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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000367536
Querying Taster for transcript #2: ENST00000367535
Querying Taster for transcript #3: ENST00000413720
Querying Taster for transcript #4: ENST00000418089
MT speed 3.07 s - this script 4.757014 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
NCF2polymorphism_automatic2.29542554397444e-06simple_aaeaffectedK181Rsingle base exchangers2274064show file
NCF2polymorphism_automatic2.29542554397444e-06simple_aaeaffectedK181Rsingle base exchangers2274064show file
NCF2polymorphism_automatic3.10050886198621e-06simple_aaeaffectedK136Rsingle base exchangers2274064show file
NCF2polymorphism_automatic0.999999999854424without_aaeaffectedsingle base exchangers2274064show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999997704574456 (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) chr1:183542387T>CN/A show variant in all transcripts   IGV
HGNC symbol NCF2
Ensembl transcript ID ENST00000367536
Genbank transcript ID NM_001127651
UniProt peptide P19878
alteration type single base exchange
alteration region CDS
DNA changes c.542A>G
cDNA.609A>G
g.17625A>G
AA changes K181R Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 181
frameshift no
known variant Reference ID: rs2274064
databasehomozygous (C/C)heterozygousallele carriers
1000G62412141838
ExAC15075261717692
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.7321
0.1010.993
(flanking)0.8780.997
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased17621wt: 0.33 / mu: 0.45wt: AGCCAGTGGTGATCCCTGTGGGCAAGCTGTTTCGACCAAAT
mu: AGCCAGTGGTGATCCCTGTGGGCAGGCTGTTTCGACCAAAT		 gtgg|GCAA
distance from splice site 41
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      181KLYEPVVIPVGKLFRPNERQVAQL
mutated  all conserved    181RLFRPNERQVAQ
Ptroglodytes  all conserved  ENSPTRG00000001766  181RLFRPNERQVAQ
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000026480  181RLFRPNERQVAQ
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000004299  181VLFKPNKHYVAE
Drerio  not conserved  ENSDARG00000005821  181LLFKPNKKYVAE
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000012530  182GRIFQPNERLVEQ
protein features
start (aa)end (aa)featuredetails 
187191HELIXmight get lost (downstream of altered splice site)
240299DOMAINSH3 1.might get lost (downstream of altered splice site)
243247STRANDmight get lost (downstream of altered splice site)
255258STRANDmight get lost (downstream of altered splice site)
266269STRANDmight get lost (downstream of altered splice site)
274276STRANDmight get lost (downstream of altered splice site)
278282STRANDmight get lost (downstream of altered splice site)
285289STRANDmight get lost (downstream of altered splice site)
294296STRANDmight get lost (downstream of altered splice site)
351429DOMAINOPR.might get lost (downstream of altered splice site)
352366STRANDmight get lost (downstream of altered splice site)
372382HELIXmight get lost (downstream of altered splice site)
387389HELIXmight get lost (downstream of altered splice site)
392394STRANDmight get lost (downstream of altered splice site)
407409TURNmight get lost (downstream of altered splice site)
410414HELIXmight get lost (downstream of altered splice site)
421426STRANDmight get lost (downstream of altered splice site)
