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: ENST00000553947
Querying Taster for transcript #2: ENST00000393080
Querying Taster for transcript #3: ENST00000467132
Querying Taster for transcript #4: ENST00000393078
MT speed 0 s - this script 4.322853 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
SERPINA3polymorphism_automatic6.63590293825678e-11simple_aaeaffectedA9Tsingle base exchangers4934show file
SERPINA3polymorphism_automatic6.63590293825678e-11simple_aaeaffectedA9Tsingle base exchangers4934show file
SERPINA3polymorphism_automatic6.63590293825678e-11simple_aaeaffectedA9Tsingle base exchangers4934show file
SERPINA3polymorphism_automatic2.87053047998143e-10simple_aaeaffectedA34Tsingle base exchangers4934show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999933641 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM950001)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:95080803G>AN/A show variant in all transcripts   IGV
HGNC symbol SERPINA3
Ensembl transcript ID ENST00000393080
Genbank transcript ID N/A
UniProt peptide P01011
alteration type single base exchange
alteration region CDS
DNA changes c.25G>A
cDNA.93G>A
g.22409G>A
AA changes A9T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 9
frameshift no
known variant Reference ID: rs4934
databasehomozygous (A/A)heterozygousallele carriers
1000G45710861543
ExAC12978681119789

known disease mutation at this position, please check HGMD for details (HGMD ID CM950001)
regulatory features H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1350.001
0.0350.002
(flanking)0.4580.013
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased22412wt: 0.58 / mu: 0.76wt: GAATGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCTGGG
mu: GAATGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCTGGG		 gctc|TGGG
Acc marginally increased22415wt: 0.9308 / mu: 0.9471 (marginal change - not scored)wt: TGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCTGGGTTC
mu: TGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCTGGGTTC		 ctgg|GGCT
Acc marginally increased22409wt: 0.9389 / mu: 0.9511 (marginal change - not scored)wt: AGAGAATGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCT
mu: AGAGAATGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCT		 ctgg|CTCT
distance from splice site 33
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      9 MERMLPLLALGLLAAGFCPAV
mutated  not conserved    9 MERMLPLLTLGLLAAGFCPAVL
Ptroglodytes  all identical  ENSPTRG00000023582  34 MERMLPLLALGLLVAGLCPAVL
Mmulatta  all identical  ENSMMUG00000011218  9 MERMLPLLALGLLVAGFCPAVL
Fcatus  no alignment  ENSFCAG00000010238  n/a
Mmusculus  all identical  ENSMUSG00000021091  6 IAALGLLMAGICPAVL
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 
123SIGNALlost
3333CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
5067HELIXmight get lost (downstream of altered splice site)
5555CONFLICTD -> S (in Ref. 12; AA sequence).might get lost (downstream of altered splice site)
6969CONFLICTP -> L (in Ref. 1; AAA51543).might get lost (downstream of altered splice site)
6971STRANDmight get lost (downstream of altered splice site)
7375STRANDmight get lost (downstream of altered splice site)
7787HELIXmight get lost (downstream of altered splice site)
8890HELIXmight get lost (downstream of altered splice site)
9393CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
93102HELIXmight get lost (downstream of altered splice site)
101101CONFLICTK -> R (in Ref. 5; BAD92297).might get lost (downstream of altered splice site)
106106CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
106106CONFLICTN -> Y (in Ref. 3; AAT08028).might get lost (downstream of altered splice site)
107109TURNmight get lost (downstream of altered splice site)
112126HELIXmight get lost (downstream of altered splice site)
127127CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
