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 5 transcript(s)...
Querying Taster for transcript #1: ENST00000479209
Querying Taster for transcript #2: ENST00000487799
Querying Taster for transcript #3: ENST00000460851
Querying Taster for transcript #4: ENST00000406576
Querying Taster for transcript #5: ENST00000273435
MT speed 9.91 s - this script 9.097263 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
EIF2Apolymorphism_automatic0.001134884899753simple_aaeaffectedT97Ssingle base exchangers1132979show file
EIF2Apolymorphism_automatic0.998505140093903simple_aaeaffectedT72Ssingle base exchangers1132979show file
EIF2Apolymorphism_automatic0.998505140093903simple_aaeaffectedT97Ssingle base exchangers1132979show file
EIF2Apolymorphism_automatic0.998505140093903simple_aaeaffectedT92Ssingle base exchangers1132979show file
SERP1polymorphism_automatic1without_aaeaffectedsingle base exchangers1132979show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.998865115100247 (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) chr3:150280445C>GN/A show variant in all transcripts   IGV
HGNC symbol EIF2A
Ensembl transcript ID ENST00000406576
Genbank transcript ID N/A
UniProt peptide Q9BY44
alteration type single base exchange
alteration region CDS
DNA changes c.290C>G
cDNA.306C>G
g.15981C>G
AA changes T97S Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
97
frameshift no
known variant Reference ID: rs1132979
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC79401688724827
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5540.899
3.8481
(flanking)1.0441
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost15982sequence motif lost- wt: ACTA|gtaa
 mu: AGTA.gtaa
Donor marginally decreased15982wt: 0.9826 / mu: 0.9823 (marginal change - not scored)wt: TACACTAGTAAGTAT
mu: TACAGTAGTAAGTAT
 CACT|agta
Donor gained159800.30mu: CTTACAGTAGTAAGT TACA|gtag
distance from splice site 3
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      97KNTVLATWQPYTNTIANKLHLQKI
mutated  all conserved    97KNTVLATWQPYSNTIANKLHLQK
Ptroglodytes  not conserved  ENSPTRG00000015528  136KK--MQNWCPSWSEDETLCARSVNNEVHFFENNNFNTIANKLHLQK
Mmulatta  not conserved  ENSMMUG00000017696  158KKT--QNWCPSWSEDETLCARNVNNEVHFFENNNFNTIANKLHLQK
Fcatus  all identical  ENSFCAG00000011331  120KNTVL-TWQPYTTS
Mmusculus  not conserved  ENSMUSG00000027810  136KK--MQNWCPSWSDDEIICARNVNNEVHFFENNNFNTIANKLHLQK
Ggallus  not conserved  ENSGALG00000010401  98KNNILATWQAYSAAKDGTAGAPNLQLYDVKTGKCLKSFIQKK
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000044479  96LNKVLATWQQYTKTQDNPQGEANLQLWDLQTGACM
Dmelanogaster  not conserved  FBgn0037135  104RGSYLCTWEHYAIT
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000020093  136KK--MENWSPCWSDDESICARNVNNEVHFFENNNFDTIANKLHLQK
protein features
start (aa)end (aa)featuredetails 
125163REPEATWD 2.might get lost (downstream of altered splice site)
150150CONFLICTV -> A (in Ref. 4; AAQ13612).might get lost (downstream of altered splice site)
173173CONFLICTF -> S (in Ref. 4; AAQ13612).might get lost (downstream of altered splice site)
261261CONFLICTT -> P (in Ref. 1; AAM83402).might get lost (downstream of altered splice site)
263263CONFLICTG -> F (in Ref. 1; AAM83402).might get lost (downstream of altered splice site)
268268CONFLICTV -> L (in Ref. 1; AAM83402).might get lost (downstream of altered splice site)
