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 4.704258 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
HLA-Cpolymorphism_automatic9.12048214729566e-13simple_aaeaffectedG16Asingle base exchangers1050451show file
HLA-Cpolymorphism_automatic9.12048214729566e-13simple_aaeaffectedG16Asingle base exchangers1050451show file
HLA-Cpolymorphism_automatic9.12048214729566e-13simple_aaeaffectedG16Asingle base exchangers1050451show file
HLA-Cpolymorphism_automatic9.12048214729566e-13simple_aaeaffectedG16Asingle base exchangers1050451show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999088 (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) chr6:31239802C>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.47G>C
cDNA.62G>C
g.106G>C
AA changes G16A Score: 60 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 16
frameshift no
known variant Reference ID: rs1050451
databasehomozygous (G/G)heterozygousallele carriers
1000G15318352366
ExAC31160-295531607
regulatory features Cfos, Transcription Factor, Cfos TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2AK9ac, Histone, Histone 2A Lysine 9 Acetylation
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
H3K36ac, Histone, Histone 3 Lysine 36 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 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
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
HNF4A, Transcription Factor, HNF4A Transcription Factor Binding
POU2F2, Transcription Factor, POU2F2 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)0.210.218
-0.0540.129
(flanking)0.5990.113
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 increased100wt: 0.7031 / mu: 0.7230 (marginal change - not scored)wt: AGCCCTCCTCCTGCTGCTCTCGGGAGGCCTGGCCCTGACCG
mu: AGCCCTCCTCCTGCTGCTCTCGGGAGCCCTGGCCCTGACCG		 tctc|GGGA
Acc marginally increased98wt: 0.4346 / mu: 0.4374 (marginal change - not scored)wt: CGAGCCCTCCTCCTGCTGCTCTCGGGAGGCCTGGCCCTGAC
mu: CGAGCCCTCCTCCTGCTGCTCTCGGGAGCCCTGGCCCTGAC		 gctc|TCGG
Donor increased99wt: 0.54 / mu: 0.70wt: TGCTCTCGGGAGGCC
mu: TGCTCTCGGGAGCCC		 CTCT|cggg
distance from splice site 27
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      16APRALLLLLSGGLALTETWACSHS
mutated  not conserved    16APRALLLLLSGALALTETWACSH
Ptroglodytes  not conserved  ENSPTRG00000041261  16APRTLILLLSGALALTETWAGSH
Mmulatta  not conserved  ENSMMUG00000029841  16APRTLLLLLSGALALTETWAGSH
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 
124SIGNALlost
25114REGIONAlpha-1.might get lost (downstream of altered splice site)
25308TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
8383MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
110110CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
115206REGIONAlpha-2.might get lost (downstream of altered splice site)
125125DISULFIDBy similarity.might get lost (downstream of altered splice site)
188188DISULFIDBy similarity.might get lost (downstream of altered splice site)
207298REGIONAlpha-3.might get lost (downstream of altered splice site)
209297DOMAINIg-like C1-type.might get lost (downstream of altered splice site)
227227DISULFIDBy similarity.might get lost (downstream of altered splice site)
283283DISULFIDBy similarity.might get lost (downstream of altered splice site)
299308REGIONConnecting peptide.might get lost (downstream of altered splice site)
309333TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
334366TOPO_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 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 47
cDNA position
(for ins/del: last normal base / first normal base)		 62
gDNA position
(for ins/del: last normal base / first normal base)		 106
chromosomal position
(for ins/del: last normal base / first normal base)		 31239802
original gDNA sequence snippet CCTCCTGCTGCTCTCGGGAGGCCTGGCCCTGACCGAGACCT
altered gDNA sequence snippet CCTCCTGCTGCTCTCGGGAGCCCTGGCCCTGACCGAGACCT
original cDNA sequence snippet CCTCCTGCTGCTCTCGGGAGGCCTGGCCCTGACCGAGACCT
altered cDNA sequence snippet CCTCCTGCTGCTCTCGGGAGCCCTGGCCCTGACCGAGACCT
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 LLLSGALALT 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*
speed 0.81 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: 0.999999999999088 (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) chr6:31239802C>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.47G>C
cDNA.62G>C
g.106G>C
AA changes G16A Score: 60 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 16
frameshift no
known variant Reference ID: rs1050451
databasehomozygous (G/G)heterozygousallele carriers
1000G15318352366
ExAC31160-295531607
regulatory features Cfos, Transcription Factor, Cfos TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2AK9ac, Histone, Histone 2A Lysine 9 Acetylation
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
H3K36ac, Histone, Histone 3 Lysine 36 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 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
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
