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 1 transcript(s)...
Querying Taster for transcript #1: ENST00000356231
MT speed 1.5 s - this script 8.043771 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CDAN1disease_causing_automatic0.999225584966962simple_aaeaffected0N599Ssingle base exchangers120074166show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999225584966962 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM023030)
  • known disease mutation: rs3178 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr15:43023473T>CN/A show variant in all transcripts   IGV
HGNC symbol CDAN1
Ensembl transcript ID ENST00000356231
Genbank transcript ID NM_138477
UniProt peptide Q8IWY9
alteration type single base exchange
alteration region CDS
DNA changes c.1796A>G
cDNA.1820A>G
g.5852A>G
AA changes N599S Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS
599
frameshift no
known variant Reference ID: rs120074166
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs3178 (pathogenic for Congenital dyserythropoietic anemia, type I) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM023030)

known disease mutation at this position, please check HGMD for details (HGMD ID CM023030)
known disease mutation at this position, please check HGMD for details (HGMD ID CM023030)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0720.601
4.8651
(flanking)1.7461
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased5843wt: 0.4596 / mu: 0.4783 (marginal change - not scored)wt: GATCCAGGAGCTCAA
mu: GATCCAGGAGCTCAG
 TCCA|ggag
Donor increased5846wt: 0.22 / mu: 0.92wt: CCAGGAGCTCAATGG
mu: CCAGGAGCTCAGTGG
 AGGA|gctc
distance from splice site 57
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      599MDSLSLKIQELNGLALPQHEPNDE
mutated  all conserved    599MDSLSLKIQELSGLALPQHEPND
Ptroglodytes  all identical  ENSPTRG00000006981  567MDSLSLKIRELNGLALPQHEPSD
Mmulatta  all identical  ENSMMUG00000015123  599MDSLSLKIRELNGLALPQHEPSD
Fcatus  all identical  ENSFCAG00000003550  599MDSLSLKIRELNSLALPQPEPSD
Mmusculus  all identical  ENSMUSG00000027284  604IRELNGLRLPQHEPGD
Ggallus  all conserved  ENSGALG00000009156  615VDSLCLKILELDGLTLVEHE--H
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000042261  661KDGLCQQLLKLDEVSILGPDASPAQGE
Dmelanogaster  all identical  FBgn0024510  595FVQLMRNNDSTFDLLQLTD
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
626646TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
669669CONFLICTQ -> P (in Ref. 4; AAQ88832).might get lost (downstream of altered splice site)
726726CONFLICTS -> C (in Ref. 1; AAO14994).might get lost (downstream of altered splice site)
946946CONFLICTR -> W (in Ref. 3; AAH01092/AAH08333/ AAH08334).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3684 / 3684
position (AA) of stopcodon in wt / mu AA sequence 1228 / 1228
position of stopcodon in wt / mu cDNA 3708 / 3708
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 25 / 25
chromosome 15
strand -1
last intron/exon boundary 3583
theoretical NMD boundary in CDS 3508
length of CDS 3684
coding sequence (CDS) position 1796
cDNA position
(for ins/del: last normal base / first normal base)
1820
gDNA position
(for ins/del: last normal base / first normal base)
