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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000422441
Querying Taster for transcript #2: ENST00000264741
MT speed 1.78 s - this script 3.816325 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ITGA9polymorphism_automatic0.999999999481893simple_aaeaffectedG507Esingle base exchangers267561show file
ITGA9polymorphism_automatic0.99999999975383simple_aaeaffectedG507Esingle base exchangers267561show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 5.18107436399236e-10 (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) chr3:37574951G>AN/A show variant in all transcripts   IGV
HGNC symbol ITGA9
Ensembl transcript ID ENST00000422441
Genbank transcript ID N/A
UniProt peptide Q13797
alteration type single base exchange
alteration region CDS
DNA changes c.1520G>A
cDNA.1780G>A
g.81346G>A
AA changes G507E Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 507
frameshift no
known variant Reference ID: rs267561
databasehomozygous (A/A)heterozygousallele carriers
1000G84911021951
ExAC20628-848912139
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)6.2681
6.2681
(flanking)1.7391
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased81349wt: 0.64 / mu: 0.82wt: AGGAGAGATTGGTAA
mu: AGAAGAGATTGGTAA		 GAGA|gatt
Donor increased81347wt: 0.56 / mu: 0.83wt: CCAGGAGAGATTGGT
mu: CCAGAAGAGATTGGT		 AGGA|gaga
Donor increased81342wt: 0.29 / mu: 0.73wt: ACGTTCCAGGAGAGA
mu: ACGTTCCAGAAGAGA		 GTTC|cagg
Donor marginally increased81344wt: 0.9881 / mu: 0.9943 (marginal change - not scored)wt: GTTCCAGGAGAGATT
mu: GTTCCAGAAGAGATT		 TCCA|ggag
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      507TCFSFHGKHVPGEIGLNYVLMADV
mutated  not conserved    507TCFSFHGKHVPEEIGLNYVLMAD
Ptroglodytes  all identical  ENSPTRG00000014748  507TCFSFHGKHVPGEIGLNYVLMAD
Mmulatta  all identical  ENSMMUG00000021927  445TCFSFRGKHVPGEIGLNYVLTAD
Fcatus  no alignment  ENSFCAG00000002281  n/a
Mmusculus  all identical  ENSMUSG00000039115  508VCFRFHGKNVPGEIGLNYNLTAD
Ggallus  all identical  ENSGALG00000012238  501ACFRFSGKHVPGEIGLNYNLTAD
Trubripes  all identical  ENSTRUG00000013012  506VCMRFRGRQLPGQIELLYNLTAD
Drerio  no homologue    
Dmelanogaster  no alignment  FBgn0034880  n/a
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000023422  501VCFRFRGKHVPGEIELYYNLTAD
protein features
start (aa)end (aa)featuredetails 
30981TOPO_DOMExtracellular (Potential).lost
555555DISULFIDBy similarity.might get lost (downstream of altered splice site)
565566SITECleavage (Potential).might get lost (downstream of altered splice site)
612612CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
620620DISULFIDBy similarity.might get lost (downstream of altered splice site)
625625DISULFIDBy similarity.might get lost (downstream of altered splice site)
654654CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
658658CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
672672CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
676676CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
696696DISULFIDBy similarity.might get lost (downstream of altered splice site)
706706DISULFIDBy similarity.might get lost (downstream of altered splice site)
807807CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
