.8732 / mu: 0.9170 (marginal change - not scored)wt: GGTCTTTTTTTTTGTTCTACCCCAGGCAGCAACAGTGCCCA
mu: GGTCTTTTTTTTTGTTCTACCCCAGCCAGCAACAGTGCCCA		 tacc|CCAG
Acc marginally increased2744wt: 0.9911 / mu: 0.9912 (marginal change - not scored)wt: CTTTTTTTTTGTTCTACCCCAGGCAGCAACAGTGCCCAGGG
mu: CTTTTTTTTTGTTCTACCCCAGCCAGCAACAGTGCCCAGGG		 ccca|GGCA
Acc marginally increased2737wt: 0.9957 / mu: 0.9962 (marginal change - not scored)wt: ACCAGGTCTTTTTTTTTGTTCTACCCCAGGCAGCAACAGTG
mu: ACCAGGTCTTTTTTTTTGTTCTACCCCAGCCAGCAACAGTG		 gttc|TACC
Acc marginally increased2743wt: 0.9642 / mu: 0.9707 (marginal change - not scored)wt: TCTTTTTTTTTGTTCTACCCCAGGCAGCAACAGTGCCCAGG
mu: TCTTTTTTTTTGTTCTACCCCAGCCAGCAACAGTGCCCAGG		 cccc|AGGC
Donor increased2749wt: 0.54 / mu: 0.61wt: AGGCAGCAACAGTGC
mu: AGCCAGCAACAGTGC		 GCAG|caac
Donor marginally increased2748wt: 0.9143 / mu: 0.9188 (marginal change - not scored)wt: CAGGCAGCAACAGTG
mu: CAGCCAGCAACAGTG		 GGCA|gcaa
Acc gained27480.87mu: TTTTTTGTTCTACCCCAGCCAGCAACAGTGCCCAGGGCTCT gcca|GCAA
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      350GGKGGSCSQAACSNSAQGSDESLI
mutated  not conserved    350GGKGGSCSQAASSNSAQGSDES
Ptroglodytes  not conserved  ENSPTRG00000041261  350GGKGGSCSQAASSNSAQGSDES
Mmulatta  not conserved  ENSMMUG00000029841  345GGKGGSYSQAAWSNGAQGSDVSR
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
334366TOPO_DOMCytoplasmic (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1101 / 1101
position (AA) of stopcodon in wt / mu AA sequence 367 / 367
position of stopcodon in wt / mu cDNA 1116 / 1116
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 16 / 16
chromosome 6
strand -1
last intron/exon boundary 1112
theoretical NMD boundary in CDS 1046
length of CDS 1101
coding sequence (CDS) position 1049
cDNA position
(for ins/del: last normal base / first normal base)		 1064
gDNA position
(for ins/del: last normal base / first normal base)		 2746
chromosomal position
(for ins/del: last normal base / first normal base)		 31237162
original gDNA sequence snippet TTTTTTTTGTTCTACCCCAGGCAGCAACAGTGCCCAGGGCT
altered gDNA sequence snippet TTTTTTTTGTTCTACCCCAGCCAGCAACAGTGCCCAGGGCT
original cDNA sequence snippet GAGCTGCTCTCAGGCTGCGTGCAGCAACAGTGCCCAGGGCT
altered cDNA sequence snippet GAGCTGCTCTCAGGCTGCGTCCAGCAACAGTGCCCAGGGCT
wildtype AA sequence MRVMAPRALL LLLSGGLALT ETWACSHSMR YFDTAVSRPG RGEPRFISVG YVDDTQFVRF
DSDAASPRGE PRAPWVEQEG PEYWDRETQK YKRQAQADRV SLRNLRGYYN QSEDGSHTLQ
RMSGCDLGPD GRLLRGYDQS AYDGKDYIAL NEDLRSWTAA DTAAQITQRK LEAARAAEQL
RAYLEGTCVE WLRRYLENGK ETLQRAEPPK THVTHHPLSD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGQEQR YTCHMQHEGL QEPLTLSWEP
SSQPTIPIMG IVAGLAVLVV LAVLGAVVTA MMCRRKSSGG KGGSCSQAAC SNSAQGSDES
LITCKA*
mutated AA sequence MRVMAPRALL LLLSGGLALT ETWACSHSMR YFDTAVSRPG RGEPRFISVG YVDDTQFVRF
DSDAASPRGE PRAPWVEQEG PEYWDRETQK YKRQAQADRV SLRNLRGYYN QSEDGSHTLQ
RMSGCDLGPD GRLLRGYDQS AYDGKDYIAL NEDLRSWTAA DTAAQITQRK LEAARAAEQL
