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: ENST00000396634
Querying Taster for transcript #2: ENST00000376806
Querying Taster for transcript #3: ENST00000376802
Querying Taster for transcript #4: ENST00000376809
MT speed 4.86 s - this script 8.06759 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
HLA-Apolymorphism_automatic2.56017429478561e-13simple_aaeaffectedQ86Esingle base exchangers1059455show file
HLA-Apolymorphism_automatic2.56017429478561e-13simple_aaeaffectedQ86Esingle base exchangers1059455show file
HLA-Apolymorphism_automatic2.56017429478561e-13simple_aaeaffectedQ86Esingle base exchangers1059455show file
HLA-Apolymorphism_automatic2.56017429478561e-13simple_aaeaffectedQ86Esingle base exchangers1059455show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999744 (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) chr6:29910716C>GN/A show variant in all transcripts   IGV
HGNC symbol HLA-A
Ensembl transcript ID ENST00000396634
Genbank transcript ID NM_002116
UniProt peptide P10314
alteration type single base exchange
alteration region CDS
DNA changes c.256C>G
cDNA.597C>G
g.1680C>G
AA changes Q86E Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS
86
frameshift no
known variant Reference ID: rs1059455
databasehomozygous (G/G)heterozygousallele carriers
1000G38411971581
ExAC68601904725907
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2AK9ac, Histone, Histone 2A Lysine 9 Acetylation
H2BK20ac, Histone, Histone 2B Lysine 20 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
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
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.6030
-2.4270
(flanking)-1.970
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased1679wt: 0.40 / mu: 0.95wt: TGGGACCAGGAGACA
mu: TGGGACGAGGAGACA
 GGAC|cagg
Donor increased1676wt: 0.54 / mu: 0.98wt: TATTGGGACCAGGAG
mu: TATTGGGACGAGGAG
 TTGG|gacc
Donor gained16740.88mu: AGTATTGGGACGAGG TATT|ggga
distance from splice site 88
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      86WIEQEGPEYWDQETRNVKAQSQTD
mutated  all conserved    86WIEQEGPEYWDEETRNVKAQSQT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000029875  86WMEQEGPEYWDQNTRICKADTQT
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 
25114REGIONAlpha-1.lost
25308TOPO_DOMExtracellular (Potential).lost
110110CARBOHYDN-linked (GlcNAc...) (By similarity).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)
209295DOMAINIg-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)
309332TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
333365TOPO_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 1098 / 1098
position (AA) of stopcodon in wt / mu AA sequence 366 / 366
position of stopcodon in wt / mu cDNA 1439 / 1439
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 342 / 342
chromosome 6
strand 1
last intron/exon boundary 1435
theoretical NMD boundary in CDS 1043
length of CDS 1098
coding sequence (CDS) position 256
cDNA position
(for ins/del: last normal base / first normal base)
597
gDNA position
(for ins/del: last normal base / first normal base)
1680
chromosomal position
(for ins/del: last normal base / first normal base)
29910716
original gDNA sequence snippet AGGGGCCGGAGTATTGGGACCAGGAGACACGGAATGTGAAG
altered gDNA sequence snippet AGGGGCCGGAGTATTGGGACGAGGAGACACGGAATGTGAAG
original cDNA sequence snippet AGGGGCCGGAGTATTGGGACCAGGAGACACGGAATGTGAAG
altered cDNA sequence snippet AGGGGCCGGAGTATTGGGACGAGGAGACACGGAATGTGAAG
wildtype AA sequence MAVMAPRTLL LLLSGALALT QTWAGSHSMR YFFTSVSRPG RGEPRFIAVG YVDDTQFVRF
DSDAASQRME PRAPWIEQEG PEYWDQETRN VKAQSQTDRV DLGTLRGYYN QSEAGSHTIQ
IMYGCDVGSD GRFLRGYRQD AYDGKDYIAL NEDLRSWTAA DMAAQITKRK WEAAHEAEQL
