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 5 transcript(s)...
Querying Taster for transcript #1: ENST00000540235
Querying Taster for transcript #2: ENST00000393939
Querying Taster for transcript #3: ENST00000347901
Querying Taster for transcript #4: ENST00000341193
Querying Taster for transcript #5: ENST00000310778
MT speed 0 s - this script 4.83639 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
HAP1polymorphism_automatic0.098042258099662simple_aaeaffectedS357Lsingle base exchangers4796693show file
HAP1polymorphism_automatic0.098042258099662simple_aaeaffectedS357Lsingle base exchangers4796693show file
HAP1polymorphism_automatic0.098042258099662simple_aaeaffectedS365Lsingle base exchangers4796693show file
HAP1polymorphism_automatic0.098042258099662simple_aaeaffectedS357Lsingle base exchangers4796693show file
JUPpolymorphism_automatic0.999998525294251without_aaeaffectedsingle base exchangers4796693show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.901957741900338 (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) chr17:39884583G>AN/A show variant in all transcripts   IGV
HGNC symbol HAP1
Ensembl transcript ID ENST00000347901
Genbank transcript ID NM_177977
UniProt peptide P54257
alteration type single base exchange
alteration region CDS
DNA changes c.1070C>T
cDNA.1080C>T
g.6314C>T
AA changes S357L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 357
frameshift no
known variant Reference ID: rs4796693
databasehomozygous (A/A)heterozygousallele carriers
1000G15667402306
ExAC---
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.6360.704
0.2680.718
(flanking)3.2770.748
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost6313.5sequence motif lost- wt: ccca|GCGG
 mu: ccca.GTGG
Acc marginally increased6313wt: 0.9164 / mu: 0.9182 (marginal change - not scored)wt: CCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGATG
mu: CCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGATG		 ccag|CGGA
Acc marginally increased6312wt: 0.9947 / mu: 0.9967 (marginal change - not scored)wt: ACCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGAT
mu: ACCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGAT		 ccca|GCGG
Acc increased6304wt: 0.26 / mu: 0.37wt: CAGGGCTGACCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGC
mu: CAGGGCTGACCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGC		 ctgc|CCTC
Acc marginally increased6307wt: 0.4322 / mu: 0.4417 (marginal change - not scored)wt: GGCTGACCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAA
mu: GGCTGACCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAA		 ccct|CCCC
Acc marginally increased6316wt: 0.8703 / mu: 0.8861 (marginal change - not scored)wt: GTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGATGGCT
mu: GTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGATGGCT		 gcgg|AGGC
Donor marginally increased6312wt: 0.9986 / mu: 0.9987 (marginal change - not scored)wt: TCCCCAGCGGAGGCC
mu: TCCCCAGTGGAGGCC		 CCCA|gcgg
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      357QMLILECVEQFSEASQQMAELSEV
mutated  not conserved    357QMLILECVEQFLEAS
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  not conserved  ENSFCAG00000002132  346XXXEASQQMAELSE
Mmusculus  all identical  ENSMUSG00000006930  310FSEASQQMAELSE
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000074508  203QRLMMVCVDELTSANKQVVSLSE
Dmelanogaster  all conserved  FBgn0262872  415RQLMADISAQLNDANSQYDNLSL
Celegans  not conserved  T27A3.1  232---LADKDKKERMISMEKEEMGA
