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 6 transcript(s)...
Querying Taster for transcript #1: ENST00000302946
Querying Taster for transcript #2: ENST00000372613
Querying Taster for transcript #3: ENST00000372611
Querying Taster for transcript #4: ENST00000359345
Querying Taster for transcript #5: ENST00000439569
Querying Taster for transcript #6: ENST00000397197
MT speed 0 s - this script 6.343492 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
SLFNL1polymorphism_automatic0.00784382452682197simple_aaeaffectedR144Tsingle base exchangers3738368show file
SLFNL1polymorphism_automatic0.093988699794145simple_aaeaffectedR144Tsingle base exchangers3738368show file
SLFNL1polymorphism_automatic0.093988699794145simple_aaeaffectedR144Tsingle base exchangers3738368show file
SLFNL1polymorphism_automatic0.093988699794145simple_aaeaffectedR144Tsingle base exchangers3738368show file
SLFNL1polymorphism_automatic0.093988699794145simple_aaeaffectedR144Tsingle base exchangers3738368show file
SLFNL1polymorphism_automatic0.093988699794145simple_aaeaffectedR144Tsingle base exchangers3738368show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.992156175473178 (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) chr1:41485902C>GN/A show variant in all transcripts   IGV
HGNC symbol SLFNL1
Ensembl transcript ID ENST00000372611
Genbank transcript ID N/A
UniProt peptide Q499Z3
alteration type single base exchange
alteration region CDS
DNA changes c.431G>C
cDNA.740G>C
g.3008G>C
AA changes R144T Score: 71 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 144
frameshift no
known variant Reference ID: rs3738368
databasehomozygous (G/G)heterozygousallele carriers
1000G113686799
ExAC46502178926439
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0990.913
1.1820.905
(flanking)0.8050.852
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 increased3001wt: 0.9336 / mu: 0.9561 (marginal change - not scored)wt: CCTTCAGCCACAGAG
mu: CCTTCAGCCACACAG		 TTCA|gcca
Donor marginally increased3011wt: 0.9967 / mu: 0.9975 (marginal change - not scored)wt: CAGAGAGGTAAGTGG
mu: CACAGAGGTAAGTGG		 GAGA|ggta
Donor increased3009wt: 0.25 / mu: 0.57wt: CACAGAGAGGTAAGT
mu: CACACAGAGGTAAGT		 CAGA|gagg
Donor increased3006wt: 0.41 / mu: 0.64wt: AGCCACAGAGAGGTA
mu: AGCCACACAGAGGTA		 CCAC|agag
distance from splice site 5
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      144LLSEAQGPFSHREQIVGKDQLFQG
mutated  not conserved    144LLSEAQGPFSHTEQIVGKDQLFQ
Ptroglodytes  all identical  ENSPTRG00000000600  144LLSEAQGPFSHREEKEEEEEDSGLSP
Mmulatta  no homologue    
Fcatus  all identical  ENSFCAG00000015323  144VLGDGRGPSRGREREDDSSRSPSPNPANSPPARAPQRSQDRPSGTRSDS
Mmusculus  no alignment  ENSMUSG00000047518  n/a
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 
261268NP_BINDATP (Potential).might get lost (downstream of altered splice site)