RAYLDGTCVE WLRRYLENGK ETLQRTDPPK THMTHHPISD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGEEQR YTCHVQHEGL PKPLTLRWEL
SSQPTIPIVG IIAGLVLLGA VITGAVVAAV MWRRKSSDRK GGSYTQAASS DSAQGSDVSL
TACKV*
mutated AA sequence MAVMAPRTLL LLLSGALALT QTWAGSHSMR YFFTSVSRPG RGEPRFIAVG YVDDTQFVRF
DSDAASQRME PRAPWIEQEG PEYWDEETRN VKAQSQTDRV DLGTLRGYYN QSEAGSHTIQ
IMYGCDVGSD GRFLRGYRQD AYDGKDYIAL NEDLRSWTAA DMAAQITKRK WEAAHEAEQL
RAYLDGTCVE WLRRYLENGK ETLQRTDPPK THMTHHPISD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGEEQR YTCHVQHEGL PKPLTLRWEL
SSQPTIPIVG IIAGLVLLGA VITGAVVAAV MWRRKSSDRK GGSYTQAASS DSAQGSDVSL
TACKV*
speed 1.46 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: 0.999999999999744 (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) chr6:29910716C>GN/A show variant in all transcripts   IGV
HGNC symbol HLA-A
Ensembl transcript ID ENST00000376806
Genbank transcript ID N/A
UniProt peptide P10314
alteration type single base exchange
alteration region CDS
DNA changes c.256C>G
cDNA.565C>G
g.1680C>G
AA changes Q86E Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS
86
frameshift no
known variant Reference ID: rs1059455
databasehomozygous (G/G)heterozygousallele carriers
1000G38411971581
ExAC68601904725907
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2AK9ac, Histone, Histone 2A Lysine 9 Acetylation
H2BK20ac, Histone, Histone 2B Lysine 20 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
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
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.6030
-2.4270
(flanking)-1.970
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased1679wt: 0.40 / mu: 0.95wt: TGGGACCAGGAGACA
mu: TGGGACGAGGAGACA
 GGAC|cagg
Donor increased1676wt: 0.54 / mu: 0.98wt: TATTGGGACCAGGAG
mu: TATTGGGACGAGGAG
 TTGG|gacc
Donor gained16740.88mu: AGTATTGGGACGAGG TATT|ggga
distance from splice site 88
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      86WIEQEGPEYWDQETRNVKAQSQTD
mutated  all conserved    86WIEQEGPEYWDEETRNVKAQSQT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000029875  86WMEQEGPEYWDQNTRICKADTQT
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 
25114REGIONAlpha-1.lost
25308TOPO_DOMExtracellular (Potential).lost
110110CARBOHYDN-linked (GlcNAc...) (By similarity).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)
209295DOMAINIg-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)
309332TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
333365TOPO_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 1116 / 1116
position (AA) of stopcodon in wt / mu AA sequence 372 / 372
position of stopcodon in wt / mu cDNA 1425 / 1425
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 310 / 310
chromosome 6
strand 1
last intron/exon boundary 1421
theoretical NMD boundary in CDS 1061
length of CDS 1116
coding sequence (CDS) position 256
cDNA position
(for ins/del: last normal base / first normal base)
565
gDNA position
(for ins/del: last normal base / first normal base)
1680
chromosomal position
(for ins/del: last normal base / first normal base)
29910716
original gDNA sequence snippet AGGGGCCGGAGTATTGGGACCAGGAGACACGGAATGTGAAG
altered gDNA sequence snippet AGGGGCCGGAGTATTGGGACGAGGAGACACGGAATGTGAAG
original cDNA sequence snippet AGGGGCCGGAGTATTGGGACCAGGAGACACGGAATGTGAAG
altered cDNA sequence snippet AGGGGCCGGAGTATTGGGACGAGGAGACACGGAATGTGAAG
wildtype AA sequence MAVMAPRTLL LLLSGALALT QTWAGSHSMR YFFTSVSRPG RGEPRFIAVG YVDDTQFVRF
DSDAASQRME PRAPWIEQEG PEYWDQETRN VKAQSQTDRV DLGTLRGYYN QSEAGSHTIQ
IMYGCDVGSD GRFLRGYRQD AYDGKDYIAL NEDLRSWTAA DMAAQITKRK WEAAHEAEQL
RAYLDGTCVE WLRRYLENGK ETLQRTDPPK THMTHHPISD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGEEQR YTCHVQHEGL PKPLTLRWEL
SSQPTIPIVG IIAGLVLLGA VITGAVVAAV MWRRKSSGGE GVKDRKGGSY TQAASSDSAQ
GSDVSLTACK V*