457516DOMAINSH3 2.might get lost (downstream of altered splice site)
460463STRANDmight get lost (downstream of altered splice site)
472475STRANDmight get lost (downstream of altered splice site)
483493STRANDmight get lost (downstream of altered splice site)
495498STRANDmight get lost (downstream of altered splice site)
503506STRANDmight get lost (downstream of altered splice site)
508510HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1581 / 1581
position (AA) of stopcodon in wt / mu AA sequence 527 / 527
position of stopcodon in wt / mu cDNA 1648 / 1648
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 68 / 68
chromosome 1
strand -1
last intron/exon boundary 1536
theoretical NMD boundary in CDS 1418
length of CDS 1581
coding sequence (CDS) position 542
cDNA position
(for ins/del: last normal base / first normal base)		 609
gDNA position
(for ins/del: last normal base / first normal base)		 17625
chromosomal position
(for ins/del: last normal base / first normal base)		 183542387
original gDNA sequence snippet AGTGGTGATCCCTGTGGGCAAGCTGTTTCGACCAAATGAGA
altered gDNA sequence snippet AGTGGTGATCCCTGTGGGCAGGCTGTTTCGACCAAATGAGA
original cDNA sequence snippet AGTGGTGATCCCTGTGGGCAAGCTGTTTCGACCAAATGAGA
altered cDNA sequence snippet AGTGGTGATCCCTGTGGGCAGGCTGTTTCGACCAAATGAGA
wildtype AA sequence MSLVEAISLW NEGVLAADKK DWKGALDAFS AVQDPHSRIC FNIGCMYTIL KNMTEAEKAF
TRSINRDKHL AVAYFQRGML YYQTEKYDLA IKDLKEALIQ LRGNQLIDYK ILGLQFKLFA
CEVLYNIAFM YAKKEEWKKA EEQLALATSM KSEPRHSKID KAMECVWKQK LYEPVVIPVG
KLFRPNERQV AQLAKKDYLG KATVVASVVD QDSFSGFAPL QPQAAEPPPR PKTPEIFRAL
EGEAHRVLFG FVPETKEELQ VMPGNIVFVL KKGNDNWATV MFNGQKGLVP CNYLEPVELR
IHPQQQPQEE SSPQSDIPAP PSSKAPGRPQ LSPGQKQKEE PKEVKLSVPM PYTLKVHYKY
TVVMKTQPGL PYSQVRDMVS KKLELRLEHT KLSYRPRDSN ELVPLSEDSM KDAWGQVKNY
CLTLWCENTV GDQGFPDEPK ESEKADANNQ TTEPQLKKGS QVEALFSYEA TQPEDLEFQE
GDIILVLSKV NEEWLEGECK GKVGIFPKVF VEDCATTDLE STRREV*
mutated AA sequence MSLVEAISLW NEGVLAADKK DWKGALDAFS AVQDPHSRIC FNIGCMYTIL KNMTEAEKAF
TRSINRDKHL AVAYFQRGML YYQTEKYDLA IKDLKEALIQ LRGNQLIDYK ILGLQFKLFA
CEVLYNIAFM YAKKEEWKKA EEQLALATSM KSEPRHSKID KAMECVWKQK LYEPVVIPVG
RLFRPNERQV AQLAKKDYLG KATVVASVVD QDSFSGFAPL QPQAAEPPPR PKTPEIFRAL
EGEAHRVLFG FVPETKEELQ VMPGNIVFVL KKGNDNWATV MFNGQKGLVP CNYLEPVELR
IHPQQQPQEE SSPQSDIPAP PSSKAPGRPQ LSPGQKQKEE PKEVKLSVPM PYTLKVHYKY
TVVMKTQPGL PYSQVRDMVS KKLELRLEHT KLSYRPRDSN ELVPLSEDSM KDAWGQVKNY
CLTLWCENTV GDQGFPDEPK ESEKADANNQ TTEPQLKKGS QVEALFSYEA TQPEDLEFQE
GDIILVLSKV NEEWLEGECK GKVGIFPKVF VEDCATTDLE STRREV*
speed 1.12 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: 0.999997704574456 (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) chr1:183542387T>CN/A show variant in all transcripts   IGV
HGNC symbol NCF2
Ensembl transcript ID ENST00000367535
Genbank transcript ID NM_000433
UniProt peptide P19878
alteration type single base exchange
alteration region CDS
DNA changes c.542A>G
cDNA.794A>G
g.17625A>G
AA changes K181R Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 181
frameshift no
known variant Reference ID: rs2274064
databasehomozygous (C/C)heterozygousallele carriers
1000G62412141838
ExAC15075261717692
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.7321
0.1010.993
(flanking)0.8780.997
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased17621wt: 0.33 / mu: 0.45wt: AGCCAGTGGTGATCCCTGTGGGCAAGCTGTTTCGACCAAAT