280280CONFLICTR -> S (in Ref. 3; AAH37879).might get lost (downstream of altered splice site)
366398COILEDPotential.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1047 / 1047
position (AA) of stopcodon in wt / mu AA sequence 349 / 349
position of stopcodon in wt / mu cDNA 1356 / 1356
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 310 / 310
chromosome 1
strand -1
last intron/exon boundary 1234
theoretical NMD boundary in CDS 874
length of CDS 1047
coding sequence (CDS) position 431
cDNA position
(for ins/del: last normal base / first normal base)		 740
gDNA position
(for ins/del: last normal base / first normal base)		 3008
chromosomal position
(for ins/del: last normal base / first normal base)		 41485902
original gDNA sequence snippet CCAAGGGCCCTTCAGCCACAGAGAGGTAAGTGGGACTTTTC
altered gDNA sequence snippet CCAAGGGCCCTTCAGCCACACAGAGGTAAGTGGGACTTTTC
original cDNA sequence snippet CCAAGGGCCCTTCAGCCACAGAGAGCAGATCGTGGGCAAGG
altered cDNA sequence snippet CCAAGGGCCCTTCAGCCACACAGAGCAGATCGTGGGCAAGG
wildtype AA sequence MTPMKRSVQT QVSEPFMESW GEESLPELPA EQSLTEYSDL EEAPSAHTLY VGHLNPQFSV
PVLACLLRDT LERLEMPVAR EHIEVVRRPR KAYALVQVTV HRDTLASLPW RLQTALEEHL
ILKELAARGK DLLLSEAQGP FSHREQIVGK DQLFQGAFLG SETRNMEFKR GSGEYLSLAF
KHHVRRYVCA FLNSEGGSLL VGVEDSGLVQ GIRCSHRDED RARLLVDSIL QGFKPQIFPD
AYTLTFIPVI STSETSVPLK VIRLTVHTPK AQSQPQLYQT DQGEVFLRRD GSIQGPLSAS
AIQEWCRQRW LVELGKLEEK MKALMMEKEQ LQQQLQQHGP VSCTCCVL*
mutated AA sequence MTPMKRSVQT QVSEPFMESW GEESLPELPA EQSLTEYSDL EEAPSAHTLY VGHLNPQFSV
PVLACLLRDT LERLEMPVAR EHIEVVRRPR KAYALVQVTV HRDTLASLPW RLQTALEEHL
ILKELAARGK DLLLSEAQGP FSHTEQIVGK DQLFQGAFLG SETRNMEFKR GSGEYLSLAF
KHHVRRYVCA FLNSEGGSLL VGVEDSGLVQ GIRCSHRDED RARLLVDSIL QGFKPQIFPD
AYTLTFIPVI STSETSVPLK VIRLTVHTPK AQSQPQLYQT DQGEVFLRRD GSIQGPLSAS
AIQEWCRQRW LVELGKLEEK MKALMMEKEQ LQQQLQQHGP VSCTCCVL*
speed 1.22 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: 0.906011300205855 (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) chr1:41485902C>GN/A show variant in all transcripts   IGV
HGNC symbol SLFNL1
Ensembl transcript ID ENST00000302946
Genbank transcript ID NM_144990
UniProt peptide Q499Z3
alteration type single base exchange
alteration region CDS
DNA changes c.431G>C
cDNA.649G>C
g.3008G>C
AA changes R144T Score: 71 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 144
frameshift no
known variant Reference ID: rs3738368
databasehomozygous (G/G)heterozygousallele carriers
1000G113686799
ExAC46502178926439
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0990.913
1.1820.905
(flanking)0.8050.852
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 increased3001wt: 0.9336 / mu: 0.9561 (marginal change - not scored)wt: CCTTCAGCCACAGAG
mu: CCTTCAGCCACACAG		 TTCA|gcca
Donor marginally increased3011wt: 0.9967 / mu: 0.9975 (marginal change - not scored)wt: CAGAGAGGTAAGTGG
mu: CACAGAGGTAAGTGG		 GAGA|ggta
Donor increased3009wt: 0.25 / mu: 0.57wt: CACAGAGAGGTAAGT
