Yum, tasty mutations...

MutationTaster - study a chromosomal position

MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000367033
MT speed 2.01 s - this script 6.77205 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
PLXNA2polymorphism_automatic0.149928559553791simple_aaeaffectedR5Qsingle base exchangers2782948show file

Taster files

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mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.850071440446209 (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) chr1:208391254C>TN/A show variant in all transcripts   IGV
HGNC symbol PLXNA2
Ensembl transcript ID ENST00000367033
Genbank transcript ID NM_025179
UniProt peptide O75051
alteration type single base exchange
alteration region CDS
DNA changes c.14G>A
cDNA.772G>A
g.26412G>A
AA changes R5Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS
5
frameshift no
known variant Reference ID: rs2782948
databasehomozygous (T/T)heterozygousallele carriers
1000G35311201473
ExAC70411868525726
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)1.160.979
4.2281
(flanking)0.7661
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased26404wt: 0.57 / mu: 0.69wt: ATGGAACAGAGGCGG
mu: ATGGAACAGAGGCAG
 GGAA|caga
Donor gained264080.87mu: AACAGAGGCAGCCCT CAGA|ggca
distance from splice site 94
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      5 MEQRRPWPRALEVDSRS
mutated  all conserved    5 MEQRQPWPRALEVDSRSVVLLS
Ptroglodytes  all identical  ENSPTRG00000001933  5 MEQRRPWPRALEVDSRSVVLLS
Mmulatta  all identical  ENSMMUG00000004563  5 MEQRRPWSRAPEVDSRSVVLLS
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000026640  5 MEQRRFYLRAMQADNLSVVLLS
Ggallus  not conserved  ENSGALG00000001264  15 MDRRRTCPWALRSDGDGRSASLLC
Trubripes  no alignment  ENSTRUG00000002260  n/a
Drerio  no alignment  ENSDARG00000060372  n/a
Dmelanogaster  no alignment  FBgn0025741  n/a
Celegans  no alignment  Y55F3AL.1  n/a
Xtropicalis  no alignment  ENSXETG00000017724  n/a
protein features
start (aa)end (aa)featuredetails 
134SIGNALPotential.lost
35508DOMAINSema.might get lost (downstream of altered splice site)
351237TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
7676CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
9191CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
9494CONFLICTC -> R (in Ref. 2; AAQ88860).might get lost (downstream of altered splice site)
9494DISULFIDBy similarity.might get lost (downstream of altered splice site)
103103DISULFIDBy similarity.might get lost (downstream of altered splice site)
129129DISULFIDBy similarity.might get lost (downstream of altered splice site)
137137DISULFIDBy similarity.might get lost (downstream of altered splice site)
284284DISULFIDBy similarity.might get lost (downstream of altered splice site)
