Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000308377
Querying Taster for transcript #2: ENST00000394566
MT speed 0 s - this script 2.28724 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
SLFN11polymorphism_automatic3.07798231347078e-12simple_aaeaffectedV121Fsingle base exchangers12453150show file
SLFN11polymorphism_automatic3.07798231347078e-12simple_aaeaffectedV121Fsingle base exchangers12453150show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999996922 (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) chr17:33690466C>AN/A show variant in all transcripts   IGV
HGNC symbol SLFN11
Ensembl transcript ID ENST00000308377
Genbank transcript ID NM_152270
UniProt peptide Q7Z7L1
alteration type single base exchange
alteration region CDS
DNA changes c.361G>T
cDNA.514G>T
g.10255G>T
AA changes V121F Score: 50 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 121
frameshift no
known variant Reference ID: rs12453150
databasehomozygous (A/A)heterozygousallele carriers
1000G53310181551
ExAC15741128517026
regulatory features H3K27me1, Histone, Histone 3 Lysine 27 mono-methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.5540
-3.6760
(flanking)-0.8150
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased10259wt: 0.28 / mu: 0.72wt: CCCTGAAGATCGCTCTGTCAAGCCCCGCCTTTGCAGCCTCA
mu: CCCTGAAGATCGCTCTTTCAAGCCCCGCCTTTGCAGCCTCA		 tcaa|GCCC
Acc marginally increased10246wt: 0.2137 / mu: 0.2380 (marginal change - not scored)wt: GCAGTGGCCCTTTCCCTGAAGATCGCTCTGTCAAGCCCCGC
mu: GCAGTGGCCCTTTCCCTGAAGATCGCTCTTTCAAGCCCCGC		 gaag|ATCG
Donor marginally increased10259wt: 0.8902 / mu: 0.9053 (marginal change - not scored)wt: TGTCAAGCCCCGCCT
mu: TTTCAAGCCCCGCCT		 TCAA|gccc
Acc gained102580.32mu: TCCCTGAAGATCGCTCTTTCAAGCCCCGCCTTTGCAGCCTC ttca|AGCC
Acc gained102640.32mu: AAGATCGCTCTTTCAAGCCCCGCCTTTGCAGCCTCAGTTCT cccc|GCCT
distance from splice site 380
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      121WSSGPFPEDRSVKPRLCSLSSSLY
mutated  not conserved    121FKPRLCSLSSSL
Ptroglodytes  all identical  ENSPTRG00000009017  121VKPRLCSLSSSL
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000072621  59TKPRICSLGSSL
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
143143CONFLICTM -> T (in Ref. 1; BAC03835).might get lost (downstream of altered splice site)
324324CONFLICTV -> M (in Ref. 2; CAD38606).might get lost (downstream of altered splice site)
599606NP_BINDATP (Potential).might get lost (downstream of altered splice site)
665665CONFLICTI -> V (in Ref. 1; BAC03835 and 2; CAD38606).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2706 / 2706
position (AA) of stopcodon in wt / mu AA sequence 902 / 902