mu: AGCCAGTGGTGATCCCTGTGGGCAGGCTGTTTCGACCAAAT		 gtgg|GCAA
distance from splice site 41
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      181KLYEPVVIPVGKLFRPNERQVAQL
mutated  all conserved    181RLFRPNERQVAQ
Ptroglodytes  all conserved  ENSPTRG00000001766  181RLFRPNERQVAQ
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000026480  181RLFRPNERQVAQ
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000004299  181VLFKPNKHYVAE
Drerio  not conserved  ENSDARG00000005821  181LLFKPNKKYVAE
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000012530  182GRIFQPNERLVEQ
protein features
start (aa)end (aa)featuredetails 
187191HELIXmight get lost (downstream of altered splice site)
240299DOMAINSH3 1.might get lost (downstream of altered splice site)
243247STRANDmight get lost (downstream of altered splice site)
255258STRANDmight get lost (downstream of altered splice site)
266269STRANDmight get lost (downstream of altered splice site)
274276STRANDmight get lost (downstream of altered splice site)
278282STRANDmight get lost (downstream of altered splice site)
285289STRANDmight get lost (downstream of altered splice site)
294296STRANDmight get lost (downstream of altered splice site)
351429DOMAINOPR.might get lost (downstream of altered splice site)
352366STRANDmight get lost (downstream of altered splice site)
372382HELIXmight get lost (downstream of altered splice site)
387389HELIXmight get lost (downstream of altered splice site)
392394STRANDmight get lost (downstream of altered splice site)
407409TURNmight get lost (downstream of altered splice site)
410414HELIXmight get lost (downstream of altered splice site)
421426STRANDmight get lost (downstream of altered splice site)
457516DOMAINSH3 2.might get lost (downstream of altered splice site)
460463STRANDmight get lost (downstream of altered splice site)
472475STRANDmight get lost (downstream of altered splice site)
483493STRANDmight get lost (downstream of altered splice site)
495498STRANDmight get lost (downstream of altered splice site)
503506STRANDmight get lost (downstream of altered splice site)
508510HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1581 / 1581
position (AA) of stopcodon in wt / mu AA sequence 527 / 527
position of stopcodon in wt / mu cDNA 1833 / 1833
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 253 / 253
chromosome 1
strand -1
last intron/exon boundary 1721
theoretical NMD boundary in CDS 1418
length of CDS 1581
coding sequence (CDS) position 542
cDNA position
(for ins/del: last normal base / first normal base)		 794
gDNA position
(for ins/del: last normal base / first normal base)		 17625
chromosomal position
(for ins/del: last normal base / first normal base)		 183542387
original gDNA sequence snippet AGTGGTGATCCCTGTGGGCAAGCTGTTTCGACCAAATGAGA
altered gDNA sequence snippet AGTGGTGATCCCTGTGGGCAGGCTGTTTCGACCAAATGAGA
original cDNA sequence snippet AGTGGTGATCCCTGTGGGCAAGCTGTTTCGACCAAATGAGA
altered cDNA sequence snippet AGTGGTGATCCCTGTGGGCAGGCTGTTTCGACCAAATGAGA
wildtype AA sequence MSLVEAISLW NEGVLAADKK DWKGALDAFS AVQDPHSRIC FNIGCMYTIL KNMTEAEKAF
TRSINRDKHL AVAYFQRGML YYQTEKYDLA IKDLKEALIQ LRGNQLIDYK ILGLQFKLFA
CEVLYNIAFM YAKKEEWKKA EEQLALATSM KSEPRHSKID KAMECVWKQK LYEPVVIPVG
KLFRPNERQV AQLAKKDYLG KATVVASVVD QDSFSGFAPL QPQAAEPPPR PKTPEIFRAL
