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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: ENST00000337963
MT speed 0.76 s - this script 2.807099 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ZMYM5polymorphism_automatic9.99200722162641e-16simple_aaeaffectedH653Rsingle base exchangers9508907show file

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 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999999 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr13:20398669T>CN/A show variant in all transcripts   IGV
HGNC symbol ZMYM5
Ensembl transcript ID ENST00000337963
Genbank transcript ID NM_001142684
UniProt peptide Q9UJ78
alteration type single base exchange
alteration region CDS
DNA changes c.1958A>G
cDNA.2223A>G
g.39108A>G
AA changes H653R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 653
frameshift no
known variant Reference ID: rs9508907
databasehomozygous (C/C)heterozygousallele carriers
1000G16606792339
ExAC---
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.9390
0.0840
(flanking)0.0070.001
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased39107wt: 0.21 / mu: 0.97wt: CAGAACACAGATTAT
mu: CAGAACGCAGATTAT		 GAAC|acag
distance from splice site 707
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      653LKKNKAIDAAEHRLYENEKNDGVL
mutated  not conserved    653LKKNKAIDAAERRLYENEK
Ptroglodytes  not conserved  ENSPTRG00000005679  652LKKNKAIDAAERRLYENEK
Mmulatta  not conserved  ENSMMUG00000001920  477LKKNKAVDAAERRLY
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000040123  618LENKTNEATEGGE---------DCV
Ggallus  no alignment  ENSGALG00000017139  n/a
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000027353  n/a
Dmelanogaster  no alignment  FBgn0010328  n/a
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000002643  n/a
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2010 / 2010
position (AA) of stopcodon in wt / mu AA sequence 670 / 670
position of stopcodon in wt / mu cDNA 2275 / 2275
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 266 / 266
chromosome 13
strand -1
last intron/exon boundary 1517
theoretical NMD boundary in CDS 1201
length of CDS 2010
coding sequence (CDS) position 1958
cDNA position
(for ins/del: last normal base / first normal base)		 2223
gDNA position
(for ins/del: last normal base / first normal base)		 39108
chromosomal position
(for ins/del: last normal base / first normal base)		 20398669
original gDNA sequence snippet AGCTATTGATGCTGCAGAACACAGATTATATGAAAATGAGA
altered gDNA sequence snippet AGCTATTGATGCTGCAGAACGCAGATTATATGAAAATGAGA
original cDNA sequence snippet AGCTATTGATGCTGCAGAACACAGATTATATGAAAATGAGA
altered cDNA sequence snippet AGCTATTGATGCTGCAGAACGCAGATTATATGAAAATGAGA
wildtype AA sequence MEKCSVGGLE LTEQTPALLG NMAMATSLMD IGDSFGHPAC PLVSRSRNSP VEDDDDDDDV
VFIESIQPPS ISAPAIADQR NFIFASSKNE KPQGNYSVIP PSSRDLASQK GNISETIVID
DEEDIETNGG AEKKSSCFIE WGLPGTKNKT NDLDFSTSSL SRSKTKTGVR PFNPGRMNVA
GDLFQNGEFA THHSPDSWIS QSASFPSNQK QPGVDSLSPV ALLRKQNFQP TAQQQLTKPA
KITCANCKKP LQKGQTAYQR KGSAHLFCST TCLSSFSHKR TQNTRSIICK KDASTKKANV
ILPVESSKSF QEFYSTSCLS PCENNWNLKK GVFNKSRCTI CSKLAEIRHE VSVNNVTHKL
CSNHCFNKYR LANGLIMNCC EHCGEYMPSK STGNNILVIG GQQKRFCCQS CINEYKQMME
TKSKKLTASE NRKRNAFREE NEKQLYGSSN TLLKKIEGIP EKKEKTSQLQ LSVECGTDTL
LIQENVNLPP SSTSTIADTF QEQLEEKNFE DSIVPVVLSA DPGTWPRILN IKQRDTLVEN
VPPQVRNFNF PKDNTGRKFS ETYYTRILPN GEKTTRSWLL YSTSKDSVFC LYCKLFGEGK
NQLKNENGCK DWQHLSHILS KHEESEMHVN NSVKYSKLKS DLKKNKAIDA AEHRLYENEK
NDGVLLLYT*
mutated AA sequence MEKCSVGGLE LTEQTPALLG NMAMATSLMD IGDSFGHPAC PLVSRSRNSP VEDDDDDDDV
VFIESIQPPS ISAPAIADQR NFIFASSKNE KPQGNYSVIP PSSRDLASQK GNISETIVID
DEEDIETNGG AEKKSSCFIE WGLPGTKNKT NDLDFSTSSL SRSKTKTGVR PFNPGRMNVA
GDLFQNGEFA THHSPDSWIS QSASFPSNQK QPGVDSLSPV ALLRKQNFQP TAQQQLTKPA
KITCANCKKP LQKGQTAYQR KGSAHLFCST TCLSSFSHKR TQNTRSIICK KDASTKKANV
ILPVESSKSF QEFYSTSCLS PCENNWNLKK GVFNKSRCTI CSKLAEIRHE VSVNNVTHKL
CSNHCFNKYR LANGLIMNCC EHCGEYMPSK STGNNILVIG GQQKRFCCQS CINEYKQMME
TKSKKLTASE NRKRNAFREE NEKQLYGSSN TLLKKIEGIP EKKEKTSQLQ LSVECGTDTL
LIQENVNLPP SSTSTIADTF QEQLEEKNFE DSIVPVVLSA DPGTWPRILN IKQRDTLVEN
VPPQVRNFNF PKDNTGRKFS ETYYTRILPN GEKTTRSWLL YSTSKDSVFC LYCKLFGEGK
NQLKNENGCK DWQHLSHILS KHEESEMHVN NSVKYSKLKS DLKKNKAIDA AERRLYENEK
NDGVLLLYT*
speed 0.76 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