Xtropicalis  all identical  ENSXETG00000012489  322SSLMLDCVEQFSEASRHVAL
protein features
start (aa)end (aa)featuredetails 
106461DOMAINHAP1 N-terminal.lost
261601COMPBIASGlu-rich.lost
573573CONFLICTP -> L (in Ref. 3; BAB13952).might get lost (downstream of altered splice site)
579579CONFLICTM -> V (in Ref. 1; AAC39861).might get lost (downstream of altered splice site)
611611CONFLICTA -> T (in Ref. 7; AAC50297).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1860 / 1860
position (AA) of stopcodon in wt / mu AA sequence 620 / 620
position of stopcodon in wt / mu cDNA 1870 / 1870
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 11 / 11
chromosome 17
strand -1
last intron/exon boundary 1417
theoretical NMD boundary in CDS 1356
length of CDS 1860
coding sequence (CDS) position 1070
cDNA position
(for ins/del: last normal base / first normal base)		 1080
gDNA position
(for ins/del: last normal base / first normal base)		 6314
chromosomal position
(for ins/del: last normal base / first normal base)		 39884583
original gDNA sequence snippet CTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGATGG
altered gDNA sequence snippet CTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGATGG
original cDNA sequence snippet GGAGTGTGTGGAGCAGTTTTCGGAGGCCAGCCAACAGATGG
altered cDNA sequence snippet GGAGTGTGTGGAGCAGTTTTTGGAGGCCAGCCAACAGATGG
wildtype AA sequence MRPKRLGRCC AGSRLGPGDP AALTCAPSPS ASPAPEPSAQ PQARGTGQRV GSRATSGSQF
LSEARTGARP ASEAGAKAGA RRPSAFSAIQ GDVRSMPDNS DAPWTRFVFQ GPFGSRATGR
GTGKAAGIWK TPAAYVGRRP GVSGPERAAF IRELEEALCP NLPPPVKKIT QEDVKVMLYL
LEELLPPVWE SVTYGMVLQR ERDLNTAARI GQSLVKQNSV LMEENSKLEA LLGSAKEEIL
YLRHQVNLRD ELLQLYSDSD EEDEDEEEEE EEKEAEEEQE EEEAEEDLQC AHPCDAPKLI
SQEALLHQHH CPQLEALQEK LRLLEEENHQ LREEASQLDT LEDEEQMLIL ECVEQFSEAS
QQMAELSEVL VLRLENYERQ QQEVARLQAQ VLKLQQRCRM YGAETEKLQK QLASEKEIQM
QLQEEETLPG FQETLAEELR TSLRRMISDP VYFMERNYEM PRGDTSSLRY DFRYSEDREQ
VRGFEAEEGL MLAADIMRGE DFTPAEEFVP QEELGAAKKV PAEEGVMEEA ELVSEETEGW
EEVELELDEA TRMNVVTSAL EASGLGPSHL DMNYVLQQLA NWQDAHYRRQ LRWKMLQKGE
CPHGALPAAS RTSCRSSCR*
mutated AA sequence MRPKRLGRCC AGSRLGPGDP AALTCAPSPS ASPAPEPSAQ PQARGTGQRV GSRATSGSQF
LSEARTGARP ASEAGAKAGA RRPSAFSAIQ GDVRSMPDNS DAPWTRFVFQ GPFGSRATGR
GTGKAAGIWK TPAAYVGRRP GVSGPERAAF IRELEEALCP NLPPPVKKIT QEDVKVMLYL
LEELLPPVWE SVTYGMVLQR ERDLNTAARI GQSLVKQNSV LMEENSKLEA LLGSAKEEIL
YLRHQVNLRD ELLQLYSDSD EEDEDEEEEE EEKEAEEEQE EEEAEEDLQC AHPCDAPKLI
SQEALLHQHH CPQLEALQEK LRLLEEENHQ LREEASQLDT LEDEEQMLIL ECVEQFLEAS
QQMAELSEVL VLRLENYERQ QQEVARLQAQ VLKLQQRCRM YGAETEKLQK QLASEKEIQM
QLQEEETLPG FQETLAEELR TSLRRMISDP VYFMERNYEM PRGDTSSLRY DFRYSEDREQ
VRGFEAEEGL MLAADIMRGE DFTPAEEFVP QEELGAAKKV PAEEGVMEEA ELVSEETEGW
EEVELELDEA TRMNVVTSAL EASGLGPSHL DMNYVLQQLA NWQDAHYRRQ LRWKMLQKGE
CPHGALPAAS RTSCRSSCR*
speed 0.99 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: 0.901957741900338 (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) chr17:39884583G>AN/A show variant in all transcripts   IGV
HGNC symbol HAP1
Ensembl transcript ID ENST00000393939
Genbank transcript ID NM_001079871
UniProt peptide P54257
alteration type single base exchange
alteration region CDS
DNA changes c.1070C>T
cDNA.1080C>T
g.6314C>T
AA changes S357L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 357
frameshift no
known variant Reference ID: rs4796693
databasehomozygous (A/A)heterozygousallele carriers
1000G15667402306
ExAC---
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.6360.704
0.2680.718
(flanking)3.2770.748
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost6313.5sequence motif lost- wt: ccca|GCGG