130132STRANDmight get lost (downstream of altered splice site)
134146STRANDmight get lost (downstream of altered splice site)
151161HELIXmight get lost (downstream of altered splice site)
164168STRANDmight get lost (downstream of altered splice site)
170172HELIXmight get lost (downstream of altered splice site)
173183HELIXmight get lost (downstream of altered splice site)
185194STRANDmight get lost (downstream of altered splice site)
186186CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
198198CONFLICTD -> N (in Ref. 3; AAT08029).might get lost (downstream of altered splice site)
199199CONFLICTL -> P (in Ref. 1; AAA51543).might get lost (downstream of altered splice site)
205219STRANDmight get lost (downstream of altered splice site)
223225HELIXmight get lost (downstream of altered splice site)
227236STRANDmight get lost (downstream of altered splice site)
234234CONFLICTS -> N (in Ref. 3; AAT08029).might get lost (downstream of altered splice site)
235237DNA_BINDmight get lost (downstream of altered splice site)
238256STRANDmight get lost (downstream of altered splice site)
257260TURNmight get lost (downstream of altered splice site)
261279STRANDmight get lost (downstream of altered splice site)
271271CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
284288HELIXmight get lost (downstream of altered splice site)
293301HELIXmight get lost (downstream of altered splice site)
304314STRANDmight get lost (downstream of altered splice site)
316323STRANDmight get lost (downstream of altered splice site)
325330HELIXmight get lost (downstream of altered splice site)
335337HELIXmight get lost (downstream of altered splice site)
339339CONFLICTS -> G (in Ref. 3; AAT08028).might get lost (downstream of altered splice site)
344347TURNmight get lost (downstream of altered splice site)
346346CONFLICTI -> S (in Ref. 3; AAT08028).might get lost (downstream of altered splice site)
348350STRANDmight get lost (downstream of altered splice site)
352365STRANDmight get lost (downstream of altered splice site)
361363CONFLICTAVL -> VVS (in Ref. 1; AAA51543).might get lost (downstream of altered splice site)
367373STRANDmight get lost (downstream of altered splice site)
369394REGIONRCL.might get lost (downstream of altered splice site)
383384SITEReactive bond.might get lost (downstream of altered splice site)
392394STRANDmight get lost (downstream of altered splice site)
399405STRANDmight get lost (downstream of altered splice site)
412418STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1272 / 1272
position (AA) of stopcodon in wt / mu AA sequence 424 / 424
position of stopcodon in wt / mu cDNA 1340 / 1340
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 69 / 69
chromosome 14
strand 1
last intron/exon boundary 1137
theoretical NMD boundary in CDS 1018
length of CDS 1272
coding sequence (CDS) position 25
cDNA position
(for ins/del: last normal base / first normal base)		 93
gDNA position
(for ins/del: last normal base / first normal base)		 22409
chromosomal position
(for ins/del: last normal base / first normal base)		 95080803
original gDNA sequence snippet AGAGAATGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCT
altered gDNA sequence snippet AGAGAATGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCT
original cDNA sequence snippet AGAGAATGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCT
altered cDNA sequence snippet AGAGAATGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCT
wildtype AA sequence MERMLPLLAL GLLAAGFCPA VLCHPNSPLD EENLTQENQD RGTHVDLGLA SANVDFAFSL
YKQLVLKAPD KNVIFSPLSI STALAFLSLG AHNTTLTEIL KGLKFNLTET SEAEIHQSFQ
HLLRTLNQSS DELQLSMGNA MFVKEQLSLL DRFTEDAKRL YGSEAFATDF QDSAAAKKLI
NDYVKNGTRG KITDLIKDLD SQTMMVLVNY IFFKAKWEMP FDPQDTHQSR FYLSKKKWVM
VPMMSLHHLT IPYFRDEELS CTVVELKYTG NASALFILPD QDKMEEVEAM LLPETLKRWR
DSLEFREIGE LYLPKFSISR DYNLNDILLQ LGIEEAFTSK ADLSGITGAR NLAVSQVVHK
AVLDVFEEGT EASAATAVKI TLLSALVETR TIVRFNRPFL MIIVPTDTQN IFFMSKVTNP