position of stopcodon in wt / mu cDNA 2859 / 2859
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 154 / 154
chromosome 17
strand -1
last intron/exon boundary 2076
theoretical NMD boundary in CDS 1872
length of CDS 2706
coding sequence (CDS) position 361
cDNA position
(for ins/del: last normal base / first normal base)		 514
gDNA position
(for ins/del: last normal base / first normal base)		 10255
chromosomal position
(for ins/del: last normal base / first normal base)		 33690466
original gDNA sequence snippet CTTTCCCTGAAGATCGCTCTGTCAAGCCCCGCCTTTGCAGC
altered gDNA sequence snippet CTTTCCCTGAAGATCGCTCTTTCAAGCCCCGCCTTTGCAGC
original cDNA sequence snippet CTTTCCCTGAAGATCGCTCTGTCAAGCCCCGCCTTTGCAGC
altered cDNA sequence snippet CTTTCCCTGAAGATCGCTCTTTCAAGCCCCGCCTTTGCAGC
wildtype AA sequence MEANQCPLVV EPSYPDLVIN VGEVTLGEEN RKKLQKIQRD QEKERVMRAA CALLNSGGGV
IRMAKKVEHP VEMGLDLEQS LRELIQSSDL QAFFETKQQG RCFYIFVKSW SSGPFPEDRS
VKPRLCSLSS SLYRRSETSV RSMDSREAFC FLKTKRKPKI LEEGPFHKIH KGVYQELPNS
DPADPNSDPA DLIFQKDYLE YGEILPFPES QLVEFKQFST KHFQEYVKRT IPEYVPAFAN
TGGGYLFIGV DDKSREVLGC AKENVDPDSL RRKIEQAIYK LPCVHFCQPQ RPITFTLKIV
NVLKRGELYG YACMIRVNPF CCAVFSEAPN SWIVEDKYVC SLTTEKWVGM MTDTDPDLLQ
LSEDFECQLS LSSGPPLSRP VYSKKGLEHK KELQQLLFSV PPGYLRYTPE SLWRDLISEH
RGLEELINKQ MQPFFRGILI FSRSWAVDLN LQEKPGVICD ALLIAQNSTP ILYTILREQD
AEGQDYCTRT AFTLKQKLVN MGGYTGKVCV RAKVLCLSPE SSAEALEAAV SPMDYPASYS
LAGTQHMEAL LQSLVIVLLG FRSLLSDQLG CEVLNLLTAQ QYEIFSRSLR KNRELFVHGL
PGSGKTIMAM KIMEKIRNVF HCEAHRILYV CENQPLRNFI SDRNICRAET RKTFLRENFE
HIQHIVIDEA QNFRTEDGDW YGKAKSITRR AKGGPGILWI FLDYFQTSHL DCSGLPPLSD
QYPREELTRI VRNADPIAKY LQKEMQVIRS NPSFNIPTGC LEVFPEAEWS QGVQGTLRIK
KYLTVEQIMT CVADTCRRFF DRGYSPKDVA VLVSTAKEVE HYKYELLKAM RKKRVVQLSD
ACDMLGDHIV LDSVRRFSGL ERSIVFGIHP RTADPAILPN VLICLASRAK QHLYIFPWGG
H*
mutated AA sequence MEANQCPLVV EPSYPDLVIN VGEVTLGEEN RKKLQKIQRD QEKERVMRAA CALLNSGGGV
IRMAKKVEHP VEMGLDLEQS LRELIQSSDL QAFFETKQQG RCFYIFVKSW SSGPFPEDRS
FKPRLCSLSS SLYRRSETSV RSMDSREAFC FLKTKRKPKI LEEGPFHKIH KGVYQELPNS
DPADPNSDPA DLIFQKDYLE YGEILPFPES QLVEFKQFST KHFQEYVKRT IPEYVPAFAN
TGGGYLFIGV DDKSREVLGC AKENVDPDSL RRKIEQAIYK LPCVHFCQPQ RPITFTLKIV
NVLKRGELYG YACMIRVNPF CCAVFSEAPN SWIVEDKYVC SLTTEKWVGM MTDTDPDLLQ
LSEDFECQLS LSSGPPLSRP VYSKKGLEHK KELQQLLFSV PPGYLRYTPE SLWRDLISEH
RGLEELINKQ MQPFFRGILI FSRSWAVDLN LQEKPGVICD ALLIAQNSTP ILYTILREQD
AEGQDYCTRT AFTLKQKLVN MGGYTGKVCV RAKVLCLSPE SSAEALEAAV SPMDYPASYS
LAGTQHMEAL LQSLVIVLLG FRSLLSDQLG CEVLNLLTAQ QYEIFSRSLR KNRELFVHGL
PGSGKTIMAM KIMEKIRNVF HCEAHRILYV CENQPLRNFI SDRNICRAET RKTFLRENFE
HIQHIVIDEA QNFRTEDGDW YGKAKSITRR AKGGPGILWI FLDYFQTSHL DCSGLPPLSD
QYPREELTRI VRNADPIAKY LQKEMQVIRS NPSFNIPTGC LEVFPEAEWS QGVQGTLRIK