292292CONFLICTY -> S (in Ref. 1; AAM83402).might get lost (downstream of altered splice site)
356401REPEATWD 3.might get lost (downstream of altered splice site)
503503MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
506506MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
512512MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
517517MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
518518MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
522522MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
531582COILEDPotential.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1575 / 1575
position (AA) of stopcodon in wt / mu AA sequence 525 / 525
position of stopcodon in wt / mu cDNA 1591 / 1591
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 17 / 17
chromosome 3
strand 1
last intron/exon boundary 1526
theoretical NMD boundary in CDS 1459
length of CDS 1575
coding sequence (CDS) position 290
cDNA position
(for ins/del: last normal base / first normal base)
306
gDNA position
(for ins/del: last normal base / first normal base)
15981
chromosomal position
(for ins/del: last normal base / first normal base)
150280445
original gDNA sequence snippet GGCAACGTGGCAGCCTTACACTAGTAAGTATTTTCTCAGTG
altered gDNA sequence snippet GGCAACGTGGCAGCCTTACAGTAGTAAGTATTTTCTCAGTG
original cDNA sequence snippet GGCAACGTGGCAGCCTTACACTAACACAATTGCAAATAAAT
altered cDNA sequence snippet GGCAACGTGGCAGCCTTACAGTAACACAATTGCAAATAAAT
wildtype AA sequence MAPSTPLLTV RGSEGLYMVN GPPHFTESTV FPRESGKNCK VCIFSKDGTL FAWGNGEKVN
IISVTNKGLL HSFDLLKAVC LEFSPKNTVL ATWQPYTNTI ANKLHLQKIN DFVLSPGPQP
YKVAVYVPGS KGAPSFVRLY QYPNFAGPHA ALANKSFFKA DKVTMLWNKK ATAVLVIAST
DVDKTGASYY GEQTLHYIAT NGESAVVQLP KNGPIYDVVW NSSSTEFCAV YGFMPAKATI
FNLKCDPVFD FGTGPRNAAY YSPHGHILVL AGFGNLRGQM EVWDVKNYKL ISKPVASDST
YFAWCPDGEH ILTATCAPRL RVNNGYKIWH YTGSILHKYD VPSNAELWQV SWQPFLDGIF
PAKTITYQAV PSEVPNEEPK VATAYRPPAL RNKPITNSKL HEEEPPQNMK PQSGNDKPLS
KTALKNQRKH EAKKAAKQEA RSDKSPDLAP TPAPQSTPRN TVSQSISGDP EIDKKIKNLK
KKLKAIEQLK EQAATGKQLE KNQLEKIQKE TALLQELEDL ELGI*
mutated AA sequence MAPSTPLLTV RGSEGLYMVN GPPHFTESTV FPRESGKNCK VCIFSKDGTL FAWGNGEKVN
IISVTNKGLL HSFDLLKAVC LEFSPKNTVL ATWQPYSNTI ANKLHLQKIN DFVLSPGPQP
YKVAVYVPGS KGAPSFVRLY QYPNFAGPHA ALANKSFFKA DKVTMLWNKK ATAVLVIAST
DVDKTGASYY GEQTLHYIAT NGESAVVQLP KNGPIYDVVW NSSSTEFCAV YGFMPAKATI
FNLKCDPVFD FGTGPRNAAY YSPHGHILVL AGFGNLRGQM EVWDVKNYKL ISKPVASDST
YFAWCPDGEH ILTATCAPRL RVNNGYKIWH YTGSILHKYD VPSNAELWQV SWQPFLDGIF
PAKTITYQAV PSEVPNEEPK VATAYRPPAL RNKPITNSKL HEEEPPQNMK PQSGNDKPLS
KTALKNQRKH EAKKAAKQEA RSDKSPDLAP TPAPQSTPRN TVSQSISGDP EIDKKIKNLK
KKLKAIEQLK EQAATGKQLE KNQLEKIQKE TALLQELEDL ELGI*
speed 2.12 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: 0.00149485990609738 (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) chr3:150280445C>GN/A show variant in all transcripts   IGV
HGNC symbol EIF2A
Ensembl transcript ID ENST00000487799
Genbank transcript ID N/A
UniProt peptide Q9BY44
alteration type single base exchange
alteration region CDS
DNA changes c.215C>G
cDNA.333C>G
g.15981C>G
AA changes T72S Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
72
frameshift no
known variant Reference ID: rs1132979
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC79401688724827
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5540.899
3.8481
(flanking)1.0441
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost15982sequence motif lost- wt: ACTA|gtaa