RAYLEGTCVE WLRRYLENGK ETLQRAEPPK THVTHHPLSD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGQEQR YTCHMQHEGL QEPLTLSWEP
SSQPTIPIMG IVAGLAVLVV LAVLGAVVTA MMCRRKSSGG KGGSCSQAAS SNSAQGSDES
LITCKA*
speed 0.73 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: 0.99999999999971 (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) chr6:31237162C>GN/A show variant in all transcripts   IGV
HGNC symbol HLA-C
Ensembl transcript ID ENST00000383329
Genbank transcript ID N/A
UniProt peptide P30501
alteration type single base exchange
alteration region CDS
DNA changes c.1067G>C
cDNA.1082G>C
g.2746G>C
AA changes C356S Score: 112 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 356
frameshift no
known variant Reference ID: rs35708511
databasehomozygous (G/G)heterozygousallele carriers
1000G15628102372
ExAC32501-32235266
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.1360
-0.4780.002
(flanking)1.8070.03
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost2745.5sequence motif lost- wt: ccca|GGCA
 mu: ccca.GCCA
Acc marginally increased2740wt: 0.9823 / mu: 0.9832 (marginal change - not scored)wt: AGGTCTTTTTTTTTGTTCTACCCCAGGCAGCAACAGTGCCC
mu: AGGTCTTTTTTTTTGTTCTACCCCAGCCAGCAACAGTGCCC		 ctac|CCCA
Acc marginally increased2741wt: 0.8732 / mu: 0.9170 (marginal change - not scored)wt: GGTCTTTTTTTTTGTTCTACCCCAGGCAGCAACAGTGCCCA
mu: GGTCTTTTTTTTTGTTCTACCCCAGCCAGCAACAGTGCCCA		 tacc|CCAG
Acc marginally increased2744wt: 0.9911 / mu: 0.9912 (marginal change - not scored)wt: CTTTTTTTTTGTTCTACCCCAGGCAGCAACAGTGCCCAGGG
mu: CTTTTTTTTTGTTCTACCCCAGCCAGCAACAGTGCCCAGGG		 ccca|GGCA
Acc marginally increased2737wt: 0.9957 / mu: 0.9962 (marginal change - not scored)wt: ACCAGGTCTTTTTTTTTGTTCTACCCCAGGCAGCAACAGTG
mu: ACCAGGTCTTTTTTTTTGTTCTACCCCAGCCAGCAACAGTG		 gttc|TACC
Acc marginally increased2743wt: 0.9642 / mu: 0.9707 (marginal change - not scored)wt: TCTTTTTTTTTGTTCTACCCCAGGCAGCAACAGTGCCCAGG
mu: TCTTTTTTTTTGTTCTACCCCAGCCAGCAACAGTGCCCAGG		 cccc|AGGC
Donor increased2749wt: 0.54 / mu: 0.61wt: AGGCAGCAACAGTGC
mu: AGCCAGCAACAGTGC		 GCAG|caac
Donor marginally increased2748wt: 0.9143 / mu: 0.9188 (marginal change - not scored)wt: CAGGCAGCAACAGTG
mu: CAGCCAGCAACAGTG		 GGCA|gcaa
Acc gained27480.87mu: TTTTTTGTTCTACCCCAGCCAGCAACAGTGCCCAGGGCTCT gcca|GCAA
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      356GGKGGSCSQAACSNSAQGSDESLI
mutated  not conserved    356GGKGGSCSQAASSNSA
Ptroglodytes  not conserved  ENSPTRG00000041261  356GGKGGSCSQAASSNSA
Mmulatta  not conserved  ENSMMUG00000029841  351GGKGGSYSQAAWSNGAQG
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
334366TOPO_DOMCytoplasmic (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1119 / 1119
position (AA) of stopcodon in wt / mu AA sequence 373 / 373
position of stopcodon in wt / mu cDNA 1134 / 1134
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 16 / 16
chromosome 6
strand -1
