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: ENST00000299440
MT speed 1.36 s - this script 5.986866 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
RAG1polymorphism_automatic6.99440505513849e-15simple_aaeH249Rsingle base exchangers3740955show file

Taster files

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documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999993 (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
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:36595600A>GN/A show variant in all transcripts   IGV
HGNC symbol RAG1
Ensembl transcript ID ENST00000299440
Genbank transcript ID NM_000448
UniProt peptide P15918
alteration type single base exchange
alteration region CDS
DNA changes c.746A>G
cDNA.858A>G
g.63342A>G
AA changes H249R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS
249
frameshift no
known variant Reference ID: rs3740955
databasehomozygous (G/G)heterozygousallele carriers
1000G101910342053
ExAC13935489718832
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.130
-0.5260
(flanking)0.1530.006
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 760
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      249TVLDQARQARQHKRRAQARISSKD
mutated  not conserved    249DQARQARQRKRRAQARISSK
Ptroglodytes  not conserved  ENSPTRG00000003512  249DQARQARQRKRRAQARISSK
Mmulatta  not conserved  ENSMMUG00000018267  249DQARQARQRKRRAQARTSSK
Fcatus  all identical  ENSFCAG00000002908  249DRARRARRHKKRARARISSK
Mmusculus  not conserved  ENSMUSG00000061311  248NHAR--RDRRKRTQARVSSK
Ggallus  not conserved  ENSGALG00000007938  248IIAERARVNRGIKNQV---IKNK
Trubripes  not conserved  ENSTRUG00000001340  252RCDNSDGNADGERRNLERPALR
Drerio  not conserved  ENSDARG00000052122  245RDSSESSRVWRQTTENPDGKEWLKLSVQRG
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
1288REGIONInteraction with importin alpha-1.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3132 / 3132
position (AA) of stopcodon in wt / mu AA sequence 1044 / 1044
position of stopcodon in wt / mu cDNA 3244 / 3244
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 113 / 113
chromosome 11
strand 1
last intron/exon boundary 99
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 3132
coding sequence (CDS) position 746
cDNA position
(for ins/del: last normal base / first normal base)
858
gDNA position
(for ins/del: last normal base / first normal base)
63342
chromosomal position
(for ins/del: last normal base / first normal base)
36595600
original gDNA sequence snippet AGCAAGACAAGCCCGTCAGCACAAGAGAAGAGCTCAGGCAA