300300DISULFIDBy similarity.might get lost (downstream of altered splice site)
327327CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
356356DISULFIDBy similarity.might get lost (downstream of altered splice site)
374374DISULFIDBy similarity.might get lost (downstream of altered splice site)
393393DISULFIDBy similarity.might get lost (downstream of altered splice site)
405405DISULFIDBy similarity.might get lost (downstream of altered splice site)
511511DISULFIDBy similarity.might get lost (downstream of altered splice site)
517517DISULFIDBy similarity.might get lost (downstream of altered splice site)
520520DISULFIDBy similarity.might get lost (downstream of altered splice site)
528528DISULFIDBy similarity.might get lost (downstream of altered splice site)
531531DISULFIDBy similarity.might get lost (downstream of altered splice site)
537537DISULFIDBy similarity.might get lost (downstream of altered splice site)
543543DISULFIDBy similarity.might get lost (downstream of altered splice site)
559559DISULFIDBy similarity.might get lost (downstream of altered splice site)
594594DISULFIDBy similarity.might get lost (downstream of altered splice site)
598598CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
599599CONFLICTL -> P (in Ref. 5; CAB57275).might get lost (downstream of altered splice site)
613613DISULFIDBy similarity.might get lost (downstream of altered splice site)
661661CONFLICTL -> P (in Ref. 5; CAB57275).might get lost (downstream of altered splice site)
696696CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
756756CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
858951DOMAINIPT/TIG 1.might get lost (downstream of altered splice site)
9541037DOMAINIPT/TIG 2.might get lost (downstream of altered splice site)
10411139DOMAINIPT/TIG 3.might get lost (downstream of altered splice site)
10851085CONFLICTN -> V (in Ref. 4; AAH09343).might get lost (downstream of altered splice site)
11431228DOMAINIPT/TIG 4.might get lost (downstream of altered splice site)
12051205CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
12381258TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
12591894TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
12611310COILEDPotential.might get lost (downstream of altered splice site)
13781378CONFLICTF -> L (in Ref. 5; CAB57275).might get lost (downstream of altered splice site)
14321432MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
14991504STRANDmight get lost (downstream of altered splice site)
15151520STRANDmight get lost (downstream of altered splice site)
15251536HELIXmight get lost (downstream of altered splice site)
15481550HELIXmight get lost (downstream of altered splice site)
15511557STRANDmight get lost (downstream of altered splice site)
15581560TURNmight get lost (downstream of altered splice site)
