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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: ENST00000408890
MT speed 1.58 s - this script 4.800432 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
POM121L12polymorphism_automatic6.3504757008559e-13simple_aaeaffectedA3Ssingle base exchangers72598684show file

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Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999365 (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
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:53103371G>TN/A show variant in all transcripts   IGV
HGNC symbol POM121L12
Ensembl transcript ID ENST00000408890
Genbank transcript ID NM_182595
UniProt peptide Q8N7R1
alteration type single base exchange
alteration region CDS
DNA changes c.7G>T
cDNA.37G>T
g.37G>T
AA changes A3S Score: 99 explain score(s)
position(s) of altered AA
if AA alteration in CDS
3
frameshift no
known variant Reference ID: rs72598684
databasehomozygous (T/T)heterozygousallele carriers
1000G2899311220
ExAC26331187014503
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.3750.002
-0.0980.003
(flanking)1.240.008
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased42wt: 0.36 / mu: 0.70wt: GCTGCAGCTCCGGCC
mu: TCTGCAGCTCCGGCC
 TGCA|gctc
distance from splice site 37
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      3 MGAAAPAESADLGNF
mutated  all conserved    3 MGSAAPAESADLGNFWKAGEPL
Ptroglodytes  all identical  ENSPTRG00000041196  3 GAAAPAESADLGNFWKAGEPL
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
144144CONFLICTP -> S (in Ref. 3; CAD38744).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 891 / 891
position (AA) of stopcodon in wt / mu AA sequence 297 / 297
position of stopcodon in wt / mu cDNA 921 / 921
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 31 / 31
chromosome 7
strand 1
last intron/exon boundary 1
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 891
coding sequence (CDS) position 7
cDNA position
(for ins/del: last normal base / first normal base)
37
gDNA position
(for ins/del: last normal base / first normal base)
37
chromosomal position
(for ins/del: last normal base / first normal base)
53103371
original gDNA sequence snippet ACGGTCCCCCAGCCATGGGCGCTGCAGCTCCGGCCGAGTCC
altered gDNA sequence snippet ACGGTCCCCCAGCCATGGGCTCTGCAGCTCCGGCCGAGTCC
original cDNA sequence snippet ACGGTCCCCCAGCCATGGGCGCTGCAGCTCCGGCCGAGTCC
altered cDNA sequence snippet ACGGTCCCCCAGCCATGGGCTCTGCAGCTCCGGCCGAGTCC
wildtype AA sequence MGAAAPAESA DLGNFWKAGE PLLQGPDALA APMSRSPSTP QTTPSPQGRQ SPWPLRSLTQ
SHIQYFQWGR PVPSTHLIEV RPTQDPAKPQ RVVSEGWRRP ALPGETALGR DLSCAWEGCM
KGGLCRAWNP GRTWSPVTIG IAPPERQESP WRSPGQRARP AGRPAAQELL DPCTRETLLG
ALSQCPKGSA RFDGPLWFEV SDSKGGRRNL QPRPSAFKPL SKNGAVASFV PRPGPLKPSL
GPWSLSFCDD AWPSVLVQPA PSAIWDFWEA TTPSCGSCSR VSFALEVTQS AGPFGS*
mutated AA sequence MGSAAPAESA DLGNFWKAGE PLLQGPDALA APMSRSPSTP QTTPSPQGRQ SPWPLRSLTQ
SHIQYFQWGR PVPSTHLIEV RPTQDPAKPQ RVVSEGWRRP ALPGETALGR DLSCAWEGCM
KGGLCRAWNP GRTWSPVTIG IAPPERQESP WRSPGQRARP AGRPAAQELL DPCTRETLLG
ALSQCPKGSA RFDGPLWFEV SDSKGGRRNL QPRPSAFKPL SKNGAVASFV PRPGPLKPSL
GPWSLSFCDD AWPSVLVQPA PSAIWDFWEA TTPSCGSCSR VSFALEVTQS AGPFGS*
speed 1.58 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