 mu: AGTA.gtaa
Donor marginally decreased15982wt: 0.9826 / mu: 0.9823 (marginal change - not scored)wt: TACACTAGTAAGTAT
mu: TACAGTAGTAAGTAT
 CACT|agta
Donor gained159800.30mu: CTTACAGTAGTAAGT TACA|gtag
distance from splice site 3
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      72KNTVLATWQPYTTSKDGTAGIPNL
mutated  all conserved    72KNTVLATWQPYSTSKDGTAGIPN
Ptroglodytes  all identical  ENSPTRG00000015528  97KNTVLATWQPYTTSKDGTAGIPN
Mmulatta  all identical  ENSMMUG00000017696  119KNTVLATWQPYTTSKDGTAGIPN
Fcatus  all identical  ENSFCAG00000011331  120KNTVL-TWQPYTTSKDGTAGVPN
Mmusculus  all identical  ENSMUSG00000027810  97NNTVLATWQPYTTSKDGTAGTPN
Ggallus  all conserved  ENSGALG00000010401  98KNNILATWQAYSAAKDGTAGAPN
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000044479  96LNKVLATWQQYTKTQDNPQGEAN
Dmelanogaster  not conserved  FBgn0037135  109RGSYLCTWEHYAITKDRPEGSPN
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000020093  97KNTILATWQTYTTGKDGTAGTPN
protein features
start (aa)end (aa)featuredetails 
8484CONFLICTS -> P (in Ref. 2; BAB55058).might get lost (downstream of altered splice site)
125163REPEATWD 2.might get lost (downstream of altered splice site)
150150CONFLICTV -> A (in Ref. 4; AAQ13612).might get lost (downstream of altered splice site)
173173CONFLICTF -> S (in Ref. 4; AAQ13612).might get lost (downstream of altered splice site)
261261CONFLICTT -> P (in Ref. 1; AAM83402).might get lost (downstream of altered splice site)
263263CONFLICTG -> F (in Ref. 1; AAM83402).might get lost (downstream of altered splice site)
268268CONFLICTV -> L (in Ref. 1; AAM83402).might get lost (downstream of altered splice site)
292292CONFLICTY -> S (in Ref. 1; AAM83402).might get lost (downstream of altered splice site)
356401REPEATWD 3.might get lost (downstream of altered splice site)
503503MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
506506MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
512512MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
517517MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
518518MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
522522MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
531582COILEDPotential.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1683 / 1683
position (AA) of stopcodon in wt / mu AA sequence 561 / 561
position of stopcodon in wt / mu cDNA 1801 / 1801
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 119 / 119
chromosome 3
strand 1
last intron/exon boundary 1736
theoretical NMD boundary in CDS 1567
length of CDS 1683
coding sequence (CDS) position 215
cDNA position
(for ins/del: last normal base / first normal base)
333
gDNA position
(for ins/del: last normal base / first normal base)
15981
chromosomal position
(for ins/del: last normal base / first normal base)
150280445
original gDNA sequence snippet GGCAACGTGGCAGCCTTACACTAGTAAGTATTTTCTCAGTG
altered gDNA sequence snippet GGCAACGTGGCAGCCTTACAGTAGTAAGTATTTTCTCAGTG
original cDNA sequence snippet GGCAACGTGGCAGCCTTACACTACTTCTAAAGATGGCACAG
altered cDNA sequence snippet GGCAACGTGGCAGCCTTACAGTACTTCTAAAGATGGCACAG
wildtype AA sequence MAPSTPLLTV RGSEGLYMVN GPPHFTESTV FPRVNIISVT NKGLLHSFDL LKAVCLEFSP
KNTVLATWQP YTTSKDGTAG IPNLQLYDVK TGTCLKSFIQ KKMQNWCPSW SEDETLCARN
VNNEVHFFEN NNFNTIANKL HLQKINDFVL SPGPQPYKVA VYVPGSKGAP SFVRLYQYPN