EGEAHRVLFG FVPETKEELQ VMPGNIVFVL KKGNDNWATV MFNGQKGLVP CNYLEPVELR
IHPQQQPQEE SSPQSDIPAP PSSKAPGRPQ LSPGQKQKEE PKEVKLSVPM PYTLKVHYKY
TVVMKTQPGL PYSQVRDMVS KKLELRLEHT KLSYRPRDSN ELVPLSEDSM KDAWGQVKNY
CLTLWCENTV GDQGFPDEPK ESEKADANNQ TTEPQLKKGS QVEALFSYEA TQPEDLEFQE
GDIILVLSKV NEEWLEGECK GKVGIFPKVF VEDCATTDLE STRREV*
mutated AA sequence MSLVEAISLW NEGVLAADKK DWKGALDAFS AVQDPHSRIC FNIGCMYTIL KNMTEAEKAF
TRSINRDKHL AVAYFQRGML YYQTEKYDLA IKDLKEALIQ LRGNQLIDYK ILGLQFKLFA
CEVLYNIAFM YAKKEEWKKA EEQLALATSM KSEPRHSKID KAMECVWKQK LYEPVVIPVG
RLFRPNERQV AQLAKKDYLG KATVVASVVD QDSFSGFAPL QPQAAEPPPR PKTPEIFRAL
EGEAHRVLFG FVPETKEELQ VMPGNIVFVL KKGNDNWATV MFNGQKGLVP CNYLEPVELR
IHPQQQPQEE SSPQSDIPAP PSSKAPGRPQ LSPGQKQKEE PKEVKLSVPM PYTLKVHYKY
TVVMKTQPGL PYSQVRDMVS KKLELRLEHT KLSYRPRDSN ELVPLSEDSM KDAWGQVKNY
CLTLWCENTV GDQGFPDEPK ESEKADANNQ TTEPQLKKGS QVEALFSYEA TQPEDLEFQE
GDIILVLSKV NEEWLEGECK GKVGIFPKVF VEDCATTDLE STRREV*
speed 0.42 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: 0.999996899491138 (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) chr1:183542387T>CN/A show variant in all transcripts   IGV
HGNC symbol NCF2
Ensembl transcript ID ENST00000413720
Genbank transcript ID NM_001190794
UniProt peptide P19878
alteration type single base exchange
alteration region CDS
DNA changes c.407A>G
cDNA.682A>G
g.17625A>G
AA changes K136R Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 136
frameshift no
known variant Reference ID: rs2274064
databasehomozygous (C/C)heterozygousallele carriers
1000G62412141838
ExAC15075261717692
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.7321
0.1010.993
(flanking)0.8780.997
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased17621wt: 0.33 / mu: 0.45wt: AGCCAGTGGTGATCCCTGTGGGCAAGCTGTTTCGACCAAAT
mu: AGCCAGTGGTGATCCCTGTGGGCAGGCTGTTTCGACCAAAT		 gtgg|GCAA
distance from splice site 41
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      136KLYEPVVIPVGKLFRPNERQVAQL
mutated  all conserved    136KLYEPVVIPVGRLFRPNERQVAQ
Ptroglodytes  all conserved  ENSPTRG00000001766  181RLFRPNERQVAQ
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000026480  181RLFRPNERQVAQ
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000004299  181VLFKPNKHYVAE
Drerio  not conserved  ENSDARG00000005821  181LLFKPNKKYVAE
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000012530  182GRIFQPNERLVEQ
protein features
start (aa)end (aa)featuredetails 
121154REPEATTPR 3.lost
137148HELIXmight get lost (downstream of altered splice site)
154157HELIXmight get lost (downstream of altered splice site)
158167HELIXmight get lost (downstream of altered splice site)
187191HELIXmight get lost (downstream of altered splice site)
240299DOMAINSH3 1.might get lost (downstream of altered splice site)
243247STRANDmight get lost (downstream of altered splice site)
255258STRANDmight get lost (downstream of altered splice site)
266269STRANDmight get lost (downstream of altered splice site)
274276STRANDmight get lost (downstream of altered splice site)
278282STRANDmight get lost (downstream of altered splice site)
285289STRANDmight get lost (downstream of altered splice site)
294296STRANDmight get lost (downstream of altered splice site)
351429DOMAINOPR.might get lost (downstream of altered splice site)
352366STRANDmight get lost (downstream of altered splice site)