KQA*
mutated AA sequence MERMLPLLTL GLLAAGFCPA VLCHPNSPLD EENLTQENQD RGTHVDLGLA SANVDFAFSL
YKQLVLKAPD KNVIFSPLSI STALAFLSLG AHNTTLTEIL KGLKFNLTET SEAEIHQSFQ
HLLRTLNQSS DELQLSMGNA MFVKEQLSLL DRFTEDAKRL YGSEAFATDF QDSAAAKKLI
NDYVKNGTRG KITDLIKDLD SQTMMVLVNY IFFKAKWEMP FDPQDTHQSR FYLSKKKWVM
VPMMSLHHLT IPYFRDEELS CTVVELKYTG NASALFILPD QDKMEEVEAM LLPETLKRWR
DSLEFREIGE LYLPKFSISR DYNLNDILLQ LGIEEAFTSK ADLSGITGAR NLAVSQVVHK
AVLDVFEEGT EASAATAVKI TLLSALVETR TIVRFNRPFL MIIVPTDTQN IFFMSKVTNP
KQA*
speed 0.63 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: 0.999999999933641 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM950001)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:95080803G>AN/A show variant in all transcripts   IGV
HGNC symbol SERPINA3
Ensembl transcript ID ENST00000467132
Genbank transcript ID N/A
UniProt peptide P01011
alteration type single base exchange
alteration region CDS
DNA changes c.25G>A
cDNA.1173G>A
g.22409G>A
AA changes A9T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 9
frameshift no
known variant Reference ID: rs4934
databasehomozygous (A/A)heterozygousallele carriers
1000G45710861543
ExAC12978681119789

known disease mutation at this position, please check HGMD for details (HGMD ID CM950001)
regulatory features H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1350.001
0.0350.002
(flanking)0.4580.013
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased22412wt: 0.58 / mu: 0.76wt: GAATGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCTGGG
mu: GAATGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCTGGG		 gctc|TGGG
Acc marginally increased22415wt: 0.9308 / mu: 0.9471 (marginal change - not scored)wt: TGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCTGGGTTC
mu: TGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCTGGGTTC		 ctgg|GGCT
Acc marginally increased22409wt: 0.9389 / mu: 0.9511 (marginal change - not scored)wt: AGAGAATGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCT
mu: AGAGAATGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCT		 ctgg|CTCT
distance from splice site 619
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      9 MERMLPLLALGLLAAGFCPAV
mutated  not conserved    9 MERMLPLLTLGLLAAGFCPAVL
Ptroglodytes  all identical  ENSPTRG00000023582  34 MERMLPLLALGLLVAGLCPAVL
Mmulatta  all identical  ENSMMUG00000011218  9 MERMLPLLALGLLVAGFCPAVL
Fcatus  no alignment  ENSFCAG00000010238  n/a
Mmusculus  all identical  ENSMUSG00000021091  6 IAALGLLMAGICPAVL
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 
123SIGNALlost
3333CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
5067HELIXmight get lost (downstream of altered splice site)
5555CONFLICTD -> S (in Ref. 12; AA sequence).might get lost (downstream of altered splice site)
6969CONFLICTP -> L (in Ref. 1; AAA51543).might get lost (downstream of altered splice site)
6971STRANDmight get lost (downstream of altered splice site)
7375STRANDmight get lost (downstream of altered splice site)
7787HELIXmight get lost (downstream of altered splice site)
8890HELIXmight get lost (downstream of altered splice site)
9393CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
93102HELIXmight get lost (downstream of altered splice site)
101101CONFLICTK -> R (in Ref. 5; BAD92297).might get lost (downstream of altered splice site)
106106CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
106106CONFLICTN -> Y (in Ref. 3; AAT08028).might get lost (downstream of altered splice site)
107109TURNmight get lost (downstream of altered splice site)
112126HELIXmight get lost (downstream of altered splice site)
127127CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
130132STRANDmight get lost (downstream of altered splice site)
134146STRANDmight get lost (downstream of altered splice site)
151161HELIXmight get lost (downstream of altered splice site)
164168STRANDmight get lost (downstream of altered splice site)