15611565STRANDmight get lost (downstream of altered splice site)
15671569STRANDmight get lost (downstream of altered splice site)
15841587HELIXmight get lost (downstream of altered splice site)
15941599STRANDmight get lost (downstream of altered splice site)
16301630MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
16331633MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
17001700CONFLICTF -> L (in Ref. 4; AAH09343).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 5685 / 5685
position (AA) of stopcodon in wt / mu AA sequence 1895 / 1895
position of stopcodon in wt / mu cDNA 6443 / 6443
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 759 / 759
chromosome 1
strand -1
last intron/exon boundary 6348
theoretical NMD boundary in CDS 5539
length of CDS 5685
coding sequence (CDS) position 14
cDNA position
(for ins/del: last normal base / first normal base)
772
gDNA position
(for ins/del: last normal base / first normal base)
26412
chromosomal position
(for ins/del: last normal base / first normal base)
208391254
original gDNA sequence snippet TCTCAGCATGGAACAGAGGCGGCCCTGGCCCCGGGCCCTGG
altered gDNA sequence snippet TCTCAGCATGGAACAGAGGCAGCCCTGGCCCCGGGCCCTGG
original cDNA sequence snippet TCTCAGCATGGAACAGAGGCGGCCCTGGCCCCGGGCCCTGG
altered cDNA sequence snippet TCTCAGCATGGAACAGAGGCAGCCCTGGCCCCGGGCCCTGG
wildtype AA sequence MEQRRPWPRA LEVDSRSVVL LSVVWVLLAP PAAGMPQFST FHSENRDWTF NHLTVHQGTG
AVYVGAINRV YKLTGNLTIQ VAHKTGPEED NKSCYPPLIV QPCSEVLTLT NNVNKLLIID
YSENRLLACG SLYQGVCKLL RLDDLFILVE PSHKKEHYLS SVNKTGTMYG VIVRSEGEDG
KLFIGTAVDG KQDYFPTLSS RKLPRDPESS AMLDYELHSD FVSSLIKIPS DTLALVSHFD
IFYIYGFASG GFVYFLTVQP ETPEGVAINS AGDLFYTSRI VRLCKDDPKF HSYVSLPFGC
TRAGVEYRLL QAAYLAKPGD SLAQAFNITS QDDVLFAIFS KGQKQYHHPP DDSALCAFPI
RAINLQIKER LQSCYQGEGN LELNWLLGKD VQCTKAPVPI DDNFCGLDIN QPLGGSTPVE
GLTLYTTSRD RMTSVASYVY NGYSVVFVGT KSGKLKKIRA DGPPHGGVQY EMVSVLKDGS
PILRDMAFSI DQRYLYVMSE RQVTRVPVES CEQYTTCGEC LSSGDPHCGW CALHNMCSRR
DKCQQAWEPN RFAASISQCV SLAVHPSSIS VSEHSRLLSL VVSDAPDLSA GIACAFGNLT
EVEGQVSGSQ VICISPGPKD VPVIPLDQDW FGLELQLRSK ETGKIFVSTE FKFYNCSAHQ
LCLSCVNSAF RCHWCKYRNL CTHDPTTCSF QEGRINISED CPQLVPTEEI LIPVGEVKPI
TLKARNLPQP QSGQRGYECV LNIQGAIHRV PALRFNSSSV QCQNSSYQYD GMDISNLAVD
FAVVWNGNFI IDNPQDLKVH LYKCAAQRES CGLCLKADRK FECGWCSGER RCTLHQHCTS
PSSPWLDWSS HNVKCSNPQI TEILTVSGPP EGGTRVTIHG VNLGLDFSEI AHHVQVAGVP
CTPLPGEYII AEQIVCEMGH ALVGTTSGPV RLCIGECKPE FMTKSHQQYT FVNPSVLSLN
PIRGPESGGT MVTITGHYLG AGSSVAVYLG NQTCEFYGRS MSEIVCVSPP SSNGLGPVPV
SVSVDRAHVD SNLQFEYIDD PRVQRIEPEW SIASGHTPLT ITGFNLDVIQ EPRIRVKFNG
KESVNVCKVV NTTTLTCLAP SLTTDYRPGL DTVERPDEFG FVFNNVQSLL IYNDTKFIYY
PNPTFELLSP TGVLDQKPGS PIILKGKNLC PPASGGAKLN YTVLIGETPC AVTVSETQLL
CEPPNLTGQH KVMVHVGGMV FSPGSVSVIS DSLLTLPAIV SIAAGGSLLL IIVIIVLIAY
KRKSRENDLT LKRLQMQMDN LESRVALECK EAFAELQTDI NELTSDLDRS GIPYLDYRTY
AMRVLFPGIE DHPVLRELEV QGNGQQHVEK ALKLFAQLIN NKVFLLTFIR TLELQRSFSM