mu: CACACAGAGGTAAGT		 CAGA|gagg
Donor increased3006wt: 0.41 / mu: 0.64wt: AGCCACAGAGAGGTA
mu: AGCCACACAGAGGTA		 CCAC|agag
distance from splice site 5
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      144LLSEAQGPFSHREEKEEEEEDSGL
mutated  not conserved    144LLSEAQGPFSHTEEKEEEEEDSG
Ptroglodytes  all identical  ENSPTRG00000000600  144LLSEAQGPFSHREEKEEEEEDSG
Mmulatta  no homologue    
Fcatus  all identical  ENSFCAG00000015323  144VLGDGRGPSRGRER----EDDSS
Mmusculus  all identical  ENSMUSG00000047518  144VLSEALESLHHREQEDSGPSPSHSPG
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 
261268NP_BINDATP (Potential).might get lost (downstream of altered splice site)
280280CONFLICTR -> S (in Ref. 3; AAH37879).might get lost (downstream of altered splice site)
366398COILEDPotential.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1224 / 1224
position (AA) of stopcodon in wt / mu AA sequence 408 / 408
position of stopcodon in wt / mu cDNA 1442 / 1442
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 219 / 219
chromosome 1
strand -1
last intron/exon boundary 1320
theoretical NMD boundary in CDS 1051
length of CDS 1224
coding sequence (CDS) position 431
cDNA position
(for ins/del: last normal base / first normal base)		 649
gDNA position
(for ins/del: last normal base / first normal base)		 3008
chromosomal position
(for ins/del: last normal base / first normal base)		 41485902
original gDNA sequence snippet CCAAGGGCCCTTCAGCCACAGAGAGGTAAGTGGGACTTTTC
altered gDNA sequence snippet CCAAGGGCCCTTCAGCCACACAGAGGTAAGTGGGACTTTTC
original cDNA sequence snippet CCAAGGGCCCTTCAGCCACAGAGAGGAGAAGGAGGAGGAGG
altered cDNA sequence snippet CCAAGGGCCCTTCAGCCACACAGAGGAGAAGGAGGAGGAGG
wildtype AA sequence MTPMKRSVQT QVSEPFMESW GEESLPELPA EQSLTEYSDL EEAPSAHTLY VGHLNPQFSV
PVLACLLRDT LERLEMPVAR EHIEVVRRPR KAYALVQVTV HRDTLASLPW RLQTALEEHL
ILKELAARGK DLLLSEAQGP FSHREEKEEE EEDSGLSPGP SPGSGVPLPT WPTHTLPDRP
QAQQLQSCQG RPSGVCSDSA IVHQQIVGKD QLFQGAFLGS ETRNMEFKRG SGEYLSLAFK
HHVRRYVCAF LNSEGGSLLV GVEDSGLVQG IRCSHRDEDR ARLLVDSILQ GFKPQIFPDA
YTLTFIPVIS TSETSVPLKV IRLTVHTPKA QSQPQLYQTD QGEVFLRRDG SIQGPLSASA
IQEWCRQRWL VELGKLEEKM KALMMEKEQL QQQLQQHGPV SCTCCVL*
mutated AA sequence MTPMKRSVQT QVSEPFMESW GEESLPELPA EQSLTEYSDL EEAPSAHTLY VGHLNPQFSV
PVLACLLRDT LERLEMPVAR EHIEVVRRPR KAYALVQVTV HRDTLASLPW RLQTALEEHL
ILKELAARGK DLLLSEAQGP FSHTEEKEEE EEDSGLSPGP SPGSGVPLPT WPTHTLPDRP
QAQQLQSCQG RPSGVCSDSA IVHQQIVGKD QLFQGAFLGS ETRNMEFKRG SGEYLSLAFK
HHVRRYVCAF LNSEGGSLLV GVEDSGLVQG IRCSHRDEDR ARLLVDSILQ GFKPQIFPDA
YTLTFIPVIS TSETSVPLKV IRLTVHTPKA QSQPQLYQTD QGEVFLRRDG SIQGPLSASA
IQEWCRQRWL VELGKLEEKM KALMMEKEQL QQQLQQHGPV SCTCCVL*
speed 1.20 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: 0.906011300205855 (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) chr1:41485902C>GN/A show variant in all transcripts   IGV
HGNC symbol SLFNL1
Ensembl transcript ID ENST00000372613
Genbank transcript ID N/A