FAGPHAALAN KSFFKADKVT MLWNKKATAV LVIASTDVDK TGASYYGEQT LHYIATNGES
AVVQLPKNGP IYDVVWNSSS TEFCAVYGFM PAKATIFNLK CDPVFDFGTG PRNAAYYSPH
GHILVLAGFG NLRGQMEVWD VKNYKLISKP VASDSTYFAW CPDGEHILTA TCAPRLRVNN
GYKIWHYTGS ILHKYDVPSN AELWQVSWQP FLDGIFPAKT ITYQAVPSEV PNEEPKVATA
YRPPALRNKP ITNSKLHEEE PPQNMKPQSG NDKPLSKTAL KNQRKHEAKK AAKQEARSDK
SPDLAPTPAP QSTPRNTVSQ SISGDPEIDK KIKNLKKKLK AIEQLKEQAA TGKQLEKNQL
EKIQKETALL QELEDLELGI *
mutated AA sequence MAPSTPLLTV RGSEGLYMVN GPPHFTESTV FPRVNIISVT NKGLLHSFDL LKAVCLEFSP
KNTVLATWQP YSTSKDGTAG IPNLQLYDVK TGTCLKSFIQ KKMQNWCPSW SEDETLCARN
VNNEVHFFEN NNFNTIANKL HLQKINDFVL SPGPQPYKVA VYVPGSKGAP SFVRLYQYPN
FAGPHAALAN KSFFKADKVT MLWNKKATAV LVIASTDVDK TGASYYGEQT LHYIATNGES
AVVQLPKNGP IYDVVWNSSS TEFCAVYGFM PAKATIFNLK CDPVFDFGTG PRNAAYYSPH
GHILVLAGFG NLRGQMEVWD VKNYKLISKP VASDSTYFAW CPDGEHILTA TCAPRLRVNN
GYKIWHYTGS ILHKYDVPSN AELWQVSWQP FLDGIFPAKT ITYQAVPSEV PNEEPKVATA
YRPPALRNKP ITNSKLHEEE PPQNMKPQSG NDKPLSKTAL KNQRKHEAKK AAKQEARSDK
SPDLAPTPAP QSTPRNTVSQ SISGDPEIDK KIKNLKKKLK AIEQLKEQAA TGKQLEKNQL
EKIQKETALL QELEDLELGI *
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: 0.00149485990609738 (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) chr3:150280445C>GN/A show variant in all transcripts   IGV
HGNC symbol EIF2A
Ensembl transcript ID ENST00000460851
Genbank transcript ID NM_032025
UniProt peptide Q9BY44
alteration type single base exchange
alteration region CDS
DNA changes c.290C>G
cDNA.399C>G
g.15981C>G
AA changes T97S Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
97
frameshift no
known variant Reference ID: rs1132979
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC79401688724827
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5540.899
3.8481
(flanking)1.0441
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost15982sequence motif lost- wt: ACTA|gtaa
 mu: AGTA.gtaa
Donor marginally decreased15982wt: 0.9826 / mu: 0.9823 (marginal change - not scored)wt: TACACTAGTAAGTAT
mu: TACAGTAGTAAGTAT
 CACT|agta
Donor gained159800.30mu: CTTACAGTAGTAAGT TACA|gtag
distance from splice site 3
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      97KNTVLATWQPYTTSKDGTAGIPNL
mutated  all conserved    97KNTVLATWQPYSTSKDGTAGIPN
Ptroglodytes  all identical  ENSPTRG00000015528  97KNTVLATWQPYTTSKDGTAGIPN
Mmulatta  all identical  ENSMMUG00000017696  119KNTVLATWQPYTTSKDGTAGIPN
Fcatus  all identical  ENSFCAG00000011331  120KNTVL-TWQPYTTSKDGTAGVPN
Mmusculus  all identical  ENSMUSG00000027810  97NNTVLATWQPYTTSKDGTAGTPN
Ggallus  all conserved  ENSGALG00000010401  98KNNILATWQAYSAAKDGTAGAPN
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000044479  96LNKVLATWQQYTKTQDNPQGEAN
Dmelanogaster  not conserved  FBgn0037135  104RGSYLCTWEHYAITKDRPEGSPN
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000020093  97KNTILATWQTYTTGKDGTAGTPN
protein features
start (aa)end (aa)featuredetails 
125163REPEATWD 2.might get lost (downstream of altered splice site)
150150CONFLICTV -> A (in Ref. 4; AAQ13612).might get lost (downstream of altered splice site)
173173CONFLICTF -> S (in Ref. 4; AAQ13612).might get lost (downstream of altered splice site)
261261CONFLICTT -> P (in Ref. 1; AAM83402).might get lost (downstream of altered splice site)
263263CONFLICTG -> F (in Ref. 1; AAM83402).might get lost (downstream of altered splice site)
268268CONFLICTV -> L (in Ref. 1; AAM83402).might get lost (downstream of altered splice site)