RDRGNVASLI MTGLQGRLEY ATDVLKQLLS DLIDKNLENK NHPKLLLRRT ESVAEKMLTN
WFAFLLHKFL KECAGEPLFM LYCAIKQQME KGPIDAITGE ARYSLSEDKL IRQQIEYKTL
ILNCVNPDNE NSPEIPVKVL NCDTITQVKE KILDAVYKNV PYSQRPRAVD MDLEWRQGRI
ARVVLQDEDI TTKIEGDWKR LNTLMHYQVS DRSVVALVPK QTSSYNIPAS ASISRTSISR
YDSSFRYTGS PDSLRSRAPM ITPDLESGVK VWHLVKNHDH GDQKEGDRGS KMVSEIYLTR
LLATKGTLQK FVDDLFETLF STVHRGSALP LAIKYMFDFL DEQADRHSIH DTDVRHTWKS
NCLPLRFWVN VIKNPQFVFD IHKGSITDAC LSVVAQTFMD SCSTSEHRLG KDSPSNKLLY
AKDIPSYKSW VERYYADIAK LPAISDQDMN AYLAEQSRLH AVEFNMLSAL NEIYSYVSKY
SEELIGALEQ DEQARRQRLA YKVEQLINAM SIES*
mutated AA sequence MEQRQPWPRA LEVDSRSVVL LSVVWVLLAP PAAGMPQFST FHSENRDWTF NHLTVHQGTG
AVYVGAINRV YKLTGNLTIQ VAHKTGPEED NKSCYPPLIV QPCSEVLTLT NNVNKLLIID
YSENRLLACG SLYQGVCKLL RLDDLFILVE PSHKKEHYLS SVNKTGTMYG VIVRSEGEDG
KLFIGTAVDG KQDYFPTLSS RKLPRDPESS AMLDYELHSD FVSSLIKIPS DTLALVSHFD
IFYIYGFASG GFVYFLTVQP ETPEGVAINS AGDLFYTSRI VRLCKDDPKF HSYVSLPFGC
TRAGVEYRLL QAAYLAKPGD SLAQAFNITS QDDVLFAIFS KGQKQYHHPP DDSALCAFPI
RAINLQIKER LQSCYQGEGN LELNWLLGKD VQCTKAPVPI DDNFCGLDIN QPLGGSTPVE
GLTLYTTSRD RMTSVASYVY NGYSVVFVGT KSGKLKKIRA DGPPHGGVQY EMVSVLKDGS
PILRDMAFSI DQRYLYVMSE RQVTRVPVES CEQYTTCGEC LSSGDPHCGW CALHNMCSRR
DKCQQAWEPN RFAASISQCV SLAVHPSSIS VSEHSRLLSL VVSDAPDLSA GIACAFGNLT
EVEGQVSGSQ VICISPGPKD VPVIPLDQDW FGLELQLRSK ETGKIFVSTE FKFYNCSAHQ
LCLSCVNSAF RCHWCKYRNL CTHDPTTCSF QEGRINISED CPQLVPTEEI LIPVGEVKPI
TLKARNLPQP QSGQRGYECV LNIQGAIHRV PALRFNSSSV QCQNSSYQYD GMDISNLAVD
FAVVWNGNFI IDNPQDLKVH LYKCAAQRES CGLCLKADRK FECGWCSGER RCTLHQHCTS
PSSPWLDWSS HNVKCSNPQI TEILTVSGPP EGGTRVTIHG VNLGLDFSEI AHHVQVAGVP
CTPLPGEYII AEQIVCEMGH ALVGTTSGPV RLCIGECKPE FMTKSHQQYT FVNPSVLSLN
PIRGPESGGT MVTITGHYLG AGSSVAVYLG NQTCEFYGRS MSEIVCVSPP SSNGLGPVPV
SVSVDRAHVD SNLQFEYIDD PRVQRIEPEW SIASGHTPLT ITGFNLDVIQ EPRIRVKFNG
KESVNVCKVV NTTTLTCLAP SLTTDYRPGL DTVERPDEFG FVFNNVQSLL IYNDTKFIYY
PNPTFELLSP TGVLDQKPGS PIILKGKNLC PPASGGAKLN YTVLIGETPC AVTVSETQLL
CEPPNLTGQH KVMVHVGGMV FSPGSVSVIS DSLLTLPAIV SIAAGGSLLL IIVIIVLIAY
KRKSRENDLT LKRLQMQMDN LESRVALECK EAFAELQTDI NELTSDLDRS GIPYLDYRTY
AMRVLFPGIE DHPVLRELEV QGNGQQHVEK ALKLFAQLIN NKVFLLTFIR TLELQRSFSM
RDRGNVASLI MTGLQGRLEY ATDVLKQLLS DLIDKNLENK NHPKLLLRRT ESVAEKMLTN
WFAFLLHKFL KECAGEPLFM LYCAIKQQME KGPIDAITGE ARYSLSEDKL IRQQIEYKTL
ILNCVNPDNE NSPEIPVKVL NCDTITQVKE KILDAVYKNV PYSQRPRAVD MDLEWRQGRI
ARVVLQDEDI TTKIEGDWKR LNTLMHYQVS DRSVVALVPK QTSSYNIPAS ASISRTSISR
YDSSFRYTGS PDSLRSRAPM ITPDLESGVK VWHLVKNHDH GDQKEGDRGS KMVSEIYLTR
LLATKGTLQK FVDDLFETLF STVHRGSALP LAIKYMFDFL DEQADRHSIH DTDVRHTWKS
NCLPLRFWVN VIKNPQFVFD IHKGSITDAC LSVVAQTFMD SCSTSEHRLG KDSPSNKLLY
AKDIPSYKSW VERYYADIAK LPAISDQDMN AYLAEQSRLH AVEFNMLSAL NEIYSYVSKY
SEELIGALEQ DEQARRQRLA YKVEQLINAM SIES*
speed 2.01 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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