Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999994167 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM1311834)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:95561459A>GN/A show variant in all transcripts   IGV
HGNC symbol PDLIM5
Ensembl transcript ID ENST00000514743
Genbank transcript ID N/A
UniProt peptide Q96HC4
alteration type single base exchange
alteration region CDS
DNA changes c.1228A>G
cDNA.1272A>G
g.188423A>G
AA changes T410A Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 410
frameshift no
known variant Reference ID: rs7690296
databasehomozygous (G/G)heterozygousallele carriers
1000G43910631502
ExAC12093858120674

known disease mutation at this position, please check HGMD for details (HGMD ID CM1311834)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-4.10
-2.6990
(flanking)0.5110
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased188430wt: 0.40 / mu: 0.59wt: CTCAAACAGCGCTACTTACTCAGGATCAGTGGCACCAGCCA
mu: CTCAAACAGCGCTGCTTACTCAGGATCAGTGGCACCAGCCA		 actc|AGGA
Donor increased188427wt: 0.34 / mu: 0.38wt: TACTTACTCAGGATC
mu: TGCTTACTCAGGATC		 CTTA|ctca
Donor marginally increased188414wt: 0.6965 / mu: 0.7610 (marginal change - not scored)wt: TCTCAAACAGCGCTA
mu: TCTCAAACAGCGCTG		 TCAA|acag
Donor gained1884170.82mu: CAAACAGCGCTGCTT AACA|gcgc
distance from splice site 33
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      410VPSTGRISNSATYSGSVAPANSAL
mutated  not conserved    410VPSTGRISNSAAYSGSVAPANS
Ptroglodytes  all identical  ENSPTRG00000016292  381VPSTGRISNSATYSGSVAPANSA
Mmulatta  all identical  ENSMMUG00000022246  381VPSTGRISNSATSSGSVAPASSA
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000028273  382APSTGRISNNARSSGT-
Ggallus  not conserved  ENSGALG00000012211  382APASGWTSNSNKTSGTTAPSQKL
Trubripes  all conserved  ENSTRUG00000005717  384LITPSFSMKGNGSASAPKGVVPARPA
Drerio  not conserved  ENSDARG00000027600  416PSAGRGVSSSVPKGPERP----
Dmelanogaster  not conserved  FBgn0083919  1999KSAGAFGATSAPKRGRGILNKA
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000019217  368TNNASNAVKPVANNKS
protein features
start (aa)end (aa)featuredetails 
409411STRANDlost
413415TURNmight get lost (downstream of altered splice site)
418477DOMAINLIM zinc-binding 1.might get lost (downstream of altered splice site)
419423STRANDmight get lost (downstream of altered splice site)
431434STRANDmight get lost (downstream of altered splice site)
437439STRANDmight get lost (downstream of altered splice site)
441443TURNmight get lost (downstream of altered splice site)
447449STRANDmight get lost (downstream of altered splice site)
454456STRANDmight get lost (downstream of altered splice site)
458463STRANDmight get lost (downstream of altered splice site)
468474HELIXmight get lost (downstream of altered splice site)
477536DOMAINLIM zinc-binding 2.might get lost (downstream of altered splice site)
536596DOMAINLIM zinc-binding 3.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1878 / 1878
position (AA) of stopcodon in wt / mu AA sequence 626 / 626
position of stopcodon in wt / mu cDNA 1922 / 1922
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 45 / 45
chromosome 4
strand 1
last intron/exon boundary 1833
theoretical NMD boundary in CDS 1738
length of CDS 1878
coding sequence (CDS) position 1228
cDNA position
(for ins/del: last normal base / first normal base)		 1272
gDNA position
(for ins/del: last normal base / first normal base)		 188423
chromosomal position
(for ins/del: last normal base / first normal base)		 95561459
original gDNA sequence snippet GAAGAATCTCAAACAGCGCTACTTACTCAGGATCAGTGGCA
altered gDNA sequence snippet GAAGAATCTCAAACAGCGCTGCTTACTCAGGATCAGTGGCA
original cDNA sequence snippet GAAGAATCTCAAACAGCGCTACTTACTCAGGATCAGTGGCA
altered cDNA sequence snippet GAAGAATCTCAAACAGCGCTGCTTACTCAGGATCAGTGGCA
wildtype AA sequence MSNYSVSLVG PAPWGFRLQG GKDFNMPLTI SSLKDGGKAA QANVRIGDVV LSIDGINAQG
MTHLEAQNKI KGCTGSLNMT LQRASAAPKP EPVPVQKPTV TSVCSETSQE LAEGQRRGSQ
GDSKQQNGKI PPKRPPRKHI VERYTEFYHV PTHSDASKKR LIEDTEDWRP RTGTTQSRSF
RILAQITGTE HLKESEADNT KKAKFDSALE DLPKSGPHPP ATPQVLTIGS QVATLSKVAT
TYSSLSSSTG NVEDSFEGFR NFSTFSSPAR YSAAVLSSAA ATVSAVIATK TRLYTPERYH
SLLDALCISP VSKPLAFSYL QSSRKSTGSI HVKKTSNSQE PSPQLASSVA STRSMPESLD
SPTSGRPGVT SLTAAAAFKP VGSTGVIKSP SWQRPNQGVP STGRISNSAT YSGSVAPANS
ALGQTQPSDQ DTLVQRAEHI PAGKRTPMCA HCNQVIRGPF LVALGKSWHP EEFNCAHCKN
TMAYIGFVEE KGALYCELCY EKFFAPECGR CQRKILGEVI SALKQTWHVS CFVCVACGKP
IRNNVFHLED GEPYCETDYY ALFGTICHGC EFPIEAGDMF LEALGYTWHD TCFVCSVCCE
SLEGQTFFSK KDKPLCKKHA HSVNF*
mutated AA sequence MSNYSVSLVG PAPWGFRLQG GKDFNMPLTI SSLKDGGKAA QANVRIGDVV LSIDGINAQG
MTHLEAQNKI KGCTGSLNMT LQRASAAPKP EPVPVQKPTV TSVCSETSQE LAEGQRRGSQ
GDSKQQNGKI PPKRPPRKHI VERYTEFYHV PTHSDASKKR LIEDTEDWRP RTGTTQSRSF
RILAQITGTE HLKESEADNT KKAKFDSALE DLPKSGPHPP ATPQVLTIGS QVATLSKVAT
TYSSLSSSTG NVEDSFEGFR NFSTFSSPAR YSAAVLSSAA ATVSAVIATK TRLYTPERYH
SLLDALCISP VSKPLAFSYL QSSRKSTGSI HVKKTSNSQE PSPQLASSVA STRSMPESLD
SPTSGRPGVT SLTAAAAFKP VGSTGVIKSP SWQRPNQGVP STGRISNSAA YSGSVAPANS
ALGQTQPSDQ DTLVQRAEHI PAGKRTPMCA HCNQVIRGPF LVALGKSWHP EEFNCAHCKN
TMAYIGFVEE KGALYCELCY EKFFAPECGR CQRKILGEVI SALKQTWHVS CFVCVACGKP
IRNNVFHLED GEPYCETDYY ALFGTICHGC EFPIEAGDMF LEALGYTWHD TCFVCSVCCE
SLEGQTFFSK KDKPLCKKHA HSVNF*
speed 1.29 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