5852
chromosomal position
(for ins/del: last normal base / first normal base)
43023473
original gDNA sequence snippet CTTGAAGATCCAGGAGCTCAATGGTCTTGCCCTGCCCCAGC
altered gDNA sequence snippet CTTGAAGATCCAGGAGCTCAGTGGTCTTGCCCTGCCCCAGC
original cDNA sequence snippet CTTGAAGATCCAGGAGCTCAATGGTCTTGCCCTGCCCCAGC
altered cDNA sequence snippet CTTGAAGATCCAGGAGCTCAGTGGTCTTGCCCTGCCCCAGC
wildtype AA sequence MAAVLESLLR EEVSVAAVVR WIARSTQGSE DNAGEAAALS SLRALRKEFV PFLLNFLREQ
SSRVLPQGPP TPAKTPGASA ALPGRPGGPP RGSRGARSQL FPPTEAQSTA AEAPLARRGG
RRRGPGPARE RGGRGLEEGV SGESLPGAGG RRLRGSGSPS RPSLTLSDPP NLSNLEEFPP
VGSVPPGPTG TKPSRRINPT PVSEERSLSK PKTCFTSPPI SCVPSSQPSA LDTSPWGLGL
PPGCRSLQEE REMLRKERSK QLQQSPTPTC PTPELGSPLP SRTGSLTDEP ADPARVSSRQ
RLELVALVYS SCIAENLVPN LFLELFFVFQ LLTARRMVTA KDSDPELSPA VLDSLESPLF
QSIHDCVFFA VQVLECHFQV LSNLDKGTLK LLAENERLLC FSPALQGRLR AAYEGSVAKV
SLVMPPSTQA VSFQPETDNR ANFSSDRAFH TFKKQRDVFY EVLREWEDHH EEPGWDFEKG
LGSRIRAMMG QLSAACSHSH FVRLFQKQLL QMCQSPGGAG GTVLGEAPDV LSMLGADKLG
RLWRLQERLM APQSSGGPCP PPTFPGCQGF FRDFILSASS FQFNQHLMDS LSLKIQELNG
LALPQHEPND EDGESDVDWQ GERKQFAVVL LSLRLLAKFL GFVAFLPYRG PEPPPTGELQ
DSILALRSQV PPVLDVRTLL QRGLQARRAV LTVPWLVEFL SFADHVVPLL EYYRDIFTLL
LRLHRSLVLS QESEGKMCFL NKLLLLAVLG WLFQIPTVPE DLFFLEEGPS YAFEVDTVAP
EHGLDNAPVV DQQLLYTCCP YIGELRKLLA SWVSGSSGRS GGFMRKITPT TTTSLGAQPS
QTSQGLQAQL AQAFFHNQPP SLRRTVEFVA ERIGSNCVKH IKATLVADLV RQAESLLQEQ
LVTQGEEGGD PAQLLEILCS QLCPHGAQAL ALGREFCQRK SPGAVRALLP EETPAAVLSS
AENIAVGLAT EKACAWLSAN ITALIRREVK AAVSRTLRAQ GPEPAARGER RGCSRACEHH
APLPSHLISE IKDVLSLAVG PRDPDEGVSP EHLEQLLGQL GQTLRCRQFL CPPAEQHLAK
CSVELASLLV ADQIPILGPP AQYRLERGQA RRLLHMLLSL WKEDFQGPVP LQLLLSPRNV
GLLADTRPRE WDLLLFLLRE LVEKGLMGRM EIEACLGSLH QAQWPGDFAE ELATLSNLFL
AEPHLPEPQL RACELVQPNR GTVLAQS*
mutated AA sequence MAAVLESLLR EEVSVAAVVR WIARSTQGSE DNAGEAAALS SLRALRKEFV PFLLNFLREQ
SSRVLPQGPP TPAKTPGASA ALPGRPGGPP RGSRGARSQL FPPTEAQSTA AEAPLARRGG
RRRGPGPARE RGGRGLEEGV SGESLPGAGG RRLRGSGSPS RPSLTLSDPP NLSNLEEFPP
VGSVPPGPTG TKPSRRINPT PVSEERSLSK PKTCFTSPPI SCVPSSQPSA LDTSPWGLGL
PPGCRSLQEE REMLRKERSK QLQQSPTPTC PTPELGSPLP SRTGSLTDEP ADPARVSSRQ
RLELVALVYS SCIAENLVPN LFLELFFVFQ LLTARRMVTA KDSDPELSPA VLDSLESPLF
QSIHDCVFFA VQVLECHFQV LSNLDKGTLK LLAENERLLC FSPALQGRLR AAYEGSVAKV
SLVMPPSTQA VSFQPETDNR ANFSSDRAFH TFKKQRDVFY EVLREWEDHH EEPGWDFEKG
LGSRIRAMMG QLSAACSHSH FVRLFQKQLL QMCQSPGGAG GTVLGEAPDV LSMLGADKLG
RLWRLQERLM APQSSGGPCP PPTFPGCQGF FRDFILSASS FQFNQHLMDS LSLKIQELSG
LALPQHEPND EDGESDVDWQ GERKQFAVVL LSLRLLAKFL GFVAFLPYRG PEPPPTGELQ
DSILALRSQV PPVLDVRTLL QRGLQARRAV LTVPWLVEFL SFADHVVPLL EYYRDIFTLL
LRLHRSLVLS QESEGKMCFL NKLLLLAVLG WLFQIPTVPE DLFFLEEGPS YAFEVDTVAP
EHGLDNAPVV DQQLLYTCCP YIGELRKLLA SWVSGSSGRS GGFMRKITPT TTTSLGAQPS
QTSQGLQAQL AQAFFHNQPP SLRRTVEFVA ERIGSNCVKH IKATLVADLV RQAESLLQEQ
LVTQGEEGGD PAQLLEILCS QLCPHGAQAL ALGREFCQRK SPGAVRALLP EETPAAVLSS
AENIAVGLAT EKACAWLSAN ITALIRREVK AAVSRTLRAQ GPEPAARGER RGCSRACEHH
APLPSHLISE IKDVLSLAVG PRDPDEGVSP EHLEQLLGQL GQTLRCRQFL CPPAEQHLAK
CSVELASLLV ADQIPILGPP AQYRLERGQA RRLLHMLLSL WKEDFQGPVP LQLLLSPRNV
GLLADTRPRE WDLLLFLLRE LVEKGLMGRM EIEACLGSLH QAQWPGDFAE ELATLSNLFL
AEPHLPEPQL RACELVQPNR GTVLAQS*
speed 1.50 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