Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999099933 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM042305)
  • known disease mutation: rs12909 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:42482193G>AN/A show variant in all transcripts   IGV
HGNC symbol ATP1A3
Ensembl transcript ID ENST00000302102
Genbank transcript ID NM_152296
UniProt peptide P13637
alteration type single base exchange
alteration region CDS
DNA changes c.1838C>T
cDNA.1989C>T
g.16192C>T
AA changes T613M Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 613
frameshift no
known variant Reference ID: rs80356534
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs12909 (pathogenic for Dystonia 12|Alternating hemiplegia of childhood 2|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM042305)

known disease mutation at this position, please check HGMD for details (HGMD ID CM042305)
known disease mutation at this position, please check HGMD for details (HGMD ID CM042305)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.3080.975
5.141
(flanking)4.2461
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 32
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      613KVIMVTGDHPITAKAIAKGVGIIS
mutated  not conserved    613KVIMVTGDHPIMAKAIAKGVGII
Ptroglodytes  no alignment  ENSPTRG00000011041  n/a
Mmulatta  all identical  ENSMMUG00000017427  613KVIMVTGDHPITAKAIAKGVGII
Fcatus  all identical  ENSFCAG00000012729  513KVIMVTGDHPITAKAIAKGVGII
Mmusculus  all identical  ENSMUSG00000040907  613KVIMVTGDHPITAKAIAKGVGII
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008243  620MVTGDHPITAKAIAKGVGII
Drerio  all identical  ENSDARG00000018259  623VTGDHPITAKAIAKGVGII
Dmelanogaster  all identical  FBgn0002921  641KVIMVTGDHPITAKAIAKSVGII
Celegans  all identical  B0365.3  596KVVMVTGDHPITAKAIAKSVGII
Xtropicalis  all identical  ENSXETG00000023811  625VIMVTGDHPITAKAIAKGVGII
protein features
start (aa)end (aa)featuredetails 
329762TOPO_DOMCytoplasmic (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3042 / 3042
position (AA) of stopcodon in wt / mu AA sequence 1014 / 1014
position of stopcodon in wt / mu cDNA 3193 / 3193
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 152 / 152
chromosome 19
strand -1
last intron/exon boundary 3165
theoretical NMD boundary in CDS 2963
length of CDS 3042
coding sequence (CDS) position 1838
cDNA position
(for ins/del: last normal base / first normal base)		 1989
gDNA position
(for ins/del: last normal base / first normal base)		 16192
chromosomal position
(for ins/del: last normal base / first normal base)		 42482193