KYLTVEQIMT CVADTCRRFF DRGYSPKDVA VLVSTAKEVE HYKYELLKAM RKKRVVQLSD
ACDMLGDHIV LDSVRRFSGL ERSIVFGIHP RTADPAILPN VLICLASRAK QHLYIFPWGG
H*
speed 0.17 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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999996922 (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) chr17:33690466C>AN/A show variant in all transcripts   IGV
HGNC symbol SLFN11
Ensembl transcript ID ENST00000394566
Genbank transcript ID NM_001104587
UniProt peptide Q7Z7L1
alteration type single base exchange
alteration region CDS
DNA changes c.361G>T
cDNA.634G>T
g.10255G>T
AA changes V121F Score: 50 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 121
frameshift no
known variant Reference ID: rs12453150
databasehomozygous (A/A)heterozygousallele carriers
1000G53310181551
ExAC15741128517026
regulatory features H3K27me1, Histone, Histone 3 Lysine 27 mono-methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.5540
-3.6760
(flanking)-0.8150
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased10259wt: 0.28 / mu: 0.72wt: CCCTGAAGATCGCTCTGTCAAGCCCCGCCTTTGCAGCCTCA
mu: CCCTGAAGATCGCTCTTTCAAGCCCCGCCTTTGCAGCCTCA		 tcaa|GCCC
Acc marginally increased10246wt: 0.2137 / mu: 0.2380 (marginal change - not scored)wt: GCAGTGGCCCTTTCCCTGAAGATCGCTCTGTCAAGCCCCGC
mu: GCAGTGGCCCTTTCCCTGAAGATCGCTCTTTCAAGCCCCGC		 gaag|ATCG
Donor marginally increased10259wt: 0.8902 / mu: 0.9053 (marginal change - not scored)wt: TGTCAAGCCCCGCCT
mu: TTTCAAGCCCCGCCT		 TCAA|gccc
Acc gained102580.32mu: TCCCTGAAGATCGCTCTTTCAAGCCCCGCCTTTGCAGCCTC ttca|AGCC
Acc gained102640.32mu: AAGATCGCTCTTTCAAGCCCCGCCTTTGCAGCCTCAGTTCT cccc|GCCT
distance from splice site 380
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      121WSSGPFPEDRSVKPRLCSLSSSLY
mutated  not conserved    121FKPRLCSLSSSL
Ptroglodytes  all identical  ENSPTRG00000009017  121VKPRLCSLSSSL
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000072621  59TKPRICSLGSSL
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
143143CONFLICTM -> T (in Ref. 1; BAC03835).might get lost (downstream of altered splice site)
324324CONFLICTV -> M (in Ref. 2; CAD38606).might get lost (downstream of altered splice site)
599606NP_BINDATP (Potential).might get lost (downstream of altered splice site)
665665CONFLICTI -> V (in Ref. 1; BAC03835 and 2; CAD38606).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2706 / 2706
position (AA) of stopcodon in wt / mu AA sequence 902 / 902
position of stopcodon in wt / mu cDNA 2979 / 2979
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 274 / 274
chromosome 17
strand -1
last intron/exon boundary 2196
theoretical NMD boundary in CDS 1872