854854CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
855855DISULFIDBy similarity.might get lost (downstream of altered splice site)
891891DISULFIDBy similarity.might get lost (downstream of altered splice site)
898898DISULFIDBy similarity.might get lost (downstream of altered splice site)
903903DISULFIDBy similarity.might get lost (downstream of altered splice site)
904904CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
9821002TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
10031035TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
10051009MOTIFGFFKR motif.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1899 / 1899
position (AA) of stopcodon in wt / mu AA sequence 633 / 633
position of stopcodon in wt / mu cDNA 2159 / 2159
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 261 / 261
chromosome 3
strand 1
last intron/exon boundary 1950
theoretical NMD boundary in CDS 1639
length of CDS 1899
coding sequence (CDS) position 1520
cDNA position
(for ins/del: last normal base / first normal base)		 1780
gDNA position
(for ins/del: last normal base / first normal base)		 81346
chromosomal position
(for ins/del: last normal base / first normal base)		 37574951
original gDNA sequence snippet CCATGGCAAACACGTTCCAGGAGAGATTGGTAATGAGCCAC
altered gDNA sequence snippet CCATGGCAAACACGTTCCAGAAGAGATTGGTAATGAGCCAC
original cDNA sequence snippet CCATGGCAAACACGTTCCAGGAGAGATTGGCCTGAATTATG
altered cDNA sequence snippet CCATGGCAAACACGTTCCAGAAGAGATTGGCCTGAATTATG
wildtype AA sequence MGGPAAPRGA GRLRALLLAL VVAGIPAGAY NLDPQRPVHF QGPADSFFGY AVLEHFHDNT
RWVLVGAPKA DSKYSPSVKS PGAVFKCRVH TNPDRRCTEL DMARGKNRGT SCGKTCREDR
DDEWMGVSLA RQPKADGRVL ACAHRWKNIY YEADHILPHG FCYIIPSNLQ AKGRTLIPCY
EEYKKKYGEE HGSCQAGIAG FFTEELVVMG APGSFYWAGT IKVLNLTDNT YLKLNDEVIM
NRRYTYLGYA VTAGHFSHPS TIDVVGGAPQ DKGIGKVYIF RADRRSGTLI KIFQASGKKM
GSYFGSSLCA VDLNGDGLSD LLVGAPMFSE IRDEGQVTVY INRGNGALEE QLALTGDGAY
NAHFGESIAS LDDLDNDGFP DVAIGAPKED DFAGAVYIYH GDAGGIVPQY SMKLSGQKIN
PVLRMFGQSI SGGIDMDGNG YPDVTVGAFM SDSVVLLRAR PVITVDVSIF LPGSINITAP
QCHDGQQPVN CLNVTTCFSF HGKHVPGEIG LNYVLMADVA KKEKGQMPRV YFVLLGETMG
QVTEKLQLTY MEETCRHYVA HVKRRVQDVI SPIVFEAAYS LSEHVTGEEE RELPPLTPVL
RWKKGQKIAQ KNQVRTLKLI LSTQGGSCTE QK*
mutated AA sequence MGGPAAPRGA GRLRALLLAL VVAGIPAGAY NLDPQRPVHF QGPADSFFGY AVLEHFHDNT
RWVLVGAPKA DSKYSPSVKS PGAVFKCRVH TNPDRRCTEL DMARGKNRGT SCGKTCREDR
DDEWMGVSLA RQPKADGRVL ACAHRWKNIY YEADHILPHG FCYIIPSNLQ AKGRTLIPCY
EEYKKKYGEE HGSCQAGIAG FFTEELVVMG APGSFYWAGT IKVLNLTDNT YLKLNDEVIM
NRRYTYLGYA VTAGHFSHPS TIDVVGGAPQ DKGIGKVYIF RADRRSGTLI KIFQASGKKM
GSYFGSSLCA VDLNGDGLSD LLVGAPMFSE IRDEGQVTVY INRGNGALEE QLALTGDGAY
NAHFGESIAS LDDLDNDGFP DVAIGAPKED DFAGAVYIYH GDAGGIVPQY SMKLSGQKIN
PVLRMFGQSI SGGIDMDGNG YPDVTVGAFM SDSVVLLRAR PVITVDVSIF LPGSINITAP
QCHDGQQPVN CLNVTTCFSF HGKHVPEEIG LNYVLMADVA KKEKGQMPRV YFVLLGETMG
QVTEKLQLTY MEETCRHYVA HVKRRVQDVI SPIVFEAAYS LSEHVTGEEE RELPPLTPVL
RWKKGQKIAQ KNQVRTLKLI LSTQGGSCTE QK*
speed 1.04 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: 2.46169807364118e-10 (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) chr3:37574951G>AN/A show variant in all transcripts   IGV
HGNC symbol ITGA9
Ensembl transcript ID ENST00000264741
Genbank transcript ID NM_002207