 mu: ccca.GTGG
Acc marginally increased6313wt: 0.9164 / mu: 0.9182 (marginal change - not scored)wt: CCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGATG
mu: CCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGATG		 ccag|CGGA
Acc marginally increased6312wt: 0.9947 / mu: 0.9967 (marginal change - not scored)wt: ACCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGAT
mu: ACCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGAT		 ccca|GCGG
Acc increased6304wt: 0.26 / mu: 0.37wt: CAGGGCTGACCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGC
mu: CAGGGCTGACCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGC		 ctgc|CCTC
Acc marginally increased6307wt: 0.4322 / mu: 0.4417 (marginal change - not scored)wt: GGCTGACCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAA
mu: GGCTGACCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAA		 ccct|CCCC
Acc marginally increased6316wt: 0.8703 / mu: 0.8861 (marginal change - not scored)wt: GTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGATGGCT
mu: GTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGATGGCT		 gcgg|AGGC
Donor marginally increased6312wt: 0.9986 / mu: 0.9987 (marginal change - not scored)wt: TCCCCAGCGGAGGCC
mu: TCCCCAGTGGAGGCC		 CCCA|gcgg
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      357QMLILECVEQFSEASQQMAELSEV
mutated  not conserved    357QMLILECVEQFLEAS
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  not conserved  ENSFCAG00000002132  346XXXEASQQMAELSE
Mmusculus  all identical  ENSMUSG00000006930  310FSEASQQMAELSE
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000074508  203QRLMMVCVDELTSANKQVVSLSE
Dmelanogaster  all conserved  FBgn0262872  415RQLMADISAQLNDANSQYDNLSL
Celegans  not conserved  T27A3.1  232---LADKDKKERMISMEKEEMGA
Xtropicalis  all identical  ENSXETG00000012489  325SSLMLDCVEQFSEASRHVALLAE
protein features
start (aa)end (aa)featuredetails 
106461DOMAINHAP1 N-terminal.lost
261601COMPBIASGlu-rich.lost
573573CONFLICTP -> L (in Ref. 3; BAB13952).might get lost (downstream of altered splice site)
579579CONFLICTM -> V (in Ref. 1; AAC39861).might get lost (downstream of altered splice site)
611611CONFLICTA -> T (in Ref. 7; AAC50297).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1785 / 1785
position (AA) of stopcodon in wt / mu AA sequence 595 / 595
position of stopcodon in wt / mu cDNA 1795 / 1795
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 11 / 11
chromosome 17
strand -1
last intron/exon boundary 1342
theoretical NMD boundary in CDS 1281
length of CDS 1785
coding sequence (CDS) position 1070
cDNA position
(for ins/del: last normal base / first normal base)		 1080
gDNA position
(for ins/del: last normal base / first normal base)		 6314
chromosomal position
(for ins/del: last normal base / first normal base)		 39884583
original gDNA sequence snippet CTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGATGG
altered gDNA sequence snippet CTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGATGG
original cDNA sequence snippet GGAGTGTGTGGAGCAGTTTTCGGAGGCCAGCCAACAGATGG
altered cDNA sequence snippet GGAGTGTGTGGAGCAGTTTTTGGAGGCCAGCCAACAGATGG
wildtype AA sequence MRPKRLGRCC AGSRLGPGDP AALTCAPSPS ASPAPEPSAQ PQARGTGQRV GSRATSGSQF
LSEARTGARP ASEAGAKAGA RRPSAFSAIQ GDVRSMPDNS DAPWTRFVFQ GPFGSRATGR
GTGKAAGIWK TPAAYVGRRP GVSGPERAAF IRELEEALCP NLPPPVKKIT QEDVKVMLYL
LEELLPPVWE SVTYGMVLQR ERDLNTAARI GQSLVKQNSV LMEENSKLEA LLGSAKEEIL
YLRHQVNLRD ELLQLYSDSD EEDEDEEEEE EEKEAEEEQE EEEAEEDLQC AHPCDAPKLI
