Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.991171534905901 (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) chr20:1115919A>GN/A show variant in all transcripts   IGV
HGNC symbol PSMF1
Ensembl transcript ID ENST00000333082
Genbank transcript ID NM_178578
UniProt peptide Q92530
alteration type single base exchange
alteration region CDS
DNA changes c.521A>G
cDNA.689A>G
g.22014A>G
AA changes H174R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 174
frameshift no
known variant Reference ID: rs2235587
databasehomozygous (G/G)heterozygousallele carriers
1000G180650830
ExAC25001640018900
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.4240.915
0.4620.91
(flanking)-0.1290.906
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased22024wt: 0.23 / mu: 0.37wt: ATTCCTCCACACCACCCACACACCAGTCGGCAGCCTCCCTG
mu: ATTCCTCCACGCCACCCACACACCAGTCGGCAGCCTCCCTG		 acac|ACCA
Acc increased22020wt: 0.41 / mu: 0.46wt: CCGGATTCCTCCACACCACCCACACACCAGTCGGCAGCCTC
mu: CCGGATTCCTCCACGCCACCCACACACCAGTCGGCAGCCTC		 accc|ACAC
Acc marginally increased22015wt: 0.9313 / mu: 0.9396 (marginal change - not scored)wt: CCACTCCGGATTCCTCCACACCACCCACACACCAGTCGGCA
mu: CCACTCCGGATTCCTCCACGCCACCCACACACCAGTCGGCA		 acac|CACC
Donor gained220130.85mu: CTCCACGCCACCCAC CCAC|gcca
Donor gained220080.41mu: GATTCCTCCACGCCA TTCC|tcca
distance from splice site 31
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      174AREVDPLRIPPHHPHTSRQPPWCD
mutated  not conserved    174AREVDPLRIPPRHPHTSR
Ptroglodytes  all identical  ENSPTRG00000013155  174AREVDPLRIPPHHPHTSR
Mmulatta  all identical  ENSMMUG00000004709  174AREVDPLRIPPHHPHTSR
Fcatus  not conserved  ENSFCAG00000010927  174XXXXXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000032869  174AREVDPLQISSHRPHTSR
Ggallus  not conserved  ENSGALG00000000259  174PLDYNPRGIPPRHPAGAR
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000022652  144RDPDSDPLLIPTRGPPAR
Dmelanogaster  not conserved  FBgn0033669  185GSDPDPLRIGEPRRGGSF
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000030118  n/a
protein features
start (aa)end (aa)featuredetails 
154271COMPBIASPro-rich.lost
251251MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
252252MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 816 / 816
position (AA) of stopcodon in wt / mu AA sequence 272 / 272
position of stopcodon in wt / mu cDNA 984 / 984
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 169 / 169
chromosome 20
strand 1
last intron/exon boundary 933
theoretical NMD boundary in CDS 714
length of CDS 816
coding sequence (CDS) position 521
cDNA position
(for ins/del: last normal base / first normal base)		 689
gDNA position
(for ins/del: last normal base / first normal base)		 22014
chromosomal position
(for ins/del: last normal base / first normal base)		 1115919
original gDNA sequence snippet CCCACTCCGGATTCCTCCACACCACCCACACACCAGTCGGC
altered gDNA sequence snippet CCCACTCCGGATTCCTCCACGCCACCCACACACCAGTCGGC
original cDNA sequence snippet CCCACTCCGGATTCCTCCACACCACCCACACACCAGTCGGC
altered cDNA sequence snippet CCCACTCCGGATTCCTCCACGCCACCCACACACCAGTCGGC
wildtype AA sequence MAGLEVLFAS AAPAITCRQD ALVCFLHWEV VTHGYFGLGV GDQPGPNDKK SELLPAGWNN
NKDLYVLRYE YKDGSRKLLV KAITVESSMI LNVLEYGSQQ VADLTLNLDD YIDAEHLGDF
HRTYKNSEEL RSRIVSGIIT PIHEQWEKAN VSSPHREFPP ATAREVDPLR IPPHHPHTSR
QPPWCDPLGP FVVGGEDLDP FGPRRGGMIV DPLRSGFPRA LIDPSSGLPN RLPPGAVPPG
ARFDPFGPIG TSPPGPNPDH LPPPGYDDMY L*
mutated AA sequence MAGLEVLFAS AAPAITCRQD ALVCFLHWEV VTHGYFGLGV GDQPGPNDKK SELLPAGWNN
NKDLYVLRYE YKDGSRKLLV KAITVESSMI LNVLEYGSQQ VADLTLNLDD YIDAEHLGDF
HRTYKNSEEL RSRIVSGIIT PIHEQWEKAN VSSPHREFPP ATAREVDPLR IPPRHPHTSR
QPPWCDPLGP FVVGGEDLDP FGPRRGGMIV DPLRSGFPRA LIDPSSGLPN RLPPGAVPPG
ARFDPFGPIG TSPPGPNPDH LPPPGYDDMY L*
speed 0.63 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