HNF4A, Transcription Factor, HNF4A Transcription Factor Binding
POU2F2, Transcription Factor, POU2F2 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)0.210.218
-0.0540.129
(flanking)0.5990.113
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 increased100wt: 0.7031 / mu: 0.7230 (marginal change - not scored)wt: AGCCCTCCTCCTGCTGCTCTCGGGAGGCCTGGCCCTGACCG
mu: AGCCCTCCTCCTGCTGCTCTCGGGAGCCCTGGCCCTGACCG		 tctc|GGGA
Acc marginally increased98wt: 0.4346 / mu: 0.4374 (marginal change - not scored)wt: CGAGCCCTCCTCCTGCTGCTCTCGGGAGGCCTGGCCCTGAC
mu: CGAGCCCTCCTCCTGCTGCTCTCGGGAGCCCTGGCCCTGAC		 gctc|TCGG
Donor increased99wt: 0.54 / mu: 0.70wt: TGCTCTCGGGAGGCC
mu: TGCTCTCGGGAGCCC		 CTCT|cggg
distance from splice site 27
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      16APRALLLLLSGGLALTETWACSHS
mutated  not conserved    16APRALLLLLSGALALTETWACSH
Ptroglodytes  not conserved  ENSPTRG00000041261  16APRTLILLLSGALALTETWAGSH
Mmulatta  not conserved  ENSMMUG00000029841  16APRTLLLLLSGALALTETWAGSH
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 
124SIGNALlost
25114REGIONAlpha-1.might get lost (downstream of altered splice site)
25308TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
8383MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
110110CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
115206REGIONAlpha-2.might get lost (downstream of altered splice site)
125125DISULFIDBy similarity.might get lost (downstream of altered splice site)
188188DISULFIDBy similarity.might get lost (downstream of altered splice site)
207298REGIONAlpha-3.might get lost (downstream of altered splice site)
209297DOMAINIg-like C1-type.might get lost (downstream of altered splice site)
227227DISULFIDBy similarity.might get lost (downstream of altered splice site)
283283DISULFIDBy similarity.might get lost (downstream of altered splice site)
299308REGIONConnecting peptide.might get lost (downstream of altered splice site)
309333TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
334366TOPO_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 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 47
cDNA position
(for ins/del: last normal base / first normal base)		 62
gDNA position
(for ins/del: last normal base / first normal base)		 106
chromosomal position
(for ins/del: last normal base / first normal base)		 31239802
original gDNA sequence snippet CCTCCTGCTGCTCTCGGGAGGCCTGGCCCTGACCGAGACCT
altered gDNA sequence snippet CCTCCTGCTGCTCTCGGGAGCCCTGGCCCTGACCGAGACCT
original cDNA sequence snippet CCTCCTGCTGCTCTCGGGAGGCCTGGCCCTGACCGAGACCT
altered cDNA sequence snippet CCTCCTGCTGCTCTCGGGAGCCCTGGCCCTGACCGAGACCT
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 LLLSGALALT 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*
speed 0.81 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: 0.999999999999088 (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) chr6:31239802C>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.47G>C
cDNA.62G>C
g.106G>C
AA changes G16A Score: 60 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 16
frameshift no
known variant Reference ID: rs1050451
databasehomozygous (G/G)heterozygousallele carriers
1000G15318352366
ExAC31160-295531607
regulatory features Cfos, Transcription Factor, Cfos TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2AK9ac, Histone, Histone 2A Lysine 9 Acetylation
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
H3K36ac, Histone, Histone 3 Lysine 36 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 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
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
HNF4A, Transcription Factor, HNF4A Transcription Factor Binding
POU2F2, Transcription Factor, POU2F2 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)0.210.218
-0.0540.129
(flanking)0.5990.113
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 increased100wt: 0.7031 / mu: 0.7230 (marginal change - not scored)wt: AGCCCTCCTCCTGCTGCTCTCGGGAGGCCTGGCCCTGACCG
mu: AGCCCTCCTCCTGCTGCTCTCGGGAGCCCTGGCCCTGACCG		 tctc|GGGA
Acc marginally increased98wt: 0.4346 / mu: 0.4374 (marginal change - not scored)wt: CGAGCCCTCCTCCTGCTGCTCTCGGGAGGCCTGGCCCTGAC
mu: CGAGCCCTCCTCCTGCTGCTCTCGGGAGCCCTGGCCCTGAC		 gctc|TCGG
Donor increased99wt: 0.54 / mu: 0.70wt: TGCTCTCGGGAGGCC
mu: TGCTCTCGGGAGCCC		 CTCT|cggg
distance from splice site 27
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      16APRALLLLLSGGLALTETWACSHS
mutated  not conserved    16APRALLLLLSGALALTETWACSH
Ptroglodytes  not conserved  ENSPTRG00000041261  16APRTLILLLSGALALTETWAGSH
Mmulatta  not conserved  ENSMMUG00000029841  16APRTLLLLLSGALALTETWAGSH
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 
124SIGNALlost
25114REGIONAlpha-1.might get lost (downstream of altered splice site)
25308TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
8383MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
110110CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
115206REGIONAlpha-2.might get lost (downstream of altered splice site)