372382HELIXmight get lost (downstream of altered splice site)
387389HELIXmight get lost (downstream of altered splice site)
392394STRANDmight get lost (downstream of altered splice site)
407409TURNmight get lost (downstream of altered splice site)
410414HELIXmight get lost (downstream of altered splice site)
421426STRANDmight get lost (downstream of altered splice site)
457516DOMAINSH3 2.might get lost (downstream of altered splice site)
460463STRANDmight get lost (downstream of altered splice site)
472475STRANDmight get lost (downstream of altered splice site)
483493STRANDmight get lost (downstream of altered splice site)
495498STRANDmight get lost (downstream of altered splice site)
503506STRANDmight get lost (downstream of altered splice site)
508510HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1446 / 1446
position (AA) of stopcodon in wt / mu AA sequence 482 / 482
position of stopcodon in wt / mu cDNA 1721 / 1721
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 276 / 276
chromosome 1
strand -1
last intron/exon boundary 1609
theoretical NMD boundary in CDS 1283
length of CDS 1446
coding sequence (CDS) position 407
cDNA position
(for ins/del: last normal base / first normal base)		 682
gDNA position
(for ins/del: last normal base / first normal base)		 17625
chromosomal position
(for ins/del: last normal base / first normal base)		 183542387
original gDNA sequence snippet AGTGGTGATCCCTGTGGGCAAGCTGTTTCGACCAAATGAGA
altered gDNA sequence snippet AGTGGTGATCCCTGTGGGCAGGCTGTTTCGACCAAATGAGA
original cDNA sequence snippet AGTGGTGATCCCTGTGGGCAAGCTGTTTCGACCAAATGAGA
altered cDNA sequence snippet AGTGGTGATCCCTGTGGGCAGGCTGTTTCGACCAAATGAGA
wildtype AA sequence MSLVEAISLW NEGVLAADKK DWKGALDAFS AVQDPHSRIC FNIGCMYTIL KNMTEAEKAF
TRSINRDKHL AVAYFQRGML YYQTEKYDLA IKDLKEALIQ LRGNQLIDYK ILGLQFKLFA
CEKQKLYEPV VIPVGKLFRP NERQVAQLAK KDYLGKATVV ASVVDQDSFS GFAPLQPQAA
EPPPRPKTPE IFRALEGEAH RVLFGFVPET KEELQVMPGN IVFVLKKGND NWATVMFNGQ
KGLVPCNYLE PVELRIHPQQ QPQEESSPQS DIPAPPSSKA PGRPQLSPGQ KQKEEPKEVK
LSVPMPYTLK VHYKYTVVMK TQPGLPYSQV RDMVSKKLEL RLEHTKLSYR PRDSNELVPL
SEDSMKDAWG QVKNYCLTLW CENTVGDQGF PDEPKESEKA DANNQTTEPQ LKKGSQVEAL
FSYEATQPED LEFQEGDIIL VLSKVNEEWL EGECKGKVGI FPKVFVEDCA TTDLESTRRE
V*
mutated AA sequence MSLVEAISLW NEGVLAADKK DWKGALDAFS AVQDPHSRIC FNIGCMYTIL KNMTEAEKAF
TRSINRDKHL AVAYFQRGML YYQTEKYDLA IKDLKEALIQ LRGNQLIDYK ILGLQFKLFA
CEKQKLYEPV VIPVGRLFRP NERQVAQLAK KDYLGKATVV ASVVDQDSFS GFAPLQPQAA
EPPPRPKTPE IFRALEGEAH RVLFGFVPET KEELQVMPGN IVFVLKKGND NWATVMFNGQ
KGLVPCNYLE PVELRIHPQQ QPQEESSPQS DIPAPPSSKA PGRPQLSPGQ KQKEEPKEVK
LSVPMPYTLK VHYKYTVVMK TQPGLPYSQV RDMVSKKLEL RLEHTKLSYR PRDSNELVPL
SEDSMKDAWG QVKNYCLTLW CENTVGDQGF PDEPKESEKA DANNQTTEPQ LKKGSQVEAL
FSYEATQPED LEFQEGDIIL VLSKVNEEWL EGECKGKVGI FPKVFVEDCA TTDLESTRRE
V*
speed 1.26 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: 1.45576414213291e-10 (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) chr1:183542387T>CN/A show variant in all transcripts   IGV
HGNC symbol NCF2
Ensembl transcript ID ENST00000418089
Genbank transcript ID NM_001190789
UniProt peptide P19878
alteration type single base exchange
alteration region intron
DNA changes g.17625A>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs2274064
databasehomozygous (C/C)heterozygousallele carriers
1000G62412141838
ExAC15075261717692