UniProt peptide Q13797
alteration type single base exchange
alteration region CDS
DNA changes c.1520G>A
cDNA.1776G>A
g.81346G>A
AA changes G507E Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 507
frameshift no
known variant Reference ID: rs267561
databasehomozygous (A/A)heterozygousallele carriers
1000G84911021951
ExAC20628-848912139
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)6.2681
6.2681
(flanking)1.7391
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased81349wt: 0.64 / mu: 0.82wt: AGGAGAGATTGGTAA
mu: AGAAGAGATTGGTAA		 GAGA|gatt
Donor increased81347wt: 0.56 / mu: 0.83wt: CCAGGAGAGATTGGT
mu: CCAGAAGAGATTGGT		 AGGA|gaga
Donor increased81342wt: 0.29 / mu: 0.73wt: ACGTTCCAGGAGAGA
mu: ACGTTCCAGAAGAGA		 GTTC|cagg
Donor marginally increased81344wt: 0.9881 / mu: 0.9943 (marginal change - not scored)wt: GTTCCAGGAGAGATT
mu: GTTCCAGAAGAGATT		 TCCA|ggag
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      507TCFSFHGKHVPGEIGLNYVLMADV
mutated  not conserved    507TCFSFHGKHVPEEIGLNYVLMAD
Ptroglodytes  all identical  ENSPTRG00000014748  507TCFSFHGKHVPGEIGLNYVLMAD
Mmulatta  all identical  ENSMMUG00000021927  445TCFSFRGKHVPGEIGLNYVLTAD
Fcatus  no alignment  ENSFCAG00000002281  n/a
Mmusculus  all identical  ENSMUSG00000039115  508VCFRFHGKNVPGEIGLNYNLTAD
Ggallus  all identical  ENSGALG00000012238  501ACFRFSGKHVPGEIGLNYNLTAD
Trubripes  all identical  ENSTRUG00000013012  506VCMRFRGRQLPGQIELLYNLTAD
Drerio  no homologue    
Dmelanogaster  not conserved  FBgn0034880  472AC---------------YRLETT
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000023422  501VCFRFRGKHVPGEIELYYNLTAD
protein features
start (aa)end (aa)featuredetails 
30981TOPO_DOMExtracellular (Potential).lost
555555DISULFIDBy similarity.might get lost (downstream of altered splice site)
565566SITECleavage (Potential).might get lost (downstream of altered splice site)
612612CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
620620DISULFIDBy similarity.might get lost (downstream of altered splice site)
625625DISULFIDBy similarity.might get lost (downstream of altered splice site)
654654CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
658658CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
672672CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
676676CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
696696DISULFIDBy similarity.might get lost (downstream of altered splice site)
706706DISULFIDBy similarity.might get lost (downstream of altered splice site)
807807CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
854854CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
855855DISULFIDBy similarity.might get lost (downstream of altered splice site)
891891DISULFIDBy similarity.might get lost (downstream of altered splice site)
898898DISULFIDBy similarity.might get lost (downstream of altered splice site)
903903DISULFIDBy similarity.might get lost (downstream of altered splice site)
904904CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
9821002TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
10031035TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
10051009MOTIFGFFKR motif.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3108 / 3108
position (AA) of stopcodon in wt / mu AA sequence 1036 / 1036