292292CONFLICTY -> S (in Ref. 1; AAM83402).might get lost (downstream of altered splice site)
356401REPEATWD 3.might get lost (downstream of altered splice site)
503503MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
506506MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
512512MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
517517MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
518518MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
522522MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
531582COILEDPotential.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1758 / 1758
position (AA) of stopcodon in wt / mu AA sequence 586 / 586
position of stopcodon in wt / mu cDNA 1867 / 1867
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 110 / 110
chromosome 3
strand 1
last intron/exon boundary 1802
theoretical NMD boundary in CDS 1642
length of CDS 1758
coding sequence (CDS) position 290
cDNA position
(for ins/del: last normal base / first normal base)
399
gDNA position
(for ins/del: last normal base / first normal base)
15981
chromosomal position
(for ins/del: last normal base / first normal base)
150280445
original gDNA sequence snippet GGCAACGTGGCAGCCTTACACTAGTAAGTATTTTCTCAGTG
altered gDNA sequence snippet GGCAACGTGGCAGCCTTACAGTAGTAAGTATTTTCTCAGTG
original cDNA sequence snippet GGCAACGTGGCAGCCTTACACTACTTCTAAAGATGGCACAG
altered cDNA sequence snippet GGCAACGTGGCAGCCTTACAGTACTTCTAAAGATGGCACAG
wildtype AA sequence MAPSTPLLTV RGSEGLYMVN GPPHFTESTV FPRESGKNCK VCIFSKDGTL FAWGNGEKVN
IISVTNKGLL HSFDLLKAVC LEFSPKNTVL ATWQPYTTSK DGTAGIPNLQ LYDVKTGTCL
KSFIQKKMQN WCPSWSEDET LCARNVNNEV HFFENNNFNT IANKLHLQKI NDFVLSPGPQ
PYKVAVYVPG SKGAPSFVRL YQYPNFAGPH AALANKSFFK ADKVTMLWNK KATAVLVIAS
TDVDKTGASY YGEQTLHYIA TNGESAVVQL PKNGPIYDVV WNSSSTEFCA VYGFMPAKAT
IFNLKCDPVF DFGTGPRNAA YYSPHGHILV LAGFGNLRGQ MEVWDVKNYK LISKPVASDS
TYFAWCPDGE HILTATCAPR LRVNNGYKIW HYTGSILHKY DVPSNAELWQ VSWQPFLDGI
FPAKTITYQA VPSEVPNEEP KVATAYRPPA LRNKPITNSK LHEEEPPQNM KPQSGNDKPL
SKTALKNQRK HEAKKAAKQE ARSDKSPDLA PTPAPQSTPR NTVSQSISGD PEIDKKIKNL
KKKLKAIEQL KEQAATGKQL EKNQLEKIQK ETALLQELED LELGI*
mutated AA sequence MAPSTPLLTV RGSEGLYMVN GPPHFTESTV FPRESGKNCK VCIFSKDGTL FAWGNGEKVN
IISVTNKGLL HSFDLLKAVC LEFSPKNTVL ATWQPYSTSK DGTAGIPNLQ LYDVKTGTCL
KSFIQKKMQN WCPSWSEDET LCARNVNNEV HFFENNNFNT IANKLHLQKI NDFVLSPGPQ
PYKVAVYVPG SKGAPSFVRL YQYPNFAGPH AALANKSFFK ADKVTMLWNK KATAVLVIAS
TDVDKTGASY YGEQTLHYIA TNGESAVVQL PKNGPIYDVV WNSSSTEFCA VYGFMPAKAT
IFNLKCDPVF DFGTGPRNAA YYSPHGHILV LAGFGNLRGQ MEVWDVKNYK LISKPVASDS
TYFAWCPDGE HILTATCAPR LRVNNGYKIW HYTGSILHKY DVPSNAELWQ VSWQPFLDGI
FPAKTITYQA VPSEVPNEEP KVATAYRPPA LRNKPITNSK LHEEEPPQNM KPQSGNDKPL
SKTALKNQRK HEAKKAAKQE ARSDKSPDLA PTPAPQSTPR NTVSQSISGD PEIDKKIKNL
KKKLKAIEQL KEQAATGKQL EKNQLEKIQK ETALLQELED LELGI*
speed 1.80 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: 0.00149485990609738 (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) chr3:150280445C>GN/A show variant in all transcripts   IGV
HGNC symbol EIF2A
Ensembl transcript ID ENST00000273435
Genbank transcript ID N/A
UniProt peptide Q9BY44
alteration type single base exchange
alteration region CDS
DNA changes c.275C>G
cDNA.284C>G
g.15981C>G
AA changes T92S Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
92
frameshift no
known variant Reference ID: rs1132979
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC79401688724827