125125DISULFIDBy similarity.might get lost (downstream of altered splice site)
188188DISULFIDBy similarity.might get lost (downstream of altered splice site)
207298REGIONAlpha-3.might get lost (downstream of altered splice site)
209297DOMAINIg-like C1-type.might get lost (downstream of altered splice site)
227227DISULFIDBy similarity.might get lost (downstream of altered splice site)
283283DISULFIDBy similarity.might get lost (downstream of altered splice site)
299308REGIONConnecting peptide.might get lost (downstream of altered splice site)
309333TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
334366TOPO_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 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 47
cDNA position
(for ins/del: last normal base / first normal base)		 62
gDNA position
(for ins/del: last normal base / first normal base)		 106
chromosomal position
(for ins/del: last normal base / first normal base)		 31239802
original gDNA sequence snippet CCTCCTGCTGCTCTCGGGAGGCCTGGCCCTGACCGAGACCT
altered gDNA sequence snippet CCTCCTGCTGCTCTCGGGAGCCCTGGCCCTGACCGAGACCT
original cDNA sequence snippet CCTCCTGCTGCTCTCGGGAGGCCTGGCCCTGACCGAGACCT
altered cDNA sequence snippet CCTCCTGCTGCTCTCGGGAGCCCTGGCCCTGACCGAGACCT
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 LLLSGALALT 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*
speed 0.77 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: 0.999999999999088 (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) chr6:31239802C>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.47G>C
cDNA.47G>C
g.106G>C
AA changes G16A Score: 60 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 16
frameshift no
known variant Reference ID: rs1050451
databasehomozygous (G/G)heterozygousallele carriers
1000G15318352366
ExAC31160-295531607
regulatory features Cfos, Transcription Factor, Cfos TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2AK9ac, Histone, Histone 2A Lysine 9 Acetylation
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
H3K36ac, Histone, Histone 3 Lysine 36 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 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
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
HNF4A, Transcription Factor, HNF4A Transcription Factor Binding
POU2F2, Transcription Factor, POU2F2 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)0.210.218
-0.0540.129
(flanking)0.5990.113
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 increased100wt: 0.7031 / mu: 0.7230 (marginal change - not scored)wt: AGCCCTCCTCCTGCTGCTCTCGGGAGGCCTGGCCCTGACCG
mu: AGCCCTCCTCCTGCTGCTCTCGGGAGCCCTGGCCCTGACCG		 tctc|GGGA
Acc marginally increased98wt: 0.4346 / mu: 0.4374 (marginal change - not scored)wt: CGAGCCCTCCTCCTGCTGCTCTCGGGAGGCCTGGCCCTGAC
mu: CGAGCCCTCCTCCTGCTGCTCTCGGGAGCCCTGGCCCTGAC		 gctc|TCGG
Donor increased99wt: 0.54 / mu: 0.70wt: TGCTCTCGGGAGGCC
mu: TGCTCTCGGGAGCCC		 CTCT|cggg
distance from splice site 47
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      16APRALLLLLSGGLALTETWACECG
mutated  not conserved    16APRALLLLLSGALALTETWACEC
Ptroglodytes  not conserved  ENSPTRG00000041261  16APRTLILLLSGALALTETWA---
Mmulatta  not conserved  ENSMMUG00000029841  16APRTLLLLLSGALALTETWA---
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 
124SIGNALlost
25114REGIONAlpha-1.might get lost (downstream of altered splice site)
25308TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
8383MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
110110CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
115206REGIONAlpha-2.might get lost (downstream of altered splice site)
125125DISULFIDBy similarity.might get lost (downstream of altered splice site)
188188DISULFIDBy similarity.might get lost (downstream of altered splice site)
207298REGIONAlpha-3.might get lost (downstream of altered splice site)
209297DOMAINIg-like C1-type.might get lost (downstream of altered splice site)
227227DISULFIDBy similarity.might get lost (downstream of altered splice site)
283283DISULFIDBy similarity.might get lost (downstream of altered splice site)
299308REGIONConnecting peptide.might get lost (downstream of altered splice site)
309333TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
334366TOPO_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 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 47
cDNA position
(for ins/del: last normal base / first normal base)		 47
gDNA position
(for ins/del: last normal base / first normal base)		 106
chromosomal position
(for ins/del: last normal base / first normal base)		 31239802
original gDNA sequence snippet CCTCCTGCTGCTCTCGGGAGGCCTGGCCCTGACCGAGACCT
altered gDNA sequence snippet CCTCCTGCTGCTCTCGGGAGCCCTGGCCCTGACCGAGACCT
original cDNA sequence snippet CCTCCTGCTGCTCTCGGGAGGCCTGGCCCTGACCGAGACCT
altered cDNA sequence snippet CCTCCTGCTGCTCTCGGGAGCCCTGGCCCTGACCGAGACCT
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 LLLSGALALT 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*
speed 1.02 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