UniProt peptide Q499Z3
alteration type single base exchange
alteration region CDS
DNA changes c.431G>C
cDNA.1496G>C
g.3008G>C
AA changes R144T Score: 71 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 144
frameshift no
known variant Reference ID: rs3738368
databasehomozygous (G/G)heterozygousallele carriers
1000G113686799
ExAC46502178926439
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0990.913
1.1820.905
(flanking)0.8050.852
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 increased3001wt: 0.9336 / mu: 0.9561 (marginal change - not scored)wt: CCTTCAGCCACAGAG
mu: CCTTCAGCCACACAG		 TTCA|gcca
Donor marginally increased3011wt: 0.9967 / mu: 0.9975 (marginal change - not scored)wt: CAGAGAGGTAAGTGG
mu: CACAGAGGTAAGTGG		 GAGA|ggta
Donor increased3009wt: 0.25 / mu: 0.57wt: CACAGAGAGGTAAGT
mu: CACACAGAGGTAAGT		 CAGA|gagg
Donor increased3006wt: 0.41 / mu: 0.64wt: AGCCACAGAGAGGTA
mu: AGCCACACAGAGGTA		 CCAC|agag
distance from splice site 5
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      144LLSEAQGPFSHREEKEEEEEDSGL
mutated  not conserved    144LLSEAQGPFSHTEEKEEEEEDSG
Ptroglodytes  all identical  ENSPTRG00000000600  144LLSEAQGPFSHREEKEEEEEDSG
Mmulatta  no homologue    
Fcatus  all identical  ENSFCAG00000015323  144VLGDGRGPSRGRER----EDDSS
Mmusculus  all identical  ENSMUSG00000047518  144VLSEALESLHHREQEDSGPSPSHSPG
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 
261268NP_BINDATP (Potential).might get lost (downstream of altered splice site)
280280CONFLICTR -> S (in Ref. 3; AAH37879).might get lost (downstream of altered splice site)
366398COILEDPotential.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1080 / 1080
position (AA) of stopcodon in wt / mu AA sequence 360 / 360
position of stopcodon in wt / mu cDNA 2145 / 2145
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 1066 / 1066
chromosome 1
strand -1
last intron/exon boundary 2023
theoretical NMD boundary in CDS 907
length of CDS 1080
coding sequence (CDS) position 431
cDNA position
(for ins/del: last normal base / first normal base)		 1496
gDNA position
(for ins/del: last normal base / first normal base)		 3008
chromosomal position
(for ins/del: last normal base / first normal base)		 41485902
original gDNA sequence snippet CCAAGGGCCCTTCAGCCACAGAGAGGTAAGTGGGACTTTTC
altered gDNA sequence snippet CCAAGGGCCCTTCAGCCACACAGAGGTAAGTGGGACTTTTC
original cDNA sequence snippet CCAAGGGCCCTTCAGCCACAGAGAGGAGAAGGAGGAGGAGG
altered cDNA sequence snippet CCAAGGGCCCTTCAGCCACACAGAGGAGAAGGAGGAGGAGG
wildtype AA sequence MTPMKRSVQT QVSEPFMESW GEESLPELPA EQSLTEYSDL EEAPSAHTLY VGHLNPQFSV
PVLACLLRDT LERLEMPVAR EHIEVVRRPR KAYALVQVTV HRDTLASLPW RLQTALEEHL
ILKELAARGK DLLLSEAQGP FSHREEKEEE EEDSGLSPGP SPGSGVPLPT WPTHTLPDRP
QAQQLQSCQG RPSGVCSDSA IVHQQIVGKD QLFQGAFLGS ETRNMEFKRG SGEYLSLAFK
HHVRRYVCAF LNSEGGSLLV GVEDSGLVQG IRCSHRDEDR ARLLVDSILQ GFKPQIFPDA
YTLTFIPVIS TSETSVPLKR WLVELGKLEE KMKALMMEKE QLQQQLQQHG PVSCTCCVL*