position of stopcodon in wt / mu cDNA 3364 / 3364
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 257 / 257
chromosome 3
strand 1
last intron/exon boundary 3266
theoretical NMD boundary in CDS 2959
length of CDS 3108
coding sequence (CDS) position 1520
cDNA position
(for ins/del: last normal base / first normal base)		 1776
gDNA position
(for ins/del: last normal base / first normal base)		 81346
chromosomal position
(for ins/del: last normal base / first normal base)		 37574951
original gDNA sequence snippet CCATGGCAAACACGTTCCAGGAGAGATTGGTAATGAGCCAC
altered gDNA sequence snippet CCATGGCAAACACGTTCCAGAAGAGATTGGTAATGAGCCAC
original cDNA sequence snippet CCATGGCAAACACGTTCCAGGAGAGATTGGCCTGAATTATG
altered cDNA sequence snippet CCATGGCAAACACGTTCCAGAAGAGATTGGCCTGAATTATG
wildtype AA sequence MGGPAAPRGA GRLRALLLAL VVAGIPAGAY NLDPQRPVHF QGPADSFFGY AVLEHFHDNT
RWVLVGAPKA DSKYSPSVKS PGAVFKCRVH TNPDRRCTEL DMARGKNRGT SCGKTCREDR
DDEWMGVSLA RQPKADGRVL ACAHRWKNIY YEADHILPHG FCYIIPSNLQ AKGRTLIPCY
EEYKKKYGEE HGSCQAGIAG FFTEELVVMG APGSFYWAGT IKVLNLTDNT YLKLNDEVIM
NRRYTYLGYA VTAGHFSHPS TIDVVGGAPQ DKGIGKVYIF RADRRSGTLI KIFQASGKKM
GSYFGSSLCA VDLNGDGLSD LLVGAPMFSE IRDEGQVTVY INRGNGALEE QLALTGDGAY
NAHFGESIAS LDDLDNDGFP DVAIGAPKED DFAGAVYIYH GDAGGIVPQY SMKLSGQKIN
PVLRMFGQSI SGGIDMDGNG YPDVTVGAFM SDSVVLLRAR PVITVDVSIF LPGSINITAP
QCHDGQQPVN CLNVTTCFSF HGKHVPGEIG LNYVLMADVA KKEKGQMPRV YFVLLGETMG
QVTEKLQLTY MEETCRHYVA HVKRRVQDVI SPIVFEAAYS LSEHVTGEEE RELPPLTPVL
RWKKGQKIAQ KNQTVFERNC RSEDCAADLQ LQGKLLLSSM DEKTLYLALG AVKNISLNIS
ISNLGDDAYD ANVSFNVSRE LFFINMWQKE EMGISCELLE SDFLKCSVGF PFMRSKSKYE
FSVIFDTSHL SGEEEVLSFI VTAQSGNTER SESLHDNTLV LMVPLMHEVD TSITGIMSPT
SFVYGESVDA ANFIQLDDLE CHFQPINITL QVYNTGPSTL PGSSVSISFP NRLSSGGAEM
FHVQEMVVGQ EKGNCSFQKN PTPCIIPQEQ ENIFHTIFAF FTKSGRKVLD CEKPGISCLT
AHCNFSALAK EESRTIDIYM LLNTEILKKD SSSVIQFMSR AKVKVDPALR VVEIAHGNPE
EVTVVFEALH NLEPRGYVVG WIIAISLLVG ILIFLLLAVL LWKMGFFRRR YKEIIEAEKN
RKENEDSWDW VQKNQ*
mutated AA sequence MGGPAAPRGA GRLRALLLAL VVAGIPAGAY NLDPQRPVHF QGPADSFFGY AVLEHFHDNT
RWVLVGAPKA DSKYSPSVKS PGAVFKCRVH TNPDRRCTEL DMARGKNRGT SCGKTCREDR
DDEWMGVSLA RQPKADGRVL ACAHRWKNIY YEADHILPHG FCYIIPSNLQ AKGRTLIPCY
EEYKKKYGEE HGSCQAGIAG FFTEELVVMG APGSFYWAGT IKVLNLTDNT YLKLNDEVIM
NRRYTYLGYA VTAGHFSHPS TIDVVGGAPQ DKGIGKVYIF RADRRSGTLI KIFQASGKKM
GSYFGSSLCA VDLNGDGLSD LLVGAPMFSE IRDEGQVTVY INRGNGALEE QLALTGDGAY
NAHFGESIAS LDDLDNDGFP DVAIGAPKED DFAGAVYIYH GDAGGIVPQY SMKLSGQKIN
PVLRMFGQSI SGGIDMDGNG YPDVTVGAFM SDSVVLLRAR PVITVDVSIF LPGSINITAP
QCHDGQQPVN CLNVTTCFSF HGKHVPEEIG LNYVLMADVA KKEKGQMPRV YFVLLGETMG
QVTEKLQLTY MEETCRHYVA HVKRRVQDVI SPIVFEAAYS LSEHVTGEEE RELPPLTPVL
RWKKGQKIAQ KNQTVFERNC RSEDCAADLQ LQGKLLLSSM DEKTLYLALG AVKNISLNIS
ISNLGDDAYD ANVSFNVSRE LFFINMWQKE EMGISCELLE SDFLKCSVGF PFMRSKSKYE
FSVIFDTSHL SGEEEVLSFI VTAQSGNTER SESLHDNTLV LMVPLMHEVD TSITGIMSPT
SFVYGESVDA ANFIQLDDLE CHFQPINITL QVYNTGPSTL PGSSVSISFP NRLSSGGAEM
FHVQEMVVGQ EKGNCSFQKN PTPCIIPQEQ ENIFHTIFAF FTKSGRKVLD CEKPGISCLT
AHCNFSALAK EESRTIDIYM LLNTEILKKD SSSVIQFMSR AKVKVDPALR VVEIAHGNPE
EVTVVFEALH NLEPRGYVVG WIIAISLLVG ILIFLLLAVL LWKMGFFRRR YKEIIEAEKN
RKENEDSWDW VQKNQ*
speed 0.74 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

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