last intron/exon boundary 1130
theoretical NMD boundary in CDS 1064
length of CDS 1119
coding sequence (CDS) position 1067
cDNA position
(for ins/del: last normal base / first normal base)		 1082
gDNA position
(for ins/del: last normal base / first normal base)		 2746
chromosomal position
(for ins/del: last normal base / first normal base)		 31237162
original gDNA sequence snippet TTTTTTTTGTTCTACCCCAGGCAGCAACAGTGCCCAGGGCT
altered gDNA sequence snippet TTTTTTTTGTTCTACCCCAGCCAGCAACAGTGCCCAGGGCT
original cDNA sequence snippet GAGCTGCTCTCAGGCTGCGTGCAGCAACAGTGCCCAGGGCT
altered cDNA sequence snippet GAGCTGCTCTCAGGCTGCGTCCAGCAACAGTGCCCAGGGCT
wildtype AA sequence MRVMAPRALL LLLSGGLALT ETWACSHSMR YFDTAVSRPG RGEPRFISVG YVDDTQFVRF
DSDAASPRGE PRAPWVEQEG PEYWDRETQK YKRQAQADRV SLRNLRGYYN QSEDGSHTLQ
RMSGCDLGPD GRLLRGYDQS AYDGKDYIAL NEDLRSWTAA DTAAQITQRK LEAARAAEQL
RAYLEGTCVE WLRRYLENGK ETLQRAEPPK THVTHHPLSD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGQEQR YTCHMQHEGL QEPLTLSWEP
SSQPTIPIMG IVAGLAVLVV LAVLGAVVTA MMCRRKSSGH FLPTGGKGGS CSQAACSNSA
QGSDESLITC KA*
mutated AA sequence MRVMAPRALL LLLSGGLALT ETWACSHSMR YFDTAVSRPG RGEPRFISVG YVDDTQFVRF
DSDAASPRGE PRAPWVEQEG PEYWDRETQK YKRQAQADRV SLRNLRGYYN QSEDGSHTLQ
RMSGCDLGPD GRLLRGYDQS AYDGKDYIAL NEDLRSWTAA DTAAQITQRK LEAARAAEQL
RAYLEGTCVE WLRRYLENGK ETLQRAEPPK THVTHHPLSD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGQEQR YTCHMQHEGL QEPLTLSWEP
SSQPTIPIMG IVAGLAVLVV LAVLGAVVTA MMCRRKSSGH FLPTGGKGGS CSQAASSNSA
QGSDESLITC KA*
speed 0.87 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: 0.999999999987455 (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) chr6:31237162C>GN/A show variant in all transcripts   IGV
HGNC symbol HLA-C
Ensembl transcript ID ENST00000396254
Genbank transcript ID N/A
UniProt peptide P30501
alteration type single base exchange
alteration region CDS
DNA changes c.1045G>C
cDNA.1060G>C
g.2746G>C
AA changes A349P Score: 27 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 349
frameshift no
known variant Reference ID: rs35708511
databasehomozygous (G/G)heterozygousallele carriers
1000G15628102372
ExAC32501-32235266
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.1360
-0.4780.002
(flanking)1.8070.03
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost2745.5sequence motif lost- wt: ccca|GGCA
 mu: ccca.GCCA
Acc marginally increased2740wt: 0.9823 / mu: 0.9832 (marginal change - not scored)wt: AGGTCTTTTTTTTTGTTCTACCCCAGGCAGCAACAGTGCCC
mu: AGGTCTTTTTTTTTGTTCTACCCCAGCCAGCAACAGTGCCC		 ctac|CCCA
Acc marginally increased2741wt: 0.8732 / mu: 0.9170 (marginal change - not scored)wt: GGTCTTTTTTTTTGTTCTACCCCAGGCAGCAACAGTGCCCA
mu: GGTCTTTTTTTTTGTTCTACCCCAGCCAGCAACAGTGCCCA		 tacc|CCAG
Acc marginally increased2744wt: 0.9911 / mu: 0.9912 (marginal change - not scored)wt: CTTTTTTTTTGTTCTACCCCAGGCAGCAACAGTGCCCAGGG
mu: CTTTTTTTTTGTTCTACCCCAGCCAGCAACAGTGCCCAGGG		 ccca|GGCA
