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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: ENST00000320256
MT speed 0.88 s - this script 2.987317 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ASPRV1polymorphism_automatic6.29496454962464e-14simple_aaeaffectedT49Asingle base exchangers3796097show file

Taster files

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 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999937 (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) chr2:70188676T>CN/A show variant in all transcripts   IGV
HGNC symbol ASPRV1
Ensembl transcript ID ENST00000320256
Genbank transcript ID NM_152792
UniProt peptide Q53RT3
alteration type single base exchange
alteration region CDS
DNA changes c.145A>G
cDNA.722A>G
g.722A>G
AA changes T49A Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 49
frameshift no
known variant Reference ID: rs3796097
databasehomozygous (C/C)heterozygousallele carriers
1000G12859262211
ExAC22473-1217910294
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.3180
-1.2470
(flanking)0.7560.001
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased730wt: 0.50 / mu: 0.57wt: CAAGTCATCCCCACTCTGCTTCGAGAGGCCCCGTTTTCCAG
mu: CAAGTCATCCCCGCTCTGCTTCGAGAGGCCCCGTTTTCCAG		 gctt|CGAG
Acc increased726wt: 0.26 / mu: 0.35wt: CGGGCAAGTCATCCCCACTCTGCTTCGAGAGGCCCCGTTTT
mu: CGGGCAAGTCATCCCCGCTCTGCTTCGAGAGGCCCCGTTTT		 ctct|GCTT
Acc marginally increased733wt: 0.8600 / mu: 0.8866 (marginal change - not scored)wt: GTCATCCCCACTCTGCTTCGAGAGGCCCCGTTTTCCAGCGT
mu: GTCATCCCCGCTCTGCTTCGAGAGGCCCCGTTTTCCAGCGT		 tcga|GAGG
Acc marginally increased732wt: 0.8596 / mu: 0.8720 (marginal change - not scored)wt: AGTCATCCCCACTCTGCTTCGAGAGGCCCCGTTTTCCAGCG
mu: AGTCATCCCCGCTCTGCTTCGAGAGGCCCCGTTTTCCAGCG		 ttcg|AGAG
distance from splice site 722
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      49SCLPKAGQVIPTLLREAPFSSVIA
mutated  not conserved    49SCLPKAGQVIPALLREAPFSSVI
Ptroglodytes  not conserved  ENSPTRG00000012024  49SCLPKAGQVIPALLREAPFSSVI
Mmulatta  not conserved  ENSMMUG00000009011  49SCLPKAGQVIPALLPEAPFSSVI
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000033508  52SSRQGKNTAQPT---EPSLSSVI
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 
155TOPO_DOMCytoplasmic (Potential).lost
1190PROPEP /FTId=PRO_0000271170.lost
5676TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
77343TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
207288DOMAINPeptidase A2.might get lost (downstream of altered splice site)
212212ACT_SITEBy similarity.might get lost (downstream of altered splice site)
212212MUTAGEND->A,E: Abolishes production of active form of enzyme.might get lost (downstream of altered splice site)
276276CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
327343PROPEP /FTId=PRO_0000271172.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1032 / 1032
position (AA) of stopcodon in wt / mu AA sequence 344 / 344
position of stopcodon in wt / mu cDNA 1609 / 1609
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 578 / 578
chromosome 2
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 1032
coding sequence (CDS) position 145
cDNA position
(for ins/del: last normal base / first normal base)		 722
gDNA position
(for ins/del: last normal base / first normal base)		 722
chromosomal position
(for ins/del: last normal base / first normal base)		 70188676
original gDNA sequence snippet AGGCCGGGCAAGTCATCCCCACTCTGCTTCGAGAGGCCCCG
altered gDNA sequence snippet AGGCCGGGCAAGTCATCCCCGCTCTGCTTCGAGAGGCCCCG
original cDNA sequence snippet AGGCCGGGCAAGTCATCCCCACTCTGCTTCGAGAGGCCCCG
altered cDNA sequence snippet AGGCCGGGCAAGTCATCCCCGCTCTGCTTCGAGAGGCCCCG
wildtype AA sequence MGSPGASLGI KKALQSEQAT ALPASAPAVS QPTAPAPSCL PKAGQVIPTL LREAPFSSVI
APTLLCGFLF LAWVAAEVPE ESSRMAGSGA RSEEGRRQHA FVPEPFDGAN VVPNLWLHSF
EVINDLNHWD HITKLRFLKE SLRGEALGVY NRLSPQDQGD YGTVKEALLK AFGVPGAAPS
HLPKEIVFAN SMGKGYYLKG KIGKVPVRFL VDSGAQVSVV HPNLWEEVTD GDLDTLQPFE
NVVKVANGAE MKILGVWDTA VSLGKLKLKA QFLVANASAE EAIIGTDVLQ DHNAILDFEH
RTCTLKGKKF RLLPVGGSLE DEFDLELIEE DPSSEEGRQE LSH*
mutated AA sequence MGSPGASLGI KKALQSEQAT ALPASAPAVS QPTAPAPSCL PKAGQVIPAL LREAPFSSVI
APTLLCGFLF LAWVAAEVPE ESSRMAGSGA RSEEGRRQHA FVPEPFDGAN VVPNLWLHSF
EVINDLNHWD HITKLRFLKE SLRGEALGVY NRLSPQDQGD YGTVKEALLK AFGVPGAAPS
HLPKEIVFAN SMGKGYYLKG KIGKVPVRFL VDSGAQVSVV HPNLWEEVTD GDLDTLQPFE
NVVKVANGAE MKILGVWDTA VSLGKLKLKA QFLVANASAE EAIIGTDVLQ DHNAILDFEH
RTCTLKGKKF RLLPVGGSLE DEFDLELIEE DPSSEEGRQE LSH*
speed 0.88 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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