mutated AA sequence MTPMKRSVQT QVSEPFMESW GEESLPELPA EQSLTEYSDL EEAPSAHTLY VGHLNPQFSV
PVLACLLRDT LERLEMPVAR EHIEVVRRPR KAYALVQVTV HRDTLASLPW RLQTALEEHL
ILKELAARGK DLLLSEAQGP FSHTEEKEEE EEDSGLSPGP SPGSGVPLPT WPTHTLPDRP
QAQQLQSCQG RPSGVCSDSA IVHQQIVGKD QLFQGAFLGS ETRNMEFKRG SGEYLSLAFK
HHVRRYVCAF LNSEGGSLLV GVEDSGLVQG IRCSHRDEDR ARLLVDSILQ GFKPQIFPDA
YTLTFIPVIS TSETSVPLKR WLVELGKLEE KMKALMMEKE QLQQQLQQHG PVSCTCCVL*
speed 1.33 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: 0.906011300205855 (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) chr1:41485902C>GN/A show variant in all transcripts   IGV
HGNC symbol SLFNL1
Ensembl transcript ID ENST00000359345
Genbank transcript ID N/A
UniProt peptide Q499Z3
alteration type single base exchange
alteration region CDS
DNA changes c.431G>C
cDNA.3008G>C
g.3008G>C
AA changes R144T Score: 71 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 144
frameshift no
known variant Reference ID: rs3738368
databasehomozygous (G/G)heterozygousallele carriers
1000G113686799
ExAC46502178926439
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0990.913
1.1820.905
(flanking)0.8050.852
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 increased3001wt: 0.9336 / mu: 0.9561 (marginal change - not scored)wt: CCTTCAGCCACAGAG
mu: CCTTCAGCCACACAG		 TTCA|gcca
Donor marginally increased3011wt: 0.9967 / mu: 0.9975 (marginal change - not scored)wt: CAGAGAGGTAAGTGG
mu: CACAGAGGTAAGTGG		 GAGA|ggta
Donor increased3009wt: 0.25 / mu: 0.57wt: CACAGAGAGGTAAGT
mu: CACACAGAGGTAAGT		 CAGA|gagg
Donor increased3006wt: 0.41 / mu: 0.64wt: AGCCACAGAGAGGTA
mu: AGCCACACAGAGGTA		 CCAC|agag
distance from splice site 5
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      144LLSEAQGPFSHREEKEEEEEDSGL
mutated  not conserved    144LLSEAQGPFSHTEEKEEEEEDSG
Ptroglodytes  all identical  ENSPTRG00000000600  144LLSEAQGPFSHREEKEEEEEDSG
Mmulatta  no homologue    
Fcatus  all identical  ENSFCAG00000015323  144VLGDGRGPSRGRER----EDDSS
Mmusculus  all identical  ENSMUSG00000047518  144VLSEALESLHHREQEDSGPSPSHSPG
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 
261268NP_BINDATP (Potential).might get lost (downstream of altered splice site)
280280CONFLICTR -> S (in Ref. 3; AAH37879).might get lost (downstream of altered splice site)
366398COILEDPotential.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1224 / 1224
position (AA) of stopcodon in wt / mu AA sequence 408 / 408
position of stopcodon in wt / mu cDNA 3801 / 3801
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 2578 / 2578
chromosome 1
strand -1
last intron/exon boundary 3679
theoretical NMD boundary in CDS 1051
length of CDS 1224
coding sequence (CDS) position 431
cDNA position
(for ins/del: last normal base / first normal base)		 3008
gDNA position
(for ins/del: last normal base / first normal base)		 3008
chromosomal position