Acc marginally increased2737wt: 0.9957 / mu: 0.9962 (marginal change - not scored)wt: ACCAGGTCTTTTTTTTTGTTCTACCCCAGGCAGCAACAGTG
mu: ACCAGGTCTTTTTTTTTGTTCTACCCCAGCCAGCAACAGTG		 gttc|TACC
Acc marginally increased2743wt: 0.9642 / mu: 0.9707 (marginal change - not scored)wt: TCTTTTTTTTTGTTCTACCCCAGGCAGCAACAGTGCCCAGG
mu: TCTTTTTTTTTGTTCTACCCCAGCCAGCAACAGTGCCCAGG		 cccc|AGGC
Donor increased2749wt: 0.54 / mu: 0.61wt: AGGCAGCAACAGTGC
mu: AGCCAGCAACAGTGC		 GCAG|caac
Donor marginally increased2748wt: 0.9143 / mu: 0.9188 (marginal change - not scored)wt: CAGGCAGCAACAGTG
mu: CAGCCAGCAACAGTG		 GGCA|gcaa
Acc gained27480.87mu: TTTTTTGTTCTACCCCAGCCAGCAACAGTGCCCAGGGCTCT gcca|GCAA
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      349SGREGVKSGVWAATVPRALMSLSS
mutated  not conserved    349SGREGVKSGVWPATVPRALMSLS
Ptroglodytes  no alignment  ENSPTRG00000041261  n/a
Mmulatta  no alignment  ENSMMUG00000029841  n/a
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
334366TOPO_DOMCytoplasmic (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1194 / 1194
position (AA) of stopcodon in wt / mu AA sequence 398 / 398
position of stopcodon in wt / mu cDNA 1209 / 1209
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 16 / 16
chromosome 6
strand -1
last intron/exon boundary 1108
theoretical NMD boundary in CDS 1042
length of CDS 1194
coding sequence (CDS) position 1045
cDNA position
(for ins/del: last normal base / first normal base)		 1060
gDNA position
(for ins/del: last normal base / first normal base)		 2746
chromosomal position
(for ins/del: last normal base / first normal base)		 31237162
original gDNA sequence snippet TTTTTTTTGTTCTACCCCAGGCAGCAACAGTGCCCAGGGCT
altered gDNA sequence snippet TTTTTTTTGTTCTACCCCAGCCAGCAACAGTGCCCAGGGCT
original cDNA sequence snippet GGGTGAAGAGCGGGGTCTGGGCAGCAACAGTGCCCAGGGCT
altered cDNA sequence snippet GGGTGAAGAGCGGGGTCTGGCCAGCAACAGTGCCCAGGGCT
wildtype AA sequence MRVMAPRALL LLLSGGLALT ETWACSHSMR YFDTAVSRPG RGEPRFISVG YVDDTQFVRF
DSDAASPRGE PRAPWVEQEG PEYWDRETQK YKRQAQADRV SLRNLRGYYN QSEDGSHTLQ
RMSGCDLGPD GRLLRGYDQS AYDGKDYIAL NEDLRSWTAA DTAAQITQRK LEAARAAEQL
RAYLEGTCVE WLRRYLENGK ETLQRAEPPK THVTHHPLSD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGQEQR YTCHMQHEGL QEPLTLSWEP
SSQPTIPIMG IVAGLAVLVV LAVLGAVVTA MMCRRKSSGR EGVKSGVWAA TVPRALMSLS
SLVKPETAAC VGLRCRISSH LSFVTSRASG ISFCKGT*
mutated AA sequence MRVMAPRALL LLLSGGLALT ETWACSHSMR YFDTAVSRPG RGEPRFISVG YVDDTQFVRF
DSDAASPRGE PRAPWVEQEG PEYWDRETQK YKRQAQADRV SLRNLRGYYN QSEDGSHTLQ
RMSGCDLGPD GRLLRGYDQS AYDGKDYIAL NEDLRSWTAA DTAAQITQRK LEAARAAEQL
RAYLEGTCVE WLRRYLENGK ETLQRAEPPK THVTHHPLSD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGQEQR YTCHMQHEGL QEPLTLSWEP
SSQPTIPIMG IVAGLAVLVV LAVLGAVVTA MMCRRKSSGR EGVKSGVWPA TVPRALMSLS
SLVKPETAAC VGLRCRISSH LSFVTSRASG ISFCKGT*
speed 0.67 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
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Problems