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5540.899
3.8481
(flanking)1.0441
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost15982sequence motif lost- wt: ACTA|gtaa
 mu: AGTA.gtaa
Donor marginally decreased15982wt: 0.9826 / mu: 0.9823 (marginal change - not scored)wt: TACACTAGTAAGTAT
mu: TACAGTAGTAAGTAT
 CACT|agta
Donor gained159800.30mu: CTTACAGTAGTAAGT TACA|gtag
distance from splice site 3
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      92KNTVLATWQPYTTSKDGTAGIPNL
mutated  all conserved    92KNTVLATWQPYSTSKDGTAGIPN
Ptroglodytes  all identical  ENSPTRG00000015528  95KNTVLATWQPYTTSKDGTAGIPN
Mmulatta  all identical  ENSMMUG00000017696  114KNTVLATWQPYTTSKDGTAGIPN
Fcatus  all identical  ENSFCAG00000011331  118KNTVL-TWQPYTTSKDGTAGVPN
Mmusculus  all identical  ENSMUSG00000027810  95NNTVLATWQPYTTSKDGTAGTPN
Ggallus  all conserved  ENSGALG00000010401  98KNNILATWQAYSAAKDGTAGAPN
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000044479  91LNKVLATWQQYTKTQDNPQGEAN
Dmelanogaster  not conserved  FBgn0037135  102RGSYLCTWEHYAITKDRPEGSPN
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000020093  95KNTILATWQTYTTGKDGTAGTPN
protein features
start (aa)end (aa)featuredetails 
125163REPEATWD 2.might get lost (downstream of altered splice site)
150150CONFLICTV -> A (in Ref. 4; AAQ13612).might get lost (downstream of altered splice site)
173173CONFLICTF -> S (in Ref. 4; AAQ13612).might get lost (downstream of altered splice site)
261261CONFLICTT -> P (in Ref. 1; AAM83402).might get lost (downstream of altered splice site)
263263CONFLICTG -> F (in Ref. 1; AAM83402).might get lost (downstream of altered splice site)
268268CONFLICTV -> L (in Ref. 1; AAM83402).might get lost (downstream of altered splice site)
292292CONFLICTY -> S (in Ref. 1; AAM83402).might get lost (downstream of altered splice site)
356401REPEATWD 3.might get lost (downstream of altered splice site)
503503MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
506506MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
512512MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
517517MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
518518MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
522522MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
531582COILEDPotential.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1743 / 1743
position (AA) of stopcodon in wt / mu AA sequence 581 / 581
position of stopcodon in wt / mu cDNA 1752 / 1752
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 10 / 10
chromosome 3
strand 1
last intron/exon boundary 1687
theoretical NMD boundary in CDS 1627
length of CDS 1743
coding sequence (CDS) position 275
cDNA position
(for ins/del: last normal base / first normal base)
284
gDNA position
(for ins/del: last normal base / first normal base)
15981
chromosomal position
(for ins/del: last normal base / first normal base)
150280445
original gDNA sequence snippet GGCAACGTGGCAGCCTTACACTAGTAAGTATTTTCTCAGTG
altered gDNA sequence snippet GGCAACGTGGCAGCCTTACAGTAGTAAGTATTTTCTCAGTG
original cDNA sequence snippet GGCAACGTGGCAGCCTTACACTACTTCTAAAGATGGCACAG
altered cDNA sequence snippet GGCAACGTGGCAGCCTTACAGTACTTCTAAAGATGGCACAG
wildtype AA sequence MAPSTPLLTV RGSEGLYMVN GPPHFTESTV FPRESGKNCK VCIFSKDGTL FAWGNGENVT
NKGLLHSFDL LKAVCLEFSP KNTVLATWQP YTTSKDGTAG IPNLQLYDVK TGTCLKSFIQ