(for ins/del: last normal base / first normal base)		 41485902
original gDNA sequence snippet CCAAGGGCCCTTCAGCCACAGAGAGGTAAGTGGGACTTTTC
altered gDNA sequence snippet CCAAGGGCCCTTCAGCCACACAGAGGTAAGTGGGACTTTTC
original cDNA sequence snippet CCAAGGGCCCTTCAGCCACAGAGAGGAGAAGGAGGAGGAGG
altered cDNA sequence snippet CCAAGGGCCCTTCAGCCACACAGAGGAGAAGGAGGAGGAGG
wildtype AA sequence MTPMKRSVQT QVSEPFMESW GEESLPELPA EQSLTEYSDL EEAPSAHTLY VGHLNPQFSV
PVLACLLRDT LERLEMPVAR EHIEVVRRPR KAYALVQVTV HRDTLASLPW RLQTALEEHL
ILKELAARGK DLLLSEAQGP FSHREEKEEE EEDSGLSPGP SPGSGVPLPT WPTHTLPDRP
QAQQLQSCQG RPSGVCSDSA IVHQQIVGKD QLFQGAFLGS ETRNMEFKRG SGEYLSLAFK
HHVRRYVCAF LNSEGGSLLV GVEDSGLVQG IRCSHRDEDR ARLLVDSILQ GFKPQIFPDA
YTLTFIPVIS TSETSVPLKV IRLTVHTPKA QSQPQLYQTD QGEVFLRRDG SIQGPLSASA
IQEWCRQRWL VELGKLEEKM KALMMEKEQL QQQLQQHGPV SCTCCVL*
mutated AA sequence MTPMKRSVQT QVSEPFMESW GEESLPELPA EQSLTEYSDL EEAPSAHTLY VGHLNPQFSV
PVLACLLRDT LERLEMPVAR EHIEVVRRPR KAYALVQVTV HRDTLASLPW RLQTALEEHL
ILKELAARGK DLLLSEAQGP FSHTEEKEEE EEDSGLSPGP SPGSGVPLPT WPTHTLPDRP
QAQQLQSCQG RPSGVCSDSA IVHQQIVGKD QLFQGAFLGS ETRNMEFKRG SGEYLSLAFK
HHVRRYVCAF LNSEGGSLLV GVEDSGLVQG IRCSHRDEDR ARLLVDSILQ GFKPQIFPDA
YTLTFIPVIS TSETSVPLKV IRLTVHTPKA QSQPQLYQTD QGEVFLRRDG SIQGPLSASA
IQEWCRQRWL VELGKLEEKM KALMMEKEQL QQQLQQHGPV SCTCCVL*
speed 0.68 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: 0.906011300205855 (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) chr1:41485902C>GN/A show variant in all transcripts   IGV
HGNC symbol SLFNL1
Ensembl transcript ID ENST00000439569
Genbank transcript ID NM_001168247
UniProt peptide Q499Z3
alteration type single base exchange
alteration region CDS
DNA changes c.431G>C
cDNA.815G>C
g.3008G>C
AA changes R144T Score: 71 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 144
frameshift no
known variant Reference ID: rs3738368
databasehomozygous (G/G)heterozygousallele carriers
1000G113686799
ExAC46502178926439
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0990.913
1.1820.905
(flanking)0.8050.852
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 increased3001wt: 0.9336 / mu: 0.9561 (marginal change - not scored)wt: CCTTCAGCCACAGAG
mu: CCTTCAGCCACACAG		 TTCA|gcca
Donor marginally increased3011wt: 0.9967 / mu: 0.9975 (marginal change - not scored)wt: CAGAGAGGTAAGTGG
mu: CACAGAGGTAAGTGG		 GAGA|ggta
Donor increased3009wt: 0.25 / mu: 0.57wt: CACAGAGAGGTAAGT
mu: CACACAGAGGTAAGT		 CAGA|gagg
Donor increased3006wt: 0.41 / mu: 0.64wt: AGCCACAGAGAGGTA
mu: AGCCACACAGAGGTA		 CCAC|agag
distance from splice site 5
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      144LLSEAQGPFSHREEKEEEEEDSGL
mutated  not conserved    144LLSEAQGPFSHTEEKEEEEEDSG
Ptroglodytes  all identical  ENSPTRG00000000600  144LLSEAQGPFSHREEKEEEEEDSG
Mmulatta  no homologue    
Fcatus  all identical  ENSFCAG00000015323  144VLGDGRGPSRGRER----EDDSS
Mmusculus  all identical  ENSMUSG00000047518  144VLSEALESLHHREQEDSGPSPSHSPG
