Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.000232683217029942 (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) chr2:54120025A>TN/A show variant in all transcripts   IGV
HGNC symbol PSME4
Ensembl transcript ID ENST00000421748
Genbank transcript ID N/A
UniProt peptide Q14997
alteration type single base exchange
alteration region CDS
DNA changes c.1543T>A
cDNA.1543T>A
g.77953T>A
AA changes S515T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 515
frameshift no
known variant Reference ID: rs805408
databasehomozygous (T/T)heterozygousallele carriers
1000G35410411395
ExAC66361949526131
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.3271
1.4611
(flanking)1.2081
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased77956wt: 0.25 / mu: 0.28wt: ATTCACATGAAAGCA
mu: ATACACATGAAAGCA		 TCAC|atga
Donor marginally increased77957wt: 0.9035 / mu: 0.9564 (marginal change - not scored)wt: TTCACATGAAAGCAC
mu: TACACATGAAAGCAC		 CACA|tgaa
Donor gained779530.42mu: CAGATACACATGAAA GATA|caca
Donor gained779490.87mu: GTTGCAGATACACAT TGCA|gata
distance from splice site 73
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      515LKPHLEHLVADSHESTQRCVAEII
mutated  all conserved    515LKPHLEHLVADTHESTQRCVAEI
Ptroglodytes  all identical  ENSPTRG00000011920  1371LKPHLERLVADSHESTQRCVAEI
Mmulatta  all identical  ENSMMUG00000008104  1249LKPHLERLVADSHESTQRCVAEI
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000040850  1371LKPHLERLVADSHESTQRCVAEI
Ggallus  all identical  ENSGALG00000008163  1293LQPHLERLVSDSHESTQRCVAEI
Trubripes  all conserved  ENSTRUG00000016378  1358LRPHMERLVADTHESKQRCVSEI
Drerio  all identical  ENSDARG00000018742  1355LKPHMERLANDSHESTQRCVAEI
Dmelanogaster  no homologue    
Celegans  all identical  C14C10.5  1424FRTQLEILLASSKEYEQKLAAEI
Xtropicalis  all identical  ENSXETG00000015195  1356LKPHLERLVADSHESTQRCAAEI
protein features
start (aa)end (aa)featuredetails 
475519REPEATHEAT 1.lost
710710CONFLICTC -> R (in Ref. 1; AAX83871).might get lost (downstream of altered splice site)
984984CONFLICTN -> S (in Ref. 1; AAX83871).might get lost (downstream of altered splice site)
9981037REPEATHEAT 2.might get lost (downstream of altered splice site)
11211121MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
11791217REPEATHEAT 3.might get lost (downstream of altered splice site)
13541392REPEATHEAT 4.might get lost (downstream of altered splice site)
14011401CONFLICTL -> F (in Ref. 2; AAH43602).might get lost (downstream of altered splice site)
16361674REPEATHEAT 5.might get lost (downstream of altered splice site)
16801718REPEATHEAT 6.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2964 / 2964
position (AA) of stopcodon in wt / mu AA sequence 988 / 988
position of stopcodon in wt / mu cDNA 2964 / 2964
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 2969
theoretical NMD boundary in CDS 2918
length of CDS 2964
coding sequence (CDS) position 1543
cDNA position
(for ins/del: last normal base / first normal base)		 1543
gDNA position
(for ins/del: last normal base / first normal base)		 77953
chromosomal position
(for ins/del: last normal base / first normal base)		 54120025
original gDNA sequence snippet TAGAACATTTGGTTGCAGATTCACATGAAAGCACCCAGCGA
altered gDNA sequence snippet TAGAACATTTGGTTGCAGATACACATGAAAGCACCCAGCGA
original cDNA sequence snippet TAGAACATTTGGTTGCAGATTCACATGAAAGCACCCAGCGA
altered cDNA sequence snippet TAGAACATTTGGTTGCAGATACACATGAAAGCACCCAGCGA
wildtype AA sequence MGENLAKKIM FFLLTIKLIL NHILDNSEDD TKSLFLIIKI IGDLLQFQGS HKHEFDSRWK
SFNLVKKSME NRLHGKKQHI RALLIDRVML QHELRTLTVE GCEYKKIHQD MIRDLLRLST
SSYSQVRNKA QQTFFAALGA YNFCCRDIIP LVLEFLRPDR QGVTQQQFKG ALYCLLGNHS
GVCLANLHDW DCIVQTWPAI VSSGLSQAMS LEKPSIVRLF DDLAEKIHRQ YETIGLDFTI
PKSCVEIAEL LQQSKNPSIN QILLSPEKIK EGIKRQQEKN ADALRNYENL VDTLLDGVEQ
RNLPWKFEHI GIGLLSLLLR DDRVLPLRAI RFFVENLNHD AIVVRKMAIS AVAGILKQLK
RTHKKLTINP CEISGCPKPT QIIAGDRPDN HWLHYDSKTI PRTKKEWESS CFVEKTHWGY
YTWPKNMVVY AGVEEQPKLG RSREDMTEAE QIIFDHFSDP KFVEQLITFL SLEDRKGKDK
FNPRRFCLFK GIFRNFDDAF LPVLKPHLEH LVADSHESTQ RCVAEIIAGL IRGSKHWTFE
KVEKLWELLC PLLRTALSNI TVETYNDWGA CIATSCESRD PRKLHWLFEL LLESPLSGEG
GSFVDACRLY VLQGGLAQQE WRVPELLHRL LKYLEPKLTQ VYKNVRERIG SVLTYIFMID
VSLPNTTPTI SPHVPEFTAR ILEKLKPLMD VDEEIQNHVM EENGIGEEDE RTQGIKLLKT
ILKWLMASAG RSFSTAVTEQ LQLLPLFFKI APVENDNSYD ELKRDAKLCL SLMSQGLLYP
HQVPLVLQVL KQTARSSSWH ARYTVLTYLQ TMVFYNLFIF LNNEDAVKDI RWLVISLLED
EQLEVREMAA TTLSGLLQCN FLTMDSPMQI HFEQLCKTKL PKKRKRDPGS VGDTIPSAEL
VKRHAGVLGL GACVLSSPYD VPTWMPQLLM NLSAHLNDPQ PIEMTVKKTL SNFRRTHHDN
WQEHKQQFTD DQLLVLTDLL VSPCYYA*
mutated AA sequence MGENLAKKIM FFLLTIKLIL NHILDNSEDD TKSLFLIIKI IGDLLQFQGS HKHEFDSRWK
SFNLVKKSME NRLHGKKQHI RALLIDRVML QHELRTLTVE GCEYKKIHQD MIRDLLRLST
SSYSQVRNKA QQTFFAALGA YNFCCRDIIP LVLEFLRPDR QGVTQQQFKG ALYCLLGNHS
GVCLANLHDW DCIVQTWPAI VSSGLSQAMS LEKPSIVRLF DDLAEKIHRQ YETIGLDFTI
PKSCVEIAEL LQQSKNPSIN QILLSPEKIK EGIKRQQEKN ADALRNYENL VDTLLDGVEQ
RNLPWKFEHI GIGLLSLLLR DDRVLPLRAI RFFVENLNHD AIVVRKMAIS AVAGILKQLK
RTHKKLTINP CEISGCPKPT QIIAGDRPDN HWLHYDSKTI PRTKKEWESS CFVEKTHWGY
YTWPKNMVVY AGVEEQPKLG RSREDMTEAE QIIFDHFSDP KFVEQLITFL SLEDRKGKDK
FNPRRFCLFK GIFRNFDDAF LPVLKPHLEH LVADTHESTQ RCVAEIIAGL IRGSKHWTFE
KVEKLWELLC PLLRTALSNI TVETYNDWGA CIATSCESRD PRKLHWLFEL LLESPLSGEG
GSFVDACRLY VLQGGLAQQE WRVPELLHRL LKYLEPKLTQ VYKNVRERIG SVLTYIFMID
VSLPNTTPTI SPHVPEFTAR ILEKLKPLMD VDEEIQNHVM EENGIGEEDE RTQGIKLLKT
ILKWLMASAG RSFSTAVTEQ LQLLPLFFKI APVENDNSYD ELKRDAKLCL SLMSQGLLYP
HQVPLVLQVL KQTARSSSWH ARYTVLTYLQ TMVFYNLFIF LNNEDAVKDI RWLVISLLED
EQLEVREMAA TTLSGLLQCN FLTMDSPMQI HFEQLCKTKL PKKRKRDPGS VGDTIPSAEL
VKRHAGVLGL GACVLSSPYD VPTWMPQLLM NLSAHLNDPQ PIEMTVKKTL SNFRRTHHDN
WQEHKQQFTD DQLLVLTDLL VSPCYYA*
speed 0.74 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