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.7321
0.1010.993
(flanking)0.8780.997
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased17621wt: 0.33 / mu: 0.45wt: AGCCAGTGGTGATCCCTGTGGGCAAGCTGTTTCGACCAAAT
mu: AGCCAGTGGTGATCCCTGTGGGCAGGCTGTTTCGACCAAAT		 gtgg|GCAA
distance from splice site 2413
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
120133HELIXmight get lost (downstream of altered splice site)
121154REPEATTPR 3.might get lost (downstream of altered splice site)
137148HELIXmight get lost (downstream of altered splice site)
154157HELIXmight get lost (downstream of altered splice site)
158167HELIXmight get lost (downstream of altered splice site)
187191HELIXmight get lost (downstream of altered splice site)
240299DOMAINSH3 1.might get lost (downstream of altered splice site)
243247STRANDmight get lost (downstream of altered splice site)
255258STRANDmight get lost (downstream of altered splice site)
266269STRANDmight get lost (downstream of altered splice site)
274276STRANDmight get lost (downstream of altered splice site)
278282STRANDmight get lost (downstream of altered splice site)
285289STRANDmight get lost (downstream of altered splice site)
294296STRANDmight get lost (downstream of altered splice site)
351429DOMAINOPR.might get lost (downstream of altered splice site)
352366STRANDmight get lost (downstream of altered splice site)
372382HELIXmight get lost (downstream of altered splice site)
387389HELIXmight get lost (downstream of altered splice site)
392394STRANDmight get lost (downstream of altered splice site)
407409TURNmight get lost (downstream of altered splice site)
410414HELIXmight get lost (downstream of altered splice site)
421426STRANDmight get lost (downstream of altered splice site)
457516DOMAINSH3 2.might get lost (downstream of altered splice site)
460463STRANDmight get lost (downstream of altered splice site)
472475STRANDmight get lost (downstream of altered splice site)
483493STRANDmight get lost (downstream of altered splice site)
495498STRANDmight get lost (downstream of altered splice site)
503506STRANDmight get lost (downstream of altered splice site)
508510HELIXmight 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 276 / 276
chromosome 1
strand -1
last intron/exon boundary 1501
theoretical NMD boundary in CDS 1175
length of CDS 1338
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)		 17625
chromosomal position
(for ins/del: last normal base / first normal base)		 183542387
original gDNA sequence snippet AGTGGTGATCCCTGTGGGCAAGCTGTTTCGACCAAATGAGA
altered gDNA sequence snippet AGTGGTGATCCCTGTGGGCAGGCTGTTTCGACCAAATGAGA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MSLVEAISLW NEGVLAADKK DWKGALDAFS AVQDPHSRIC FNIGCMYTIL KNMTEAEKAF
TRSINRDKHL AVAYFQRGML YYQTEKYDLA IKDLKEALIQ LRGNQLIDYK ILGLQFKLFA
CEVVASVVDQ DSFSGFAPLQ PQAAEPPPRP KTPEIFRALE GEAHRVLFGF VPETKEELQV
MPGNIVFVLK KGNDNWATVM FNGQKGLVPC NYLEPVELRI HPQQQPQEES SPQSDIPAPP
SSKAPGRPQL SPGQKQKEEP KEVKLSVPMP YTLKVHYKYT VVMKTQPGLP YSQVRDMVSK
KLELRLEHTK LSYRPRDSNE LVPLSEDSMK DAWGQVKNYC LTLWCENTVG DQGFPDEPKE
SEKADANNQT TEPQLKKGSQ VEALFSYEAT QPEDLEFQEG DIILVLSKVN EEWLEGECKG
KVGIFPKVFV EDCATTDLES TRREV*
mutated AA sequence N/A
speed 0.27 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
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Problems