170172HELIXmight get lost (downstream of altered splice site)
173183HELIXmight get lost (downstream of altered splice site)
185194STRANDmight get lost (downstream of altered splice site)
186186CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
198198CONFLICTD -> N (in Ref. 3; AAT08029).might get lost (downstream of altered splice site)
199199CONFLICTL -> P (in Ref. 1; AAA51543).might get lost (downstream of altered splice site)
205219STRANDmight get lost (downstream of altered splice site)
223225HELIXmight get lost (downstream of altered splice site)
227236STRANDmight get lost (downstream of altered splice site)
234234CONFLICTS -> N (in Ref. 3; AAT08029).might get lost (downstream of altered splice site)
235237DNA_BINDmight get lost (downstream of altered splice site)
238256STRANDmight get lost (downstream of altered splice site)
257260TURNmight get lost (downstream of altered splice site)
261279STRANDmight get lost (downstream of altered splice site)
271271CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
284288HELIXmight get lost (downstream of altered splice site)
293301HELIXmight get lost (downstream of altered splice site)
304314STRANDmight get lost (downstream of altered splice site)
316323STRANDmight get lost (downstream of altered splice site)
325330HELIXmight get lost (downstream of altered splice site)
335337HELIXmight get lost (downstream of altered splice site)
339339CONFLICTS -> G (in Ref. 3; AAT08028).might get lost (downstream of altered splice site)
344347TURNmight get lost (downstream of altered splice site)
346346CONFLICTI -> S (in Ref. 3; AAT08028).might get lost (downstream of altered splice site)
348350STRANDmight get lost (downstream of altered splice site)
352365STRANDmight get lost (downstream of altered splice site)
361363CONFLICTAVL -> VVS (in Ref. 1; AAA51543).might get lost (downstream of altered splice site)
367373STRANDmight get lost (downstream of altered splice site)
369394REGIONRCL.might get lost (downstream of altered splice site)
383384SITEReactive bond.might get lost (downstream of altered splice site)
392394STRANDmight get lost (downstream of altered splice site)
399405STRANDmight get lost (downstream of altered splice site)
412418STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1272 / 1272
position (AA) of stopcodon in wt / mu AA sequence 424 / 424
position of stopcodon in wt / mu cDNA 2420 / 2420
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 1149 / 1149
chromosome 14
strand 1
last intron/exon boundary 2217
theoretical NMD boundary in CDS 1018
length of CDS 1272
coding sequence (CDS) position 25
cDNA position
(for ins/del: last normal base / first normal base)		 1173
gDNA position
(for ins/del: last normal base / first normal base)		 22409
chromosomal position
(for ins/del: last normal base / first normal base)		 95080803
original gDNA sequence snippet AGAGAATGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCT
altered gDNA sequence snippet AGAGAATGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCT
original cDNA sequence snippet AGAGAATGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCT
altered cDNA sequence snippet AGAGAATGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCT
wildtype AA sequence MERMLPLLAL GLLAAGFCPA VLCHPNSPLD EENLTQENQD RGTHVDLGLA SANVDFAFSL
YKQLVLKAPD KNVIFSPLSI STALAFLSLG AHNTTLTEIL KGLKFNLTET SEAEIHQSFQ
HLLRTLNQSS DELQLSMGNA MFVKEQLSLL DRFTEDAKRL YGSEAFATDF QDSAAAKKLI
NDYVKNGTRG KITDLIKDLD SQTMMVLVNY IFFKAKWEMP FDPQDTHQSR FYLSKKKWVM
VPMMSLHHLT IPYFRDEELS CTVVELKYTG NASALFILPD QDKMEEVEAM LLPETLKRWR
DSLEFREIGE LYLPKFSISR DYNLNDILLQ LGIEEAFTSK ADLSGITGAR NLAVSQVVHK
AVLDVFEEGT EASAATAVKI TLLSALVETR TIVRFNRPFL MIIVPTDTQN IFFMSKVTNP
KQA*
mutated AA sequence MERMLPLLTL GLLAAGFCPA VLCHPNSPLD EENLTQENQD RGTHVDLGLA SANVDFAFSL
YKQLVLKAPD KNVIFSPLSI STALAFLSLG AHNTTLTEIL KGLKFNLTET SEAEIHQSFQ