mutated AA sequence MAVMAPRTLL LLLSGALALT QTWAGSHSMR YFFTSVSRPG RGEPRFIAVG YVDDTQFVRF
DSDAASQRME PRAPWIEQEG PEYWDEETRN VKAQSQTDRV DLGTLRGYYN QSEAGSHTIQ
IMYGCDVGSD GRFLRGYRQD AYDGKDYIAL NEDLRSWTAA DMAAQITKRK WEAAHEAEQL
RAYLDGTCVE WLRRYLENGK ETLQRTDPPK THMTHHPISD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGEEQR YTCHVQHEGL PKPLTLRWEL
SSQPTIPIVG IIAGLVLLGA VITGAVVAAV MWRRKSSGGE GVKDRKGGSY TQAASSDSAQ
GSDVSLTACK V*
speed 0.99 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: 0.999999999999744 (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) chr6:29910716C>GN/A show variant in all transcripts   IGV
HGNC symbol HLA-A
Ensembl transcript ID ENST00000376802
Genbank transcript ID N/A
UniProt peptide P10314
alteration type single base exchange
alteration region CDS
DNA changes c.256C>G
cDNA.261C>G
g.1680C>G
AA changes Q86E Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS
86
frameshift no
known variant Reference ID: rs1059455
databasehomozygous (G/G)heterozygousallele carriers
1000G38411971581
ExAC68601904725907
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2AK9ac, Histone, Histone 2A Lysine 9 Acetylation
H2BK20ac, Histone, Histone 2B Lysine 20 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
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
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.6030
-2.4270
(flanking)-1.970
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased1679wt: 0.40 / mu: 0.95wt: TGGGACCAGGAGACA
mu: TGGGACGAGGAGACA
 GGAC|cagg
Donor increased1676wt: 0.54 / mu: 0.98wt: TATTGGGACCAGGAG
mu: TATTGGGACGAGGAG
 TTGG|gacc
Donor gained16740.88mu: AGTATTGGGACGAGG TATT|ggga
distance from splice site 88
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      86WIEQEGPEYWDQETRNVKAQSQTD
mutated  all conserved    86WIEQEGPEYWDEETRNVKAQSQT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000029875  86WMEQEGPEYWDQNTRICKADTQT
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 
25114REGIONAlpha-1.lost
25308TOPO_DOMExtracellular (Potential).lost
110110CARBOHYDN-linked (GlcNAc...) (By similarity).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)
209295DOMAINIg-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)
309332TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
333365TOPO_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 900 / 900
position (AA) of stopcodon in wt / mu AA sequence 300 / 300
position of stopcodon in wt / mu cDNA 905 / 905
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 6 / 6
chromosome 6
strand 1
last intron/exon boundary 901
theoretical NMD boundary in CDS 845
length of CDS 900
coding sequence (CDS) position 256
cDNA position
(for ins/del: last normal base / first normal base)
261
gDNA position
(for ins/del: last normal base / first normal base)
1680
chromosomal position
(for ins/del: last normal base / first normal base)
29910716
original gDNA sequence snippet AGGGGCCGGAGTATTGGGACCAGGAGACACGGAATGTGAAG
altered gDNA sequence snippet AGGGGCCGGAGTATTGGGACGAGGAGACACGGAATGTGAAG
original cDNA sequence snippet AGGGGCCGGAGTATTGGGACCAGGAGACACGGAATGTGAAG
altered cDNA sequence snippet AGGGGCCGGAGTATTGGGACGAGGAGACACGGAATGTGAAG
wildtype AA sequence MAVMAPRTLL LLLSGALALT QTWAGSHSMR YFFTSVSRPG RGEPRFIAVG YVDDTQFVRF
DSDAASQRME PRAPWIEQEG PEYWDQETRN VKAQSQTDRV DLGTLRGYYN QSEAGSHTIQ
IMYGCDVGSD GRFLRGYRQD AYDGKDYIAL NEDLRSWTAA DMAAQITKRK WEAAHEAEQL
RAYLDGTCVE WLRRYLENGK ETLQRTDPPK THMTHHPISD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGEEQR YTCHVQHEGL PKPLTLRWV*
mutated AA sequence MAVMAPRTLL LLLSGALALT QTWAGSHSMR YFFTSVSRPG RGEPRFIAVG YVDDTQFVRF
DSDAASQRME PRAPWIEQEG PEYWDEETRN VKAQSQTDRV DLGTLRGYYN QSEAGSHTIQ
IMYGCDVGSD GRFLRGYRQD AYDGKDYIAL NEDLRSWTAA DMAAQITKRK WEAAHEAEQL
