Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999976362 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM043341)
  • known disease mutation: rs21531 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:51058302C>TN/A show variant in all transcripts   IGV
HGNC symbol ATL1
Ensembl transcript ID ENST00000354525
Genbank transcript ID NM_181598
UniProt peptide Q8WXF7
alteration type single base exchange
alteration region CDS
DNA changes c.467C>T
cDNA.708C>T
g.59076C>T
AA changes T156I Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 156
frameshift no
known variant Reference ID: rs137852657
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs21531 (pathogenic for Hereditary spastic paraplegia 3A|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM043341)

known disease mutation at this position, please check HGMD for details (HGMD ID CM043341)
known disease mutation at this position, please check HGMD for details (HGMD ID CM043341)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.8021
5.8121
(flanking)0.3110.999
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 increased59070wt: 0.9885 / mu: 0.9897 (marginal change - not scored)wt: TAGTCAGTCAACTTT
mu: TAGTCAGTCAATTTT		 GTCA|gtca
distance from splice site 50
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      156MDTQGTFDSQSTLRDSATVFALST
mutated  not conserved    156MDTQGTFDSQSILRDSATVFALS
Ptroglodytes  all identical  ENSPTRG00000023829  156MDTQGTFDSQSTLRDSATVFALS
Mmulatta  all identical  ENSMMUG00000009577  145MDTQGTFDSQSTLRDSATVFALS
Fcatus  no alignment  ENSFCAG00000006674  n/a
Mmusculus  all identical  ENSMUSG00000021066  156MDTQGTFDSQSTLRDSATVFALS
Ggallus  all identical  ENSGALG00000012339  144MDTQGTFDSQSTLRDSATVFALS
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000060481  157MDTQGTFDSQSTLRDSATVFALS
Dmelanogaster  all identical  FBgn0039213  131FDSQSTVRDCATVFALS
Celegans  all identical  Y54G2A.2  167MDTQGAFDSQSTVKDCATIFALS
Xtropicalis  all identical  ENSXETG00000009126  156MDTQGTFDSQSTLRDSATVFALS
protein features
start (aa)end (aa)featuredetails 
1449TOPO_DOMCytoplasmic.lost
154170HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1662 / 1662
position (AA) of stopcodon in wt / mu AA sequence 554 / 554
position of stopcodon in wt / mu cDNA 1903 / 1903
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 242 / 242
chromosome 14
strand 1
last intron/exon boundary 1793
theoretical NMD boundary in CDS 1501
length of CDS 1662
coding sequence (CDS) position 467
cDNA position
(for ins/del: last normal base / first normal base)		 708
gDNA position
(for ins/del: last normal base / first normal base)		 59076
chromosomal position
(for ins/del: last normal base / first normal base)		 51058302
original gDNA sequence snippet AACCTTTGATAGTCAGTCAACTTTGAGAGATTCAGCCACAG
altered gDNA sequence snippet AACCTTTGATAGTCAGTCAATTTTGAGAGATTCAGCCACAG
original cDNA sequence snippet AACCTTTGATAGTCAGTCAACTTTGAGAGATTCAGCCACAG
altered cDNA sequence snippet AACCTTTGATAGTCAGTCAATTTTGAGAGATTCAGCCACAG
wildtype AA sequence MAKNRRDRNS WGGFSEKTYE WSSEEEEPVK KAGPVQVLIV KDDHSFELDE TALNRILLSE
AVRDKEVVAV SVAGAFRKGK SFLMDFMLRY MYNQESVDWV GDYNEPLTGF SWRGGSERET
TGIQIWSEIF LINKPDGKKV AVLLMDTQGT FDSQSTLRDS ATVFALSTMI SSIQVYNLSQ
NVQEDDLQHL QLFTEYGRLA MEETFLKPFQ SLIFLVRDWS FPYEFSYGAD GGAKFLEKRL
KVSGNQHEEL QNVRKHIHSC FTNISCFLLP HPGLKVATNP NFDGKLKEID DEFIKNLKIL
IPWLLSPESL DIKEINGNKI TCRGLVEYFK AYIKIYQGEE LPHPKSMLQA TAEANNLAAV
ATAKDTYNKK MEEICGGDKP FLAPNDLQTK HLQLKEESVK LFRGVKKMGG EEFSRRYLQQ
LESEIDELYI QYIKHNDSKN IFHAARTPAT LFVVIFITYV IAGVTGFIGL DIIASLCNMI
MGLTLITLCT WAYIRYSGEY RELGAVIDQV AAALWDQALY KLYSAAATHR HLYHQAFPTP
KSESTEQSEK KKM*
mutated AA sequence MAKNRRDRNS WGGFSEKTYE WSSEEEEPVK KAGPVQVLIV KDDHSFELDE TALNRILLSE
AVRDKEVVAV SVAGAFRKGK SFLMDFMLRY MYNQESVDWV GDYNEPLTGF SWRGGSERET
TGIQIWSEIF LINKPDGKKV AVLLMDTQGT FDSQSILRDS ATVFALSTMI SSIQVYNLSQ
NVQEDDLQHL QLFTEYGRLA MEETFLKPFQ SLIFLVRDWS FPYEFSYGAD GGAKFLEKRL
KVSGNQHEEL QNVRKHIHSC FTNISCFLLP HPGLKVATNP NFDGKLKEID DEFIKNLKIL
IPWLLSPESL DIKEINGNKI TCRGLVEYFK AYIKIYQGEE LPHPKSMLQA TAEANNLAAV
ATAKDTYNKK MEEICGGDKP FLAPNDLQTK HLQLKEESVK LFRGVKKMGG EEFSRRYLQQ
LESEIDELYI QYIKHNDSKN IFHAARTPAT LFVVIFITYV IAGVTGFIGL DIIASLCNMI
MGLTLITLCT WAYIRYSGEY RELGAVIDQV AAALWDQALY KLYSAAATHR HLYHQAFPTP
KSESTEQSEK KKM*
speed 0.57 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