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 
261268NP_BINDATP (Potential).might get lost (downstream of altered splice site)
280280CONFLICTR -> S (in Ref. 3; AAH37879).might get lost (downstream of altered splice site)
366398COILEDPotential.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1224 / 1224
position (AA) of stopcodon in wt / mu AA sequence 408 / 408
position of stopcodon in wt / mu cDNA 1608 / 1608
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 385 / 385
chromosome 1
strand -1
last intron/exon boundary 1486
theoretical NMD boundary in CDS 1051
length of CDS 1224
coding sequence (CDS) position 431
cDNA position
(for ins/del: last normal base / first normal base)		 815
gDNA position
(for ins/del: last normal base / first normal base)		 3008
chromosomal position
(for ins/del: last normal base / first normal base)		 41485902
original gDNA sequence snippet CCAAGGGCCCTTCAGCCACAGAGAGGTAAGTGGGACTTTTC
altered gDNA sequence snippet CCAAGGGCCCTTCAGCCACACAGAGGTAAGTGGGACTTTTC
original cDNA sequence snippet CCAAGGGCCCTTCAGCCACAGAGAGGAGAAGGAGGAGGAGG
altered cDNA sequence snippet CCAAGGGCCCTTCAGCCACACAGAGGAGAAGGAGGAGGAGG
wildtype AA sequence MTPMKRSVQT QVSEPFMESW GEESLPELPA EQSLTEYSDL EEAPSAHTLY VGHLNPQFSV
PVLACLLRDT LERLEMPVAR EHIEVVRRPR KAYALVQVTV HRDTLASLPW RLQTALEEHL
ILKELAARGK DLLLSEAQGP FSHREEKEEE EEDSGLSPGP SPGSGVPLPT WPTHTLPDRP
QAQQLQSCQG RPSGVCSDSA IVHQQIVGKD QLFQGAFLGS ETRNMEFKRG SGEYLSLAFK
HHVRRYVCAF LNSEGGSLLV GVEDSGLVQG IRCSHRDEDR ARLLVDSILQ GFKPQIFPDA
YTLTFIPVIS TSETSVPLKV IRLTVHTPKA QSQPQLYQTD QGEVFLRRDG SIQGPLSASA
IQEWCRQRWL VELGKLEEKM KALMMEKEQL QQQLQQHGPV SCTCCVL*
mutated AA sequence MTPMKRSVQT QVSEPFMESW GEESLPELPA EQSLTEYSDL EEAPSAHTLY VGHLNPQFSV
PVLACLLRDT LERLEMPVAR EHIEVVRRPR KAYALVQVTV HRDTLASLPW RLQTALEEHL
ILKELAARGK DLLLSEAQGP FSHTEEKEEE EEDSGLSPGP SPGSGVPLPT WPTHTLPDRP
QAQQLQSCQG RPSGVCSDSA IVHQQIVGKD QLFQGAFLGS ETRNMEFKRG SGEYLSLAFK
HHVRRYVCAF LNSEGGSLLV GVEDSGLVQG IRCSHRDEDR ARLLVDSILQ GFKPQIFPDA
YTLTFIPVIS TSETSVPLKV IRLTVHTPKA QSQPQLYQTD QGEVFLRRDG SIQGPLSASA
IQEWCRQRWL VELGKLEEKM KALMMEKEQL QQQLQQHGPV SCTCCVL*
speed 1.24 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: 0.906011300205855 (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) chr1:41485902C>GN/A show variant in all transcripts   IGV
HGNC symbol SLFNL1
Ensembl transcript ID ENST00000397197
Genbank transcript ID N/A
UniProt peptide Q499Z3
alteration type single base exchange
alteration region CDS
DNA changes c.431G>C
cDNA.815G>C
g.3008G>C
AA changes R144T Score: 71 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 144
frameshift no
known variant Reference ID: rs3738368
databasehomozygous (G/G)heterozygousallele carriers
1000G113686799
ExAC46502178926439
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0990.913
1.1820.905
(flanking)0.8050.852