KKMQNWCPSW SEDETLCARN VNNEVHFFEN NNFNTIANKL HLQKINDFVL SPGPQPYKVA
VYVPGSKGAP SFVRLYQYPN FAGPHAALAN KSFFKADKVT MLWNKKATAV LVIASTDVDK
TGASYYGEQT LHYIATNGES AVVQLPKNGP IYDVVWNSSS TEFCAVYGFM PAKATIFNLK
CDPVFDFGTG PRNAAYYSPH GHILVLAGFG NLRGQMEVWD VKNYKLISKP VASDSTYFAW
CPDGEHILTA TCAPRLRVNN GYKIWHYTGS ILHKYDVPSN AELWQVSWQP FLDGIFPAKT
ITYQAVPSEV PNEEPKVATA YRPPALRNKP ITNSKLHEEE PPQNMKPQSG NDKPLSKTAL
KNQRKHEAKK AAKQEARSDK SPDLAPTPAP QSTPRNTVSQ SISGDPEIDK KIKNLKKKLK
AIEQLKEQAA TGKQLEKNQL EKIQKETALL QELEDLELGI *
mutated AA sequence MAPSTPLLTV RGSEGLYMVN GPPHFTESTV FPRESGKNCK VCIFSKDGTL FAWGNGENVT
NKGLLHSFDL LKAVCLEFSP KNTVLATWQP YSTSKDGTAG IPNLQLYDVK TGTCLKSFIQ
KKMQNWCPSW SEDETLCARN VNNEVHFFEN NNFNTIANKL HLQKINDFVL SPGPQPYKVA
VYVPGSKGAP SFVRLYQYPN FAGPHAALAN KSFFKADKVT MLWNKKATAV LVIASTDVDK
TGASYYGEQT LHYIATNGES AVVQLPKNGP IYDVVWNSSS TEFCAVYGFM PAKATIFNLK
CDPVFDFGTG PRNAAYYSPH GHILVLAGFG NLRGQMEVWD VKNYKLISKP VASDSTYFAW
CPDGEHILTA TCAPRLRVNN GYKIWHYTGS ILHKYDVPSN AELWQVSWQP FLDGIFPAKT
ITYQAVPSEV PNEEPKVATA YRPPALRNKP ITNSKLHEEE PPQNMKPQSG NDKPLSKTAL
KNQRKHEAKK AAKQEARSDK SPDLAPTPAP QSTPRNTVSQ SISGDPEIDK KIKNLKKKLK
AIEQLKEQAA TGKQLEKNQL EKIQKETALL QELEDLELGI *
speed 2.13 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: without_aae, prob: 3.61570111501746e-30 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • 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) chr3:150280445C>GN/A show variant in all transcripts   IGV
HGNC symbol SERP1
Ensembl transcript ID ENST00000479209
Genbank transcript ID N/A
UniProt peptide Q9Y6X1
alteration type single base exchange
alteration region intron
DNA changes g.40571G>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs1132979
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC79401688724827
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5540.899
3.8481
(flanking)1.0441
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -346) |
effectgDNA positionscoredetection sequence  exon-intron border
Donor marginally increased40571wt: 0.7369 / mu: 0.7602 (marginal change - not scored)wt: TACTAGTGTAAGGCT
mu: TACTACTGTAAGGCT
 CTAG|tgta
Donor marginally increased40572wt: 0.7646 / mu: 0.8072 (marginal change - not scored)wt: ACTAGTGTAAGGCTG
mu: ACTACTGTAAGGCTG
 TAGT|gtaa
Acc gained405760.53mu: AGAAAATACTTACTACTGTAAGGCTGCCACGTTGCCAGGAC gtaa|GGCT
distance from splice site 15481
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
N/A
protein features
start (aa)end (aa)featuredetails 
138TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
3959TRANSMEMHelical; Anchor for type IV membrane protein; (Potential).might get lost (downstream of altered splice site)
6066TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 1274 / 1274
chromosome 3
strand -1
last intron/exon boundary 1434
theoretical NMD boundary in CDS 110
length of CDS 201
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)
N/A
gDNA position
(for ins/del: last normal base / first normal base)
40571
chromosomal position
(for ins/del: last normal base / first normal base)
150280445
original gDNA sequence snippet CACTGAGAAAATACTTACTAGTGTAAGGCTGCCACGTTGCC
altered gDNA sequence snippet CACTGAGAAAATACTTACTACTGTAAGGCTGCCACGTTGCC
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MVAKQRIRMA NEKHSKNITQ RGNVAKTSRN APEEKASVGP WLLALFIFVV CGSAIFQIIQ
SIRMGM*
mutated AA sequence N/A
speed 2.40 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

Problems