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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: ENST00000329321
MT speed 0 s - this script 2.545825 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GPR39polymorphism_automatic0.000679035849613041simple_aaeaffectedA50Vsingle base exchangers2241764show file

Taster files

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 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999320964150387 (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) chr2:133174764C>TN/A show variant in all transcripts   IGV
HGNC symbol GPR39
Ensembl transcript ID ENST00000329321
Genbank transcript ID NM_001508
UniProt peptide O43194
alteration type single base exchange
alteration region CDS
DNA changes c.149C>T
cDNA.618C>T
g.618C>T
AA changes A50V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 50
frameshift no
known variant Reference ID: rs2241764
databasehomozygous (T/T)heterozygousallele carriers
1000G39810981496
ExAC72041835925563
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)0.7250.989
2.5321
(flanking)1.2721
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased623wt: 0.7162 / mu: 0.7538 (marginal change - not scored)wt: CCACCATTCGGGTCA
mu: TCACCATTCGGGTCA		 ACCA|ttcg
Donor gained6110.59mu: TGGGGAACAGCGTCA GGGA|acag
distance from splice site 618
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      50IIFVMGLLGNSATIRVTQVLQKKG
mutated  not conserved    50IIFVMGLLGNSVTIRVTQVLQK
Ptroglodytes  not conserved  ENSPTRG00000012477  50IIFVMGLLGNSVTIRVTQVLQK
Mmulatta  no homologue    
Fcatus  not conserved  ENSFCAG00000000023  50AIFVVGILGNSVTIWVTQVLQK
Mmusculus  not conserved  ENSMUSG00000026343  50IIFVVGILGNSVTIRVTQVLQK
Ggallus  not conserved  ENSGALG00000012171  50CIFVAGILGNSITIKATRILQKK
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000042939  40LILSLGVLGNSATIHVAQVLQRN
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
4771TOPO_DOMCytoplasmic (Potential).lost
7292TRANSMEMHelical; Name=2; (Potential).might get lost (downstream of altered splice site)
93109TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
108108DISULFIDmight get lost (downstream of altered splice site)
110131TRANSMEMHelical; Name=3; (Potential).might get lost (downstream of altered splice site)
132154TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
155175TRANSMEMHelical; Name=4; (Potential).might get lost (downstream of altered splice site)
176223TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
191191DISULFIDmight get lost (downstream of altered splice site)
192192CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
206206CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
210210DISULFIDmight get lost (downstream of altered splice site)
212212CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
224243TRANSMEMHelical; Name=5; (Potential).might get lost (downstream of altered splice site)
244280TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
281301TRANSMEMHelical; Name=6; (Potential).might get lost (downstream of altered splice site)
302321TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
312312MUTAGENH->A: Not affect constitutive or Zn(2+)- induced activation.might get lost (downstream of altered splice site)
313313MUTAGEND->A: Induces very high constitutive activity and eliminates Zn(2+)-induced activation.might get lost (downstream of altered splice site)
322347TRANSMEMHelical; Name=7; (Potential).might get lost (downstream of altered splice site)
348428TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
380380MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1362 / 1362
position (AA) of stopcodon in wt / mu AA sequence 454 / 454
position of stopcodon in wt / mu cDNA 1831 / 1831
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 470 / 470
chromosome 2
strand 1
last intron/exon boundary 1326
theoretical NMD boundary in CDS 806
length of CDS 1362
coding sequence (CDS) position 149
cDNA position
(for ins/del: last normal base / first normal base)		 618
gDNA position
(for ins/del: last normal base / first normal base)		 618
chromosomal position
(for ins/del: last normal base / first normal base)		 133174764
original gDNA sequence snippet GGGCCTTCTGGGGAACAGCGCCACCATTCGGGTCACCCAGG
altered gDNA sequence snippet GGGCCTTCTGGGGAACAGCGTCACCATTCGGGTCACCCAGG
original cDNA sequence snippet GGGCCTTCTGGGGAACAGCGCCACCATTCGGGTCACCCAGG
altered cDNA sequence snippet GGGCCTTCTGGGGAACAGCGTCACCATTCGGGTCACCCAGG
wildtype AA sequence MASPSLPGSD CSQIIDHSHV PEFEVATWIK ITLILVYLII FVMGLLGNSA TIRVTQVLQK
KGYLQKEVTD HMVSLACSDI LVFLIGMPME FYSIIWNPLT TSSYTLSCKL HTFLFEACSY
ATLLHVLTLS FERYIAICHP FRYKAVSGPC QVKLLIGFVW VTSALVALPL LFAMGTEYPL
VNVPSHRGLT CNRSSTRHHE QPETSNMSIC TNLSSRWTVF QSSIFGAFVV YLVVLLSVAF
MCWNMMQVLM KSQKGSLAGG TRPPQLRKSE SEESRTARRQ TIIFLRLIVV TLAVCWMPNQ
IRRIMAAAKP KHDWTRSYFR AYMILLPFSE TFFYLSSVIN PLLYTVSSQQ FRRVFVQVLC
CRLSLQHANH EKRLRVHAHS TTDSARFVQR PLLFASRRQS SARRTEKIFL STFQSEAEPQ
SKSQSLSLES LEPNSGAKPA NSAAENGFQE HEV*
mutated AA sequence MASPSLPGSD CSQIIDHSHV PEFEVATWIK ITLILVYLII FVMGLLGNSV TIRVTQVLQK
KGYLQKEVTD HMVSLACSDI LVFLIGMPME FYSIIWNPLT TSSYTLSCKL HTFLFEACSY
ATLLHVLTLS FERYIAICHP FRYKAVSGPC QVKLLIGFVW VTSALVALPL LFAMGTEYPL
VNVPSHRGLT CNRSSTRHHE QPETSNMSIC TNLSSRWTVF QSSIFGAFVV YLVVLLSVAF
MCWNMMQVLM KSQKGSLAGG TRPPQLRKSE SEESRTARRQ TIIFLRLIVV TLAVCWMPNQ
IRRIMAAAKP KHDWTRSYFR AYMILLPFSE TFFYLSSVIN PLLYTVSSQQ FRRVFVQVLC
CRLSLQHANH EKRLRVHAHS TTDSARFVQR PLLFASRRQS SARRTEKIFL STFQSEAEPQ
SKSQSLSLES LEPNSGAKPA NSAAENGFQE HEV*
speed 0.48 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
back to results table

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