altered gDNA sequence snippet AGCAAGACAAGCCCGTCAGCGCAAGAGAAGAGCTCAGGCAA
original cDNA sequence snippet AGCAAGACAAGCCCGTCAGCACAAGAGAAGAGCTCAGGCAA
altered cDNA sequence snippet AGCAAGACAAGCCCGTCAGCGCAAGAGAAGAGCTCAGGCAA
wildtype AA sequence MAASFPPTLG LSSAPDEIQH PHIKFSEWKF KLFRVRSFEK TPEEAQKEKK DSFEGKPSLE
QSPAVLDKAD GQKPVPTQPL LKAHPKFSKK FHDNEKARGK AIHQANLRHL CRICGNSFRA
DEHNRRYPVH GPVDGKTLGL LRKKEKRATS WPDLIAKVFR IDVKADVDSI HPTEFCHNCW
SIMHRKFSSA PCEVYFPRNV TMEWHPHTPS CDICNTARRG LKRKSLQPNL QLSKKLKTVL
DQARQARQHK RRAQARISSK DVMKKIANCS KIHLSTKLLA VDFPEHFVKS ISCQICEHIL
ADPVETNCKH VFCRVCILRC LKVMGSYCPS CRYPCFPTDL ESPVKSFLSV LNSLMVKCPA
KECNEEVSLE KYNHHISSHK ESKEIFVHIN KGGRPRQHLL SLTRRAQKHR LRELKLQVKA
FADKEEGGDV KSVCMTLFLL ALRARNEHRQ ADELEAIMQG KGSGLQPAVC LAIRVNTFLS
CSQYHKMYRT VKAITGRQIF QPLHALRNAE KVLLPGYHHF EWQPPLKNVS SSTDVGIIDG
LSGLSSSVDD YPVDTIAKRF RYDSALVSAL MDMEEDILEG MRSQDLDDYL NGPFTVVVKE
SCDGMGDVSE KHGSGPVVPE KAVRFSFTIM KITIAHSSQN VKVFEEAKPN SELCCKPLCL
MLADESDHET LTAILSPLIA EREAMKSSEL MLELGGILRT FKFIFRGTGY DEKLVREVEG
LEASGSVYIC TLCDATRLEA SQNLVFHSIT RSHAENLERY EVWRSNPYHE SVEELRDRVK
GVSAKPFIET VPSIDALHCD IGNAAEFYKI FQLEIGEVYK NPNASKEERK RWQATLDKHL
RKKMNLKPIM RMNGNFARKL MTKETVDAVC ELIPSEERHE ALRELMDLYL KMKPVWRSSC
PAKECPESLC QYSFNSQRFA ELLSTKFKYR YEGKITNYFH KTLAHVPEII ERDGSIGAWA
SEGNESGNKL FRRFRKMNAR QSKCYEMEDV LKHHWLYTSK YLQKFMNAHN ALKTSGFTMN
PQASLGDPLG IEDSLESQDS MEF*
mutated AA sequence MAASFPPTLG LSSAPDEIQH PHIKFSEWKF KLFRVRSFEK TPEEAQKEKK DSFEGKPSLE
QSPAVLDKAD GQKPVPTQPL LKAHPKFSKK FHDNEKARGK AIHQANLRHL CRICGNSFRA
DEHNRRYPVH GPVDGKTLGL LRKKEKRATS WPDLIAKVFR IDVKADVDSI HPTEFCHNCW
SIMHRKFSSA PCEVYFPRNV TMEWHPHTPS CDICNTARRG LKRKSLQPNL QLSKKLKTVL
DQARQARQRK RRAQARISSK DVMKKIANCS KIHLSTKLLA VDFPEHFVKS ISCQICEHIL
ADPVETNCKH VFCRVCILRC LKVMGSYCPS CRYPCFPTDL ESPVKSFLSV LNSLMVKCPA
KECNEEVSLE KYNHHISSHK ESKEIFVHIN KGGRPRQHLL SLTRRAQKHR LRELKLQVKA
FADKEEGGDV KSVCMTLFLL ALRARNEHRQ ADELEAIMQG KGSGLQPAVC LAIRVNTFLS
CSQYHKMYRT VKAITGRQIF QPLHALRNAE KVLLPGYHHF EWQPPLKNVS SSTDVGIIDG
LSGLSSSVDD YPVDTIAKRF RYDSALVSAL MDMEEDILEG MRSQDLDDYL NGPFTVVVKE
SCDGMGDVSE KHGSGPVVPE KAVRFSFTIM KITIAHSSQN VKVFEEAKPN SELCCKPLCL
MLADESDHET LTAILSPLIA EREAMKSSEL MLELGGILRT FKFIFRGTGY DEKLVREVEG
LEASGSVYIC TLCDATRLEA SQNLVFHSIT RSHAENLERY EVWRSNPYHE SVEELRDRVK
GVSAKPFIET VPSIDALHCD IGNAAEFYKI FQLEIGEVYK NPNASKEERK RWQATLDKHL
RKKMNLKPIM RMNGNFARKL MTKETVDAVC ELIPSEERHE ALRELMDLYL KMKPVWRSSC
PAKECPESLC QYSFNSQRFA ELLSTKFKYR YEGKITNYFH KTLAHVPEII ERDGSIGAWA
SEGNESGNKL FRRFRKMNAR QSKCYEMEDV LKHHWLYTSK YLQKFMNAHN ALKTSGFTMN
PQASLGDPLG IEDSLESQDS MEF*
speed 1.36 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