Yum, tasty mutations...

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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000476620
Querying Taster for transcript #2: ENST00000436072
MT speed 3.51 s - this script 5.414841 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
SFRP4polymorphism_automatic0.012560373521934simple_aaeaffectedP320Tsingle base exchangers1802073show file
EPDR1polymorphism_automatic0.999954859428354without_aaeaffectedsingle base exchangers1802073show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.987439626478066 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:37947164G>TN/A show variant in all transcripts   IGV
HGNC symbol SFRP4
Ensembl transcript ID ENST00000436072
Genbank transcript ID NM_003014
UniProt peptide Q6FHJ7
alteration type single base exchange
alteration region CDS
DNA changes c.958C>A
cDNA.1336C>A
g.118134C>A
AA changes P320T Score: 38 explain score(s)
position(s) of altered AA
if AA alteration in CDS
320
frameshift no
known variant Reference ID: rs1802073
databasehomozygous (T/T)heterozygousallele carriers
1000G76411901954
ExAC12116853520651
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.0240.519
0.3720.669
(flanking)1.7180.975
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased118128wt: 0.23 / mu: 0.29wt: CAAAGGGAAAGCCTC
mu: CAAAGGGAAAGACTC
 AAGG|gaaa
Donor marginally increased118126wt: 0.9965 / mu: 0.9980 (marginal change - not scored)wt: ACCAAAGGGAAAGCC
mu: ACCAAAGGGAAAGAC
 CAAA|ggga
distance from splice site 103
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      320SRSNPPKPKGKPPAPKPASPKKNI
mutated  not conserved    320SRSNPPKPKGKTPAPKPASPKKN
Ptroglodytes  all identical  ENSPTRG00000019092  317SRSNPPKPKGKPPAPKPTSPKKN
Mmulatta  all identical  ENSMMUG00000021089  320SRSNPPKPKGKPPAPKPASPKKN
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000021319  320SRSNPPKSKGRPPAPKPASPKKN
Ggallus  not conserved  ENSGALG00000012073  338GRSGASKPSNKNTNTLVSSPKKA
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1041 / 1041
position (AA) of stopcodon in wt / mu AA sequence 347 / 347
position of stopcodon in wt / mu cDNA 1419 / 1419
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 379 / 379
chromosome 7
strand -1
last intron/exon boundary 1234
theoretical NMD boundary in CDS 805
length of CDS 1041
coding sequence (CDS) position 958
cDNA position
(for ins/del: last normal base / first normal base)
1336
gDNA position
(for ins/del: last normal base / first normal base)
118134
chromosomal position
(for ins/del: last normal base / first normal base)
37947164
original gDNA sequence snippet CCCCCAAACCAAAGGGAAAGCCTCCTGCTCCCAAACCAGCC
altered gDNA sequence snippet CCCCCAAACCAAAGGGAAAGACTCCTGCTCCCAAACCAGCC
original cDNA sequence snippet CCCCCAAACCAAAGGGAAAGCCTCCTGCTCCCAAACCAGCC
altered cDNA sequence snippet CCCCCAAACCAAAGGGAAAGACTCCTGCTCCCAAACCAGCC
wildtype AA sequence MFLSILVALC LWLHLALGVR GAPCEAVRIP MCRHMPWNIT RMPNHLHHST QENAILAIEQ
YEELVDVNCS AVLRFFLCAM YAPICTLEFL HDPIKPCKSV CQRARDDCEP LMKMYNHSWP
ESLACDELPV YDRGVCISPE AIVTDLPEDV KWIDITPDMM VQERPLDVDC KRLSPDRCKC
KKVKPTLATY LSKNYSYVIH AKIKAVQRSG CNEVTTVVDV KEIFKSSSPI PRTQVPLITN
SSCQCPHILP HQDVLIMCYE WRSRMMLLEN CLVEKWRDQL SKRSIQWEER LQEQRRTVQD
KKKTAGRTSR SNPPKPKGKP PAPKPASPKK NIKTRSAQKR TNPKRV*
mutated AA sequence MFLSILVALC LWLHLALGVR GAPCEAVRIP MCRHMPWNIT RMPNHLHHST QENAILAIEQ
YEELVDVNCS AVLRFFLCAM YAPICTLEFL HDPIKPCKSV CQRARDDCEP LMKMYNHSWP
ESLACDELPV YDRGVCISPE AIVTDLPEDV KWIDITPDMM VQERPLDVDC KRLSPDRCKC
KKVKPTLATY LSKNYSYVIH AKIKAVQRSG CNEVTTVVDV KEIFKSSSPI PRTQVPLITN
SSCQCPHILP HQDVLIMCYE WRSRMMLLEN CLVEKWRDQL SKRSIQWEER LQEQRRTVQD
KKKTAGRTSR SNPPKPKGKT PAPKPASPKK NIKTRSAQKR TNPKRV*
speed 2.34 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
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 4.51405716462715e-05 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • 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) chr7:37947164G>TN/A show variant in all transcripts   IGV
HGNC symbol EPDR1
Ensembl transcript ID ENST00000476620
Genbank transcript ID N/A
UniProt peptide Q9UM22
alteration type single base exchange
alteration region intron
DNA changes g.223719G>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs1802073
databasehomozygous (T/T)heterozygousallele carriers
1000G76411901954
ExAC12116853520651
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.0240.519
0.3720.669
(flanking)1.7180.975
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -11) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc increased223730wt: 0.80 / mu: 0.95wt: GAGCAGGAGGCTTTCCCTTTGGTTTGGGGGGATTACTACGA
mu: GAGCAGGAGTCTTTCCCTTTGGTTTGGGGGGATTACTACGA
 tttg|GTTT
Donor increased223712wt: 0.31 / mu: 0.92wt: TGGGAGCAGGAGGCT
mu: TGGGAGCAGGAGTCT
 GGAG|cagg
Acc gained2237290.32mu: GGAGCAGGAGTCTTTCCCTTTGGTTTGGGGGGATTACTACG cttt|GGTT
distance from splice site 41278
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
N/A
protein features
start (aa)end (aa)featuredetails 
137SIGNALPotential.might get lost (downstream of altered splice site)
130130CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
182182CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
207207CONFLICTP -> S (in Ref. 7; CAB60269).might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 171 / 171
chromosome 7
strand 1
last intron/exon boundary 343
theoretical NMD boundary in CDS 122
length of CDS 369
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)
N/A
gDNA position
(for ins/del: last normal base / first normal base)
223719
chromosomal position
(for ins/del: last normal base / first normal base)
37947164
original gDNA sequence snippet GGCTGGTTTGGGAGCAGGAGGCTTTCCCTTTGGTTTGGGGG
altered gDNA sequence snippet GGCTGGTTTGGGAGCAGGAGTCTTTCCCTTTGGTTTGGGGG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MFQIDQATKQ CSKMTLTQPW DPLDIPQNST FEDQYSIGGP QEQITVQEWS DRKSARSYET
WIGIYTVKDC YPVQETFTIN YSVILSTRFF DIQLGIKDPS VFTPPSTCQM AQLEKMSEDC
SW*
mutated AA sequence N/A
speed 1.17 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

Problems