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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: ENST00000408934
MT speed 0 s - this script 3.623362 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
PRR21polymorphism_automatic1.29896093881143e-14simple_aaeG58Ssingle base exchangers10439373show file

Taster files

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Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999987 (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
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:240982228C>TN/A show variant in all transcripts   IGV
HGNC symbol PRR21
Ensembl transcript ID ENST00000408934
Genbank transcript ID NM_001080835
UniProt peptide Q8WXC7
alteration type single base exchange
alteration region CDS
DNA changes c.172G>A
cDNA.172G>A
g.172G>A
AA changes G58S Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS
58
frameshift no
known variant Reference ID: rs10439373
databasehomozygous (T/T)heterozygousallele carriers
1000G47016742144
ExAC106421148322125
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.2560
-2.1090
(flanking)-1.9430
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased183wt: 0.8710 / mu: 0.8787 (marginal change - not scored)wt: TTCACCCACGGCCCTTCATCCACGGCTCTTCACCCATGTCC
mu: TTCACCCACAGCCCTTCATCCACGGCTCTTCACCCATGTCC
 atcc|ACGG
Acc marginally increased169wt: 0.9482 / mu: 0.9544 (marginal change - not scored)wt: TTCATCCACGGCTCTTCACCCACGGCCCTTCATCCACGGCT
mu: TTCATCCACGGCTCTTCACCCACAGCCCTTCATCCACGGCT
 accc|ACGG
Acc marginally increased173wt: 0.2958 / mu: 0.3146 (marginal change - not scored)wt: TCCACGGCTCTTCACCCACGGCCCTTCATCCACGGCTCTTC
mu: TCCACGGCTCTTCACCCACAGCCCTTCATCCACGGCTCTTC
 acgg|CCCT
distance from splice site 172
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      58PMALHPRLFTHGPSSTALHPCPFT
mutated  not conserved    58PMALHPRLFTHSPS
Ptroglodytes  not conserved  ENSPTRG00000040883  3HACSSTALHPRPF
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 
38320COMPBIASPro-rich.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1170 / 1170
position (AA) of stopcodon in wt / mu AA sequence 390 / 390
position of stopcodon in wt / mu cDNA 1170 / 1170
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 1 / 1
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 1170
coding sequence (CDS) position 172
cDNA position
(for ins/del: last normal base / first normal base)
172
gDNA position
(for ins/del: last normal base / first normal base)
172
chromosomal position
(for ins/del: last normal base / first normal base)
240982228
original gDNA sequence snippet ATCCACGGCTCTTCACCCACGGCCCTTCATCCACGGCTCTT
altered gDNA sequence snippet ATCCACGGCTCTTCACCCACAGCCCTTCATCCACGGCTCTT
original cDNA sequence snippet ATCCACGGCTCTTCACCCACGGCCCTTCATCCACGGCTCTT
altered cDNA sequence snippet ATCCACGGCTCTTCACCCACAGCCCTTCATCCACGGCTCTT
wildtype AA sequence MHACSSTALH PRPFIHGFSF TTFLQQLFPH GSSTALHPWP FIHGSSPMAL HPRLFTHGPS
STALHPCPFT HGSSPMSLHP RLFTHSPSSM PLHPRPFVHA SSPTALRPCL FTHGPSSMPL
HPRPFVHASS PTALPPCLFT HGPSSMPLHP RPFLHASSPT ALPPCLFTHG PSSMPLHPRP
FVHASSPTAL RPCLFTHGPS SMPLHPRPFV HASSPTALPP CLFTHGPSSM PLHPRPFVHA
SSPTALRPCL FTHGPSSMPL HPRPFLHASS PTALRPCLFT HGPSSMPLHP RPFVHASSPT
ALRPCLFTHG PSSMPLHPRP FVHASSSTSL HPRPFIHASS SKSLHLRLFS HSSCLVGFSQ
QGNVLLLSAR ATFNTCLLVS NMYFLIISY*
mutated AA sequence MHACSSTALH PRPFIHGFSF TTFLQQLFPH GSSTALHPWP FIHGSSPMAL HPRLFTHSPS
STALHPCPFT HGSSPMSLHP RLFTHSPSSM PLHPRPFVHA SSPTALRPCL FTHGPSSMPL
HPRPFVHASS PTALPPCLFT HGPSSMPLHP RPFLHASSPT ALPPCLFTHG PSSMPLHPRP
FVHASSPTAL RPCLFTHGPS SMPLHPRPFV HASSPTALPP CLFTHGPSSM PLHPRPFVHA
SSPTALRPCL FTHGPSSMPL HPRPFLHASS PTALRPCLFT HGPSSMPLHP RPFVHASSPT
ALRPCLFTHG PSSMPLHPRP FVHASSSTSL HPRPFIHASS SKSLHLRLFS HSSCLVGFSQ
QGNVLLLSAR ATFNTCLLVS NMYFLIISY*
speed 1.46 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