SQEALLHQHH CPQLEALQEK LRLLEEENHQ LREEASQLDT LEDEEQMLIL ECVEQFSEAS
QQMAELSEVL VLRLENYERQ QQEVARLQAQ VLKLQQRCRM ETLPGFQETL AEELRTSLRR
MISDPVYFME RNYEMPRGDT SSLRYDFRYS EDREQVRGFE AEEGLMLAAD IMRGEDFTPA
EEFVPQEELG AAKKVPAEEG VMEEAELVSE ETEGWEEVEL ELDEATRMNV VTSALEASGL
GPSHLDMNYV LQQLANWQDA HYRRQLRWKM LQKGECPHGA LPAASRTSCR SSCR*
mutated AA sequence MRPKRLGRCC AGSRLGPGDP AALTCAPSPS ASPAPEPSAQ PQARGTGQRV GSRATSGSQF
LSEARTGARP ASEAGAKAGA RRPSAFSAIQ GDVRSMPDNS DAPWTRFVFQ GPFGSRATGR
GTGKAAGIWK TPAAYVGRRP GVSGPERAAF IRELEEALCP NLPPPVKKIT QEDVKVMLYL
LEELLPPVWE SVTYGMVLQR ERDLNTAARI GQSLVKQNSV LMEENSKLEA LLGSAKEEIL
YLRHQVNLRD ELLQLYSDSD EEDEDEEEEE EEKEAEEEQE EEEAEEDLQC AHPCDAPKLI
SQEALLHQHH CPQLEALQEK LRLLEEENHQ LREEASQLDT LEDEEQMLIL ECVEQFLEAS
QQMAELSEVL VLRLENYERQ QQEVARLQAQ VLKLQQRCRM ETLPGFQETL AEELRTSLRR
MISDPVYFME RNYEMPRGDT SSLRYDFRYS EDREQVRGFE AEEGLMLAAD IMRGEDFTPA
EEFVPQEELG AAKKVPAEEG VMEEAELVSE ETEGWEEVEL ELDEATRMNV VTSALEASGL
GPSHLDMNYV LQQLANWQDA HYRRQLRWKM LQKGECPHGA LPAASRTSCR SSCR*
speed 1.21 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: 0.901957741900338 (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) chr17:39884583G>AN/A show variant in all transcripts   IGV
HGNC symbol HAP1
Ensembl transcript ID ENST00000341193
Genbank transcript ID NM_001079870
UniProt peptide P54257
alteration type single base exchange
alteration region CDS
DNA changes c.1094C>T
cDNA.1104C>T
g.6314C>T
AA changes S365L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 365
frameshift no
known variant Reference ID: rs4796693
databasehomozygous (A/A)heterozygousallele carriers
1000G15667402306
ExAC---
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.6360.704
0.2680.718
(flanking)3.2770.748
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost6313.5sequence motif lost- wt: ccca|GCGG
 mu: ccca.GTGG
Acc marginally increased6313wt: 0.9164 / mu: 0.9182 (marginal change - not scored)wt: CCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGATG
mu: CCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGATG		 ccag|CGGA
Acc marginally increased6312wt: 0.9947 / mu: 0.9967 (marginal change - not scored)wt: ACCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGAT
mu: ACCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGAT		 ccca|GCGG
Acc increased6304wt: 0.26 / mu: 0.37wt: CAGGGCTGACCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGC
mu: CAGGGCTGACCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGC		 ctgc|CCTC
Acc marginally increased6307wt: 0.4322 / mu: 0.4417 (marginal change - not scored)wt: GGCTGACCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAA
mu: GGCTGACCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAA		 ccct|CCCC
Acc marginally increased6316wt: 0.8703 / mu: 0.8861 (marginal change - not scored)wt: GTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGATGGCT
mu: GTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGATGGCT		 gcgg|AGGC
Donor marginally increased6312wt: 0.9986 / mu: 0.9987 (marginal change - not scored)wt: TCCCCAGCGGAGGCC
mu: TCCCCAGTGGAGGCC		 CCCA|gcgg
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      365QMLILECVEQFSEASQQMAELSEV
mutated  not conserved    365VEQFLEASQQMAELSE
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  not conserved  ENSFCAG00000002132  346XXXXXXXXXXXEASQQMAELSE
Mmusculus  all identical  ENSMUSG00000006930  310LILECVEQFSEASQQMAELSE
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000074508  203QRLMMVCVDELTSANKQVVSLSE
Dmelanogaster  all conserved  FBgn0262872  418RQLMADISAQLNDANSQYDN
Celegans  not conