Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999995 (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) chr17:42398052A>GN/A show variant in all transcripts   IGV
HGNC symbol SLC25A39
Ensembl transcript ID ENST00000225308
Genbank transcript ID NM_016016
UniProt peptide Q9BZJ4
alteration type single base exchange
alteration region CDS
DNA changes c.715T>C
cDNA.890T>C
g.4187T>C
AA changes F239L Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 239
frameshift no
known variant Reference ID: rs2011951
databasehomozygous (G/G)heterozygousallele carriers
1000G12469192165
ExAC18508-424914259
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.3040
-0.140
(flanking)-0.0220
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased4185wt: 0.32 / mu: 0.36wt: CAATGGGTTCAGGCC
mu: CAATGGGCTCAGGCC		 ATGG|gttc
Donor marginally increased4192wt: 0.9768 / mu: 0.9780 (marginal change - not scored)wt: TTCAGGCCGAAGGAC
mu: CTCAGGCCGAAGGAC		 CAGG|ccga
distance from splice site 48
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      239NYELVKSWLNGFRPKDQTSVGMSF
mutated  not conserved    239NYELVKSWLNGLRPKDQTSVGMS
Ptroglodytes  not conserved  ENSPTRG00000009272  247KSWLNGLRPKDQTSVGMS
Mmulatta  not conserved  ENSMMUG00000017944  247KSWLNGLRPKDQTSVGMS
Fcatus  not conserved  ENSFCAG00000003053  247KSWLSGLRPKDQTSVGIS
Mmusculus  not conserved  ENSMUSG00000018677  247KSWLSGLRPKDQTSVGIS
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000000159  246NYELLKSRLCQWCQLTEANVSIS
Drerio  not conserved  ENSDARG00000007449  245NYELVKAQLCEHYRTPQ
Dmelanogaster  not conserved  FBgn0031039  267SSFGVVEP----TFSFS
Celegans  not conserved  C16C10.1  260QRRQGPDHNPFVVS
Xtropicalis  not conserved  ENSXETG00000011613  251NYELVKKKMSNTKAAVESPFLVS
protein features
start (aa)end (aa)featuredetails 
159243REPEATSolcar 2.lost
253347REPEATSolcar 3.might get lost (downstream of altered splice site)
259279TRANSMEMHelical; Name=5; (Potential).might get lost (downstream of altered splice site)
266266CONFLICTG -> R (in Ref. 7; AAF69618).might get lost (downstream of altered splice site)
318338TRANSMEMHelical; Name=6; (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1056 / 1056
position (AA) of stopcodon in wt / mu AA sequence 352 / 352
position of stopcodon in wt / mu cDNA 1231 / 1231
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 176 / 176
chromosome 17
strand -1
last intron/exon boundary 1116
theoretical NMD boundary in CDS 890
length of CDS 1056
coding sequence (CDS) position 715
cDNA position
(for ins/del: last normal base / first normal base)		 890
gDNA position
(for ins/del: last normal base / first normal base)		 4187
chromosomal position
(for ins/del: last normal base / first normal base)		 42398052
original gDNA sequence snippet TGAAGAGCTGGCTCAATGGGTTCAGGCCGAAGGACCAGACT
altered gDNA sequence snippet TGAAGAGCTGGCTCAATGGGCTCAGGCCGAAGGACCAGACT
original cDNA sequence snippet TGAAGAGCTGGCTCAATGGGTTCAGGCCGAAGGACCAGACT
altered cDNA sequence snippet TGAAGAGCTGGCTCAATGGGCTCAGGCCGAAGGACCAGACT
wildtype AA sequence MADQDPAGIS PLQQMVASGT GAVVTSLFMT PLDVVKVRLQ SQRPSMASEL MPSSRLWSLS
YTKWKCLLYC NGVLEPLYLC PNGARCATWF QDPTRFTGTM DAFVKIVRHE GTRTLWSGLP
ATLVMTVPAT AIYFTAYDQL KAFLCGRALT SDLYAPMVAG ALARLGTVTV ISPLELMRTK
LQAQHVSYRE LGACVRTAVA QGGWRSLWLG WGPTALRDVP FSALYWFNYE LVKSWLNGFR
PKDQTSVGMS FVAGGISGTV AAVLTLPFDV VKTQRQVALG AMEAVRVNPL HVDSTWLLLR
RIRAESGTKG LFAGFLPRII KAAPSCAIMI STYEFGKSFF QRLNQDRLLG G*
mutated AA sequence MADQDPAGIS PLQQMVASGT GAVVTSLFMT PLDVVKVRLQ SQRPSMASEL MPSSRLWSLS
YTKWKCLLYC NGVLEPLYLC PNGARCATWF QDPTRFTGTM DAFVKIVRHE GTRTLWSGLP
ATLVMTVPAT AIYFTAYDQL KAFLCGRALT SDLYAPMVAG ALARLGTVTV ISPLELMRTK
LQAQHVSYRE LGACVRTAVA QGGWRSLWLG WGPTALRDVP FSALYWFNYE LVKSWLNGLR
PKDQTSVGMS FVAGGISGTV AAVLTLPFDV VKTQRQVALG AMEAVRVNPL HVDSTWLLLR
RIRAESGTKG LFAGFLPRII KAAPSCAIMI STYEFGKSFF QRLNQDRLLG G*
speed 1.09 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