length of CDS 2706
coding sequence (CDS) position 361
cDNA position
(for ins/del: last normal base / first normal base)		 634
gDNA position
(for ins/del: last normal base / first normal base)		 10255
chromosomal position
(for ins/del: last normal base / first normal base)		 33690466
original gDNA sequence snippet CTTTCCCTGAAGATCGCTCTGTCAAGCCCCGCCTTTGCAGC
altered gDNA sequence snippet CTTTCCCTGAAGATCGCTCTTTCAAGCCCCGCCTTTGCAGC
original cDNA sequence snippet CTTTCCCTGAAGATCGCTCTGTCAAGCCCCGCCTTTGCAGC
altered cDNA sequence snippet CTTTCCCTGAAGATCGCTCTTTCAAGCCCCGCCTTTGCAGC
wildtype AA sequence MEANQCPLVV EPSYPDLVIN VGEVTLGEEN RKKLQKIQRD QEKERVMRAA CALLNSGGGV
IRMAKKVEHP VEMGLDLEQS LRELIQSSDL QAFFETKQQG RCFYIFVKSW SSGPFPEDRS
VKPRLCSLSS SLYRRSETSV RSMDSREAFC FLKTKRKPKI LEEGPFHKIH KGVYQELPNS
DPADPNSDPA DLIFQKDYLE YGEILPFPES QLVEFKQFST KHFQEYVKRT IPEYVPAFAN
TGGGYLFIGV DDKSREVLGC AKENVDPDSL RRKIEQAIYK LPCVHFCQPQ RPITFTLKIV
NVLKRGELYG YACMIRVNPF CCAVFSEAPN SWIVEDKYVC SLTTEKWVGM MTDTDPDLLQ
LSEDFECQLS LSSGPPLSRP VYSKKGLEHK KELQQLLFSV PPGYLRYTPE SLWRDLISEH
RGLEELINKQ MQPFFRGILI FSRSWAVDLN LQEKPGVICD ALLIAQNSTP ILYTILREQD
AEGQDYCTRT AFTLKQKLVN MGGYTGKVCV RAKVLCLSPE SSAEALEAAV SPMDYPASYS
LAGTQHMEAL LQSLVIVLLG FRSLLSDQLG CEVLNLLTAQ QYEIFSRSLR KNRELFVHGL
PGSGKTIMAM KIMEKIRNVF HCEAHRILYV CENQPLRNFI SDRNICRAET RKTFLRENFE
HIQHIVIDEA QNFRTEDGDW YGKAKSITRR AKGGPGILWI FLDYFQTSHL DCSGLPPLSD
QYPREELTRI VRNADPIAKY LQKEMQVIRS NPSFNIPTGC LEVFPEAEWS QGVQGTLRIK
KYLTVEQIMT CVADTCRRFF DRGYSPKDVA VLVSTAKEVE HYKYELLKAM RKKRVVQLSD
ACDMLGDHIV LDSVRRFSGL ERSIVFGIHP RTADPAILPN VLICLASRAK QHLYIFPWGG
H*
mutated AA sequence MEANQCPLVV EPSYPDLVIN VGEVTLGEEN RKKLQKIQRD QEKERVMRAA CALLNSGGGV
IRMAKKVEHP VEMGLDLEQS LRELIQSSDL QAFFETKQQG RCFYIFVKSW SSGPFPEDRS
FKPRLCSLSS SLYRRSETSV RSMDSREAFC FLKTKRKPKI LEEGPFHKIH KGVYQELPNS
DPADPNSDPA DLIFQKDYLE YGEILPFPES QLVEFKQFST KHFQEYVKRT IPEYVPAFAN
TGGGYLFIGV DDKSREVLGC AKENVDPDSL RRKIEQAIYK LPCVHFCQPQ RPITFTLKIV
NVLKRGELYG YACMIRVNPF CCAVFSEAPN SWIVEDKYVC SLTTEKWVGM MTDTDPDLLQ
LSEDFECQLS LSSGPPLSRP VYSKKGLEHK KELQQLLFSV PPGYLRYTPE SLWRDLISEH
RGLEELINKQ MQPFFRGILI FSRSWAVDLN LQEKPGVICD ALLIAQNSTP ILYTILREQD
AEGQDYCTRT AFTLKQKLVN MGGYTGKVCV RAKVLCLSPE SSAEALEAAV SPMDYPASYS
LAGTQHMEAL LQSLVIVLLG FRSLLSDQLG CEVLNLLTAQ QYEIFSRSLR KNRELFVHGL
PGSGKTIMAM KIMEKIRNVF HCEAHRILYV CENQPLRNFI SDRNICRAET RKTFLRENFE
HIQHIVIDEA QNFRTEDGDW YGKAKSITRR AKGGPGILWI FLDYFQTSHL DCSGLPPLSD
QYPREELTRI VRNADPIAKY LQKEMQVIRS NPSFNIPTGC LEVFPEAEWS QGVQGTLRIK
KYLTVEQIMT CVADTCRRFF DRGYSPKDVA VLVSTAKEVE HYKYELLKAM RKKRVVQLSD
ACDMLGDHIV LDSVRRFSGL ERSIVFGIHP RTADPAILPN VLICLASRAK QHLYIFPWGG
H*
speed 0.11 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