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 increased3001wt: 0.9336 / mu: 0.9561 (marginal change - not scored)wt: CCTTCAGCCACAGAG
mu: CCTTCAGCCACACAG		 TTCA|gcca
Donor marginally increased3011wt: 0.9967 / mu: 0.9975 (marginal change - not scored)wt: CAGAGAGGTAAGTGG
mu: CACAGAGGTAAGTGG		 GAGA|ggta
Donor increased3009wt: 0.25 / mu: 0.57wt: CACAGAGAGGTAAGT
mu: CACACAGAGGTAAGT		 CAGA|gagg
Donor increased3006wt: 0.41 / mu: 0.64wt: AGCCACAGAGAGGTA
mu: AGCCACACAGAGGTA		 CCAC|agag
distance from splice site 5
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      144LLSEAQGPFSHREEKEEEEEDSGL
mutated  not conserved    144LLSEAQGPFSHTEEKEEEEEDSG
Ptroglodytes  all identical  ENSPTRG00000000600  144LLSEAQGPFSHREEKEEEEEDSG
Mmulatta  no homologue    
Fcatus  all identical  ENSFCAG00000015323  144VLGDGRGPSRGRER----EDDSS
Mmusculus  all identical  ENSMUSG00000047518  144VLSEALESLHHREQEDSGPSPSHSPG
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 
261268NP_BINDATP (Potential).might get lost (downstream of altered splice site)
280280CONFLICTR -> S (in Ref. 3; AAH37879).might get lost (downstream of altered splice site)
366398COILEDPotential.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1080 / 1080
position (AA) of stopcodon in wt / mu AA sequence 360 / 360
position of stopcodon in wt / mu cDNA 1464 / 1464
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 385 / 385
chromosome 1
strand -1
last intron/exon boundary 1342
theoretical NMD boundary in CDS 907
length of CDS 1080
coding sequence (CDS) position 431
cDNA position
(for ins/del: last normal base / first normal base)		 815
gDNA position
(for ins/del: last normal base / first normal base)		 3008
chromosomal position
(for ins/del: last normal base / first normal base)		 41485902
original gDNA sequence snippet CCAAGGGCCCTTCAGCCACAGAGAGGTAAGTGGGACTTTTC
altered gDNA sequence snippet CCAAGGGCCCTTCAGCCACACAGAGGTAAGTGGGACTTTTC
original cDNA sequence snippet CCAAGGGCCCTTCAGCCACAGAGAGGAGAAGGAGGAGGAGG
altered cDNA sequence snippet CCAAGGGCCCTTCAGCCACACAGAGGAGAAGGAGGAGGAGG
wildtype AA sequence MTPMKRSVQT QVSEPFMESW GEESLPELPA EQSLTEYSDL EEAPSAHTLY VGHLNPQFSV
PVLACLLRDT LERLEMPVAR EHIEVVRRPR KAYALVQVTV HRDTLASLPW RLQTALEEHL
ILKELAARGK DLLLSEAQGP FSHREEKEEE EEDSGLSPGP SPGSGVPLPT WPTHTLPDRP
QAQQLQSCQG RPSGVCSDSA IVHQQIVGKD QLFQGAFLGS ETRNMEFKRG SGEYLSLAFK
HHVRRYVCAF LNSEGGSLLV GVEDSGLVQG IRCSHRDEDR ARLLVDSILQ GFKPQIFPDA
YTLTFIPVIS TSETSVPLKR WLVELGKLEE KMKALMMEKE QLQQQLQQHG PVSCTCCVL*
mutated AA sequence MTPMKRSVQT QVSEPFMESW GEESLPELPA EQSLTEYSDL EEAPSAHTLY VGHLNPQFSV
PVLACLLRDT LERLEMPVAR EHIEVVRRPR KAYALVQVTV HRDTLASLPW RLQTALEEHL
ILKELAARGK DLLLSEAQGP FSHTEEKEEE EEDSGLSPGP SPGSGVPLPT WPTHTLPDRP
QAQQLQSCQG RPSGVCSDSA IVHQQIVGKD QLFQGAFLGS ETRNMEFKRG SGEYLSLAFK
HHVRRYVCAF LNSEGGSLLV GVEDSGLVQG IRCSHRDEDR ARLLVDSILQ GFKPQIFPDA
YTLTFIPVIS TSETSVPLKR WLVELGKLEE KMKALMMEKE QLQQQLQQHG PVSCTCCVL*
speed 0.98 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