RAYLDGTCVE WLRRYLENGK ETLQRTDPPK THMTHHPISD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGEEQR YTCHVQHEGL PKPLTLRWV*
speed 1.46 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: 0.999999999999744 (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) chr6:29910716C>GN/A show variant in all transcripts   IGV
HGNC symbol HLA-A
Ensembl transcript ID ENST00000376809
Genbank transcript ID N/A
UniProt peptide P10314
alteration type single base exchange
alteration region CDS
DNA changes c.256C>G
cDNA.278C>G
g.1680C>G
AA changes Q86E Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS
86
frameshift no
known variant Reference ID: rs1059455
databasehomozygous (G/G)heterozygousallele carriers
1000G38411971581
ExAC68601904725907
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2AK9ac, Histone, Histone 2A Lysine 9 Acetylation
H2BK20ac, Histone, Histone 2B Lysine 20 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
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
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.6030
-2.4270
(flanking)-1.970
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased1679wt: 0.40 / mu: 0.95wt: TGGGACCAGGAGACA
mu: TGGGACGAGGAGACA
 GGAC|cagg
Donor increased1676wt: 0.54 / mu: 0.98wt: TATTGGGACCAGGAG
mu: TATTGGGACGAGGAG
 TTGG|gacc
Donor gained16740.88mu: AGTATTGGGACGAGG TATT|ggga
distance from splice site 88
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      86WIEQEGPEYWDQETRNVKAQSQTD
mutated  all conserved    86WIEQEGPEYWDEETRNVKAQSQT
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000029875  86WMEQEGPEYWDQNTRICKADTQT
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 
25114REGIONAlpha-1.lost
25308TOPO_DOMExtracellular (Potential).lost
110110CARBOHYDN-linked (GlcNAc...) (By similarity).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)
209295DOMAINIg-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)
309332TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
333365TOPO_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 1098 / 1098
position (AA) of stopcodon in wt / mu AA sequence 366 / 366
position of stopcodon in wt / mu cDNA 1120 / 1120
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 23 / 23
chromosome 6
strand 1
last intron/exon boundary 1116
theoretical NMD boundary in CDS 1043
length of CDS 1098
coding sequence (CDS) position 256
cDNA position
(for ins/del: last normal base / first normal base)
278
gDNA position
(for ins/del: last normal base / first normal base)
1680
chromosomal position
(for ins/del: last normal base / first normal base)
29910716
original gDNA sequence snippet AGGGGCCGGAGTATTGGGACCAGGAGACACGGAATGTGAAG
altered gDNA sequence snippet AGGGGCCGGAGTATTGGGACGAGGAGACACGGAATGTGAAG
original cDNA sequence snippet AGGGGCCGGAGTATTGGGACCAGGAGACACGGAATGTGAAG
altered cDNA sequence snippet AGGGGCCGGAGTATTGGGACGAGGAGACACGGAATGTGAAG
wildtype AA sequence MAVMAPRTLL LLLSGALALT QTWAGSHSMR YFFTSVSRPG RGEPRFIAVG YVDDTQFVRF
DSDAASQRME PRAPWIEQEG PEYWDQETRN VKAQSQTDRV DLGTLRGYYN QSEAGSHTIQ
IMYGCDVGSD GRFLRGYRQD AYDGKDYIAL NEDLRSWTAA DMAAQITKRK WEAAHEAEQL
RAYLDGTCVE WLRRYLENGK ETLQRTDPPK THMTHHPISD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGEEQR YTCHVQHEGL PKPLTLRWEL
SSQPTIPIVG IIAGLVLLGA VITGAVVAAV MWRRKSSDRK GGSYTQAASS DSAQGSDVSL
TACKV*
mutated AA sequence MAVMAPRTLL LLLSGALALT QTWAGSHSMR YFFTSVSRPG RGEPRFIAVG YVDDTQFVRF
DSDAASQRME PRAPWIEQEG PEYWDEETRN VKAQSQTDRV DLGTLRGYYN QSEAGSHTIQ
IMYGCDVGSD GRFLRGYRQD AYDGKDYIAL NEDLRSWTAA DMAAQITKRK WEAAHEAEQL
RAYLDGTCVE WLRRYLENGK ETLQRTDPPK THMTHHPISD HEATLRCWAL GFYPAEITLT
WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGEEQR YTCHVQHEGL PKPLTLRWEL
SSQPTIPIVG IIAGLVLLGA VITGAVVAAV MWRRKSSDRK GGSYTQAASS DSAQGSDVSL
TACKV*
speed 0.95 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