original gDNA sequence snippet CACCGGCGATCACCCCATCACGGCCAAGGCCATTGCCAAGG
altered gDNA sequence snippet CACCGGCGATCACCCCATCATGGCCAAGGCCATTGCCAAGG
original cDNA sequence snippet CACCGGCGATCACCCCATCACGGCCAAGGCCATTGCCAAGG
altered cDNA sequence snippet CACCGGCGATCACCCCATCATGGCCAAGGCCATTGCCAAGG
wildtype AA sequence MGDKKDDKDS PKKNKGKERR DLDDLKKEVA MTEHKMSVEE VCRKYNTDCV QGLTHSKAQE
ILARDGPNAL TPPPTTPEWV KFCRQLFGGF SILLWIGAIL CFLAYGIQAG TEDDPSGDNL
YLGIVLAAVV IITGCFSYYQ EAKSSKIMES FKNMVPQQAL VIREGEKMQV NAEEVVVGDL
VEIKGGDRVP ADLRIISAHG CKVDNSSLTG ESEPQTRSPD CTHDNPLETR NITFFSTNCV
EGTARGVVVA TGDRTVMGRI ATLASGLEVG KTPIAIEIEH FIQLITGVAV FLGVSFFILS
LILGYTWLEA VIFLIGIIVA NVPEGLLATV TVCLTLTAKR MARKNCLVKN LEAVETLGST
STICSDKTGT LTQNRMTVAH MWFDNQIHEA DTTEDQSGTS FDKSSHTWVA LSHIAGLCNR
AVFKGGQDNI PVLKRDVAGD ASESALLKCI ELSSGSVKLM RERNKKVAEI PFNSTNKYQL
SIHETEDPND NRYLLVMKGA PERILDRCST ILLQGKEQPL DEEMKEAFQN AYLELGGLGE
RVLGFCHYYL PEEQFPKGFA FDCDDVNFTT DNLCFVGLMS MIDPPRAAVP DAVGKCRSAG
IKVIMVTGDH PITAKAIAKG VGIISEGNET VEDIAARLNI PVSQVNPRDA KACVIHGTDL
KDFTSEQIDE ILQNHTEIVF ARTSPQQKLI IVEGCQRQGA IVAVTGDGVN DSPALKKADI
GVAMGIAGSD VSKQAADMIL LDDNFASIVT GVEEGRLIFD NLKKSIAYTL TSNIPEITPF
LLFIMANIPL PLGTITILCI DLGTDMVPAI SLAYEAAESD IMKRQPRNPR TDKLVNERLI
SMAYGQIGMI QALGGFFSYF VILAENGFLP GNLVGIRLNW DDRTVNDLED SYGQQWTYEQ
RKVVEFTCHT AFFVSIVVVQ WADLIICKTR RNSVFQQGMK NKILIFGLFE ETALAAFLSY
CPGMDVALRM YPLKPSWWFC AFPYSFLIFV YDEIRKLILR RNPGGWVEKE TYY*
mutated AA sequence MGDKKDDKDS PKKNKGKERR DLDDLKKEVA MTEHKMSVEE VCRKYNTDCV QGLTHSKAQE
ILARDGPNAL TPPPTTPEWV KFCRQLFGGF SILLWIGAIL CFLAYGIQAG TEDDPSGDNL
YLGIVLAAVV IITGCFSYYQ EAKSSKIMES FKNMVPQQAL VIREGEKMQV NAEEVVVGDL
VEIKGGDRVP ADLRIISAHG CKVDNSSLTG ESEPQTRSPD CTHDNPLETR NITFFSTNCV
EGTARGVVVA TGDRTVMGRI ATLASGLEVG KTPIAIEIEH FIQLITGVAV FLGVSFFILS
LILGYTWLEA VIFLIGIIVA NVPEGLLATV TVCLTLTAKR MARKNCLVKN LEAVETLGST
STICSDKTGT LTQNRMTVAH MWFDNQIHEA DTTEDQSGTS FDKSSHTWVA LSHIAGLCNR
AVFKGGQDNI PVLKRDVAGD ASESALLKCI ELSSGSVKLM RERNKKVAEI PFNSTNKYQL
SIHETEDPND NRYLLVMKGA PERILDRCST ILLQGKEQPL DEEMKEAFQN AYLELGGLGE
RVLGFCHYYL PEEQFPKGFA FDCDDVNFTT DNLCFVGLMS MIDPPRAAVP DAVGKCRSAG
IKVIMVTGDH PIMAKAIAKG VGIISEGNET VEDIAARLNI PVSQVNPRDA KACVIHGTDL
KDFTSEQIDE ILQNHTEIVF ARTSPQQKLI IVEGCQRQGA IVAVTGDGVN DSPALKKADI
GVAMGIAGSD VSKQAADMIL LDDNFASIVT GVEEGRLIFD NLKKSIAYTL TSNIPEITPF
LLFIMANIPL PLGTITILCI DLGTDMVPAI SLAYEAAESD IMKRQPRNPR TDKLVNERLI
SMAYGQIGMI QALGGFFSYF VILAENGFLP GNLVGIRLNW DDRTVNDLED SYGQQWTYEQ
RKVVEFTCHT AFFVSIVVVQ WADLIICKTR RNSVFQQGMK NKILIFGLFE ETALAAFLSY
CPGMDVALRM YPLKPSWWFC AFPYSFLIFV YDEIRKLILR RNPGGWVEKE TYY*
speed 1.18 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