HLLRTLNQSS DELQLSMGNA MFVKEQLSLL DRFTEDAKRL YGSEAFATDF QDSAAAKKLI
NDYVKNGTRG KITDLIKDLD SQTMMVLVNY IFFKAKWEMP FDPQDTHQSR FYLSKKKWVM
VPMMSLHHLT IPYFRDEELS CTVVELKYTG NASALFILPD QDKMEEVEAM LLPETLKRWR
DSLEFREIGE LYLPKFSISR DYNLNDILLQ LGIEEAFTSK ADLSGITGAR NLAVSQVVHK
AVLDVFEEGT EASAATAVKI TLLSALVETR TIVRFNRPFL MIIVPTDTQN IFFMSKVTNP
KQA*
speed 0.65 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: 0.999999999933641 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM950001)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:95080803G>AN/A show variant in all transcripts   IGV
HGNC symbol SERPINA3
Ensembl transcript ID ENST00000393078
Genbank transcript ID N/A
UniProt peptide P01011
alteration type single base exchange
alteration region CDS
DNA changes c.25G>A
cDNA.104G>A
g.22409G>A
AA changes A9T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 9
frameshift no
known variant Reference ID: rs4934
databasehomozygous (A/A)heterozygousallele carriers
1000G45710861543
ExAC12978681119789

known disease mutation at this position, please check HGMD for details (HGMD ID CM950001)
regulatory features H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1350.001
0.0350.002
(flanking)0.4580.013
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased22412wt: 0.58 / mu: 0.76wt: GAATGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCTGGG
mu: GAATGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCTGGG		 gctc|TGGG
Acc marginally increased22415wt: 0.9308 / mu: 0.9471 (marginal change - not scored)wt: TGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCTGGGTTC
mu: TGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCTGGGTTC		 ctgg|GGCT
Acc marginally increased22409wt: 0.9389 / mu: 0.9511 (marginal change - not scored)wt: AGAGAATGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCT
mu: AGAGAATGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCT		 ctgg|CTCT
distance from splice site 33
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      9 MERMLPLLALGLLAAGFCPAV
mutated  not conserved    9 MERMLPLLTLGLLAAGFCPAVL
Ptroglodytes  all identical  ENSPTRG00000023582  34 MERMLPLLALGLLVAGLCPAVL
Mmulatta  all identical  ENSMMUG00000011218  9 MERMLPLLALGLLVAGFCPAVL
Fcatus  no alignment  ENSFCAG00000010238  n/a
Mmusculus  all identical  ENSMUSG00000021091  6 IAALGLLMAGICPAVL
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 
123SIGNALlost
3333CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
5067HELIXmight get lost (downstream of altered splice site)
5555CONFLICTD -> S (in Ref. 12; AA sequence).might get lost (downstream of altered splice site)
6969CONFLICTP -> L (in Ref. 1; AAA51543).might get lost (downstream of altered splice site)
6971STRANDmight get lost (downstream of altered splice site)
7375STRANDmight get lost (downstream of altered splice site)
7787HELIXmight get lost (downstream of altered splice site)
8890HELIXmight get lost (downstream of altered splice site)
9393CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
93102HELIXmight get lost (downstream of altered splice site)
101101CONFLICTK -> R (in Ref. 5; BAD92297).might get lost (downstream of altered splice site)
106106CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
106106CONFLICTN -> Y (in Ref. 3; AAT08028).might get lost (downstream of altered splice site)
107109TURNmight get lost (downstream of altered splice site)
112126HELIXmight get lost (downstream of altered splice site)
127127CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
130132STRANDmight get lost (downstream of altered splice site)
134146STRANDmight get lost (downstream of altered splice site)
151161HELIXmight get lost (downstream of altered splice site)
164168STRANDmight get lost (downstream of altered splice site)
170172HELIXmight get lost (downstream of altered splice site)
173183HELIXmight get lost (downstream of altered splice site)
185194STRANDmight get lost (downstream of altered splice site)
186186CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
198198CONFLICTD -> N (in Ref. 3; AAT08029).might get lost (downstream of altered splice site)
199199CONFLICTL -> P (in Ref. 1; AAA51543).might get lost (downstream of altered splice site)
205219STRANDmight get lost (downstream of altered splice site)
223225HELIXmight get lost (downstream of altered splice site)
227236STRANDmight get lost (downstream of altered splice site)
234234CONFLICTS -> N (in Ref. 3; AAT08029).might get lost (downstream of altered splice site)
235237DNA_BINDmight get lost (downstream of altered splice site)
238256STRANDmight get lost (downstream of altered splice site)
257260TURNmight get lost (downstream of altered splice site)
261279STRANDmight get lost (downstream of altered splice site)
271271CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
284288HELIXmight get lost (downstream of altered splice site)
293301HELIXmight get lost (downstream of altered splice site)
304314STRANDmight get lost (downstream of altered splice site)
316323STRANDmight get lost (downstream of altered splice site)
325330HELIXmight get lost (downstream of altered splice site)
335337HELIXmight get lost (downstream of altered splice site)
339339CONFLICTS -> G (in Ref. 3; AAT08028).might get lost (downstream of altered splice site)
344347TURNmight get lost (downstream of altered splice site)
346346CONFLICTI -> S (in Ref. 3; AAT08028).might get lost (downstream of altered splice site)
348350STRANDmight get lost (downstream of altered splice site)
352365STRANDmight get lost (downstream of altered splice site)
361363CONFLICTAVL -> VVS (in Ref. 1; AAA51543).might get lost (downstream of altered splice site)
367373STRANDmight get lost (downstream of altered splice site)
369394REGIONRCL.might get lost (downstream of altered splice site)
383384SITEReactive bond.might get lost (downstream of altered splice site)
392394STRANDmight get lost (downstream of altered splice site)
399405STRANDmight get lost (downstream of altered splice site)
412418STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1272 / 1272
position (AA) of stopcodon in wt / mu AA sequence 424 / 424
position of stopcodon in wt / mu cDNA 1351 / 1351
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 14
strand 1
last intron/exon boundary 1148
theoretical NMD boundary in CDS 1018
length of CDS 1272
coding sequence (CDS) position 25
cDNA position
(for ins/del: last normal base / first normal base)		 104
gDNA position
(for ins/del: last normal base / first normal base)		 22409
chromosomal position
(for ins/del: last normal base / first normal base)		 95080803
original gDNA sequence snippet AGAGAATGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCT
altered gDNA sequence snippet AGAGAATGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCT
original cDNA sequence snippet AGAGAATGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCT
altered cDNA sequence snippet AGAGAATGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCT
wildtype AA sequence MERMLPLLAL GLLAAGFCPA VLCHPNSPLD EENLTQENQD RGTHVDLGLA SANVDFAFSL
YKQLVLKAPD KNVIFSPLSI STALAFLSLG AHNTTLTEIL KGLKFNLTET SEAEIHQSFQ
HLLRTLNQSS DELQLSMGNA MFVKEQLSLL DRFTEDAKRL YGSEAFATDF QDSAAAKKLI
NDYVKNGTRG KITDLIKDLD SQTMMVLVNY IFFKAKWEMP FDPQDTHQSR FYLSKKKWVM
VPMMSLHHLT IPYFRDEELS CTVVELKYTG NASALFILPD QDKMEEVEAM LLPETLKRWR
DSLEFREIGE LYLPKFSISR DYNLNDILLQ LGIEEAFTSK ADLSGITGAR NLAVSQVVHK
AVLDVFEEGT EASAATAVKI TLLSALVETR TIVRFNRPFL MIIVPTDTQN IFFMSKVTNP
KQA*
mutated AA sequence MERMLPLLTL GLLAAGFCPA VLCHPNSPLD EENLTQENQD RGTHVDLGLA SANVDFAFSL
YKQLVLKAPD KNVIFSPLSI STALAFLSLG AHNTTLTEIL KGLKFNLTET SEAEIHQSFQ
HLLRTLNQSS DELQLSMGNA MFVKEQLSLL DRFTEDAKRL YGSEAFATDF QDSAAAKKLI
NDYVKNGTRG KITDLIKDLD SQTMMVLVNY IFFKAKWEMP FDPQDTHQSR FYLSKKKWVM
VPMMSLHHLT IPYFRDEELS CTVVELKYTG NASALFILPD QDKMEEVEAM LLPETLKRWR
DSLEFREIGE LYLPKFSISR DYNLNDILLQ LGIEEAFTSK ADLSGITGAR NLAVSQVVHK
AVLDVFEEGT EASAATAVKI TLLSALVETR TIVRFNRPFL MIIVPTDTQN IFFMSKVTNP
KQA*
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
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Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999712947 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM950001)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:95080803G>AN/A show variant in all transcripts   IGV
HGNC symbol SERPINA3
Ensembl transcript ID ENST00000553947
Genbank transcript ID NM_001085
UniProt peptide P01011
alteration type single base exchange
alteration region CDS
DNA changes c.100G>A
cDNA.988G>A
g.22409G>A
AA changes A34T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 34
frameshift no
known variant Reference ID: rs4934
databasehomozygous (A/A)heterozygousallele carriers
1000G45710861543
ExAC12978681119789

known disease mutation at this position, please check HGMD for details (HGMD ID CM950001)
regulatory features H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1350.001
0.0350.002
(flanking)0.4580.013
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased22412wt: 0.58 / mu: 0.76wt: GAATGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCTGGG
mu: GAATGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCTGGG		 gctc|TGGG
Acc marginally increased22415wt: 0.9308 / mu: 0.9471 (marginal change - not scored)wt: TGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCTGGGTTC
mu: TGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCTGGGTTC		 ctgg|GGCT
Acc marginally increased22409wt: 0.9389 / mu: 0.9511 (marginal change - not scored)wt: AGAGAATGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCT
mu: AGAGAATGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCT		 ctgg|CTCT
distance from splice site 33
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      34ELRMERMLPLLALGLLAAGFCPAV
mutated  not conserved    34ELRMERMLPLLTLGLLAAGFCPA
Ptroglodytes  all identical  ENSPTRG00000023582  34ELRMERMLPLLALGLLVAGLCPA
Mmulatta  all identical  ENSMMUG00000011218  9MERMLPLLALGLLVAGFCPA
Fcatus  no alignment  ENSFCAG00000010238  n/a
Mmusculus  all identical  ENSMUSG00000021091  6IAALGLLMAGICPA
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 
5067HELIXmight get lost (downstream of altered splice site)
5555CONFLICTD -> S (in Ref. 12; AA sequence).might get lost (downstream of altered splice site)
6969CONFLICTP -> L (in Ref. 1; AAA51543).might get lost (downstream of altered splice site)
6971STRANDmight get lost (downstream of altered splice site)
7375STRANDmight get lost (downstream of altered splice site)
7787HELIXmight get lost (downstream of altered splice site)
8890HELIXmight get lost (downstream of altered splice site)
9393CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
93102HELIXmight get lost (downstream of altered splice site)
101101CONFLICTK -> R (in Ref. 5; BAD92297).might get lost (downstream of altered splice site)
106106CONFLICTN -> Y (in Ref. 3; AAT08028).might get lost (downstream of altered splice site)
106106CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
107109TURNmight get lost (downstream of altered splice site)
112126HELIXmight get lost (downstream of altered splice site)
127127CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
130132STRANDmight get lost (downstream of altered splice site)
134146STRANDmight get lost (downstream of altered splice site)
151161HELIXmight get lost (downstream of altered splice site)
164168STRANDmight get lost (downstream of altered splice site)
170172HELIXmight get lost (downstream of altered splice site)
173183HELIXmight get lost (downstream of altered splice site)
185194STRANDmight get lost (downstream of altered splice site)
186186CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
198198CONFLICTD -> N (in Ref. 3; AAT08029).might get lost (downstream of altered splice site)
199199CONFLICTL -> P (in Ref. 1; AAA51543).might get lost (downstream of altered splice site)
205219STRANDmight get lost (downstream of altered splice site)
223225HELIXmight get lost (downstream of altered splice site)
227236STRANDmight get lost (downstream of altered splice site)
234234CONFLICTS -> N (in Ref. 3; AAT08029).might get lost (downstream of altered splice site)
235237DNA_BINDmight get lost (downstream of altered splice site)
238256STRANDmight get lost (downstream of altered splice site)
257260TURNmight get lost (downstream of altered splice site)
261279STRANDmight get lost (downstream of altered splice site)
271271CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
284288HELIXmight get lost (downstream of altered splice site)
293301HELIXmight get lost (downstream of altered splice site)
304314STRANDmight get lost (downstream of altered splice site)
316323STRANDmight get lost (downstream of altered splice site)
325330HELIXmight get lost (downstream of altered splice site)
335337HELIXmight get lost (downstream of altered splice site)
339339CONFLICTS -> G (in Ref. 3; AAT08028).might get lost (downstream of altered splice site)
344347TURNmight get lost (downstream of altered splice site)
346346CONFLICTI -> S (in Ref. 3; AAT08028).might get lost (downstream of altered splice site)
348350STRANDmight get lost (downstream of altered splice site)
352365STRANDmight get lost (downstream of altered splice site)
361363CONFLICTAVL -> VVS (in Ref. 1; AAA51543).might get lost (downstream of altered splice site)
367373STRANDmight get lost (downstream of altered splice site)
369394REGIONRCL.might get lost (downstream of altered splice site)
383384SITEReactive bond.might get lost (downstream of altered splice site)
392394STRANDmight get lost (downstream of altered splice site)
399405STRANDmight get lost (downstream of altered splice site)
412418STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1347 / 1347
position (AA) of stopcodon in wt / mu AA sequence 449 / 449
position of stopcodon in wt / mu cDNA 2235 / 2235
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 889 / 889
chromosome 14
strand 1
last intron/exon boundary 2032
theoretical NMD boundary in CDS 1093
length of CDS 1347
coding sequence (CDS) position 100
cDNA position
(for ins/del: last normal base / first normal base)		 988
gDNA position
(for ins/del: last normal base / first normal base)		 22409
chromosomal position
(for ins/del: last normal base / first normal base)		 95080803
original gDNA sequence snippet AGAGAATGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCT
altered gDNA sequence snippet AGAGAATGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCT
original cDNA sequence snippet AGAGAATGTTACCTCTCCTGGCTCTGGGGCTCTTGGCGGCT
altered cDNA sequence snippet AGAGAATGTTACCTCTCCTGACTCTGGGGCTCTTGGCGGCT
wildtype AA sequence MKIHYSRQTA LESTSYIQLP EAELRMERML PLLALGLLAA GFCPAVLCHP NSPLDEENLT
QENQDRGTHV DLGLASANVD FAFSLYKQLV LKAPDKNVIF SPLSISTALA FLSLGAHNTT
LTEILKGLKF NLTETSEAEI HQSFQHLLRT LNQSSDELQL SMGNAMFVKE QLSLLDRFTE
DAKRLYGSEA FATDFQDSAA AKKLINDYVK NGTRGKITDL IKDLDSQTMM VLVNYIFFKA
KWEMPFDPQD THQSRFYLSK KKWVMVPMMS LHHLTIPYFR DEELSCTVVE LKYTGNASAL
FILPDQDKME EVEAMLLPET LKRWRDSLEF REIGELYLPK FSISRDYNLN DILLQLGIEE
AFTSKADLSG ITGARNLAVS QVVHKAVLDV FEEGTEASAA TAVKITLLSA LVETRTIVRF
NRPFLMIIVP TDTQNIFFMS KVTNPKQA*
mutated AA sequence MKIHYSRQTA LESTSYIQLP EAELRMERML PLLTLGLLAA GFCPAVLCHP NSPLDEENLT
QENQDRGTHV DLGLASANVD FAFSLYKQLV LKAPDKNVIF SPLSISTALA FLSLGAHNTT
LTEILKGLKF NLTETSEAEI HQSFQHLLRT LNQSSDELQL SMGNAMFVKE QLSLLDRFTE
DAKRLYGSEA FATDFQDSAA AKKLINDYVK NGTRGKITDL IKDLDSQTMM VLVNYIFFKA
KWEMPFDPQD THQSRFYLSK KKWVMVPMMS LHHLTIPYFR DEELSCTVVE LKYTGNASAL
FILPDQDKME EVEAMLLPET LKRWRDSLEF REIGELYLPK FSISRDYNLN DILLQLGIEE
AFTSKADLSG ITGARNLAVS QVVHKAVLDV FEEGTEASAA TAVKITLLSA LVETRTIVRF
NRPFLMIIVP TDTQNIFFMS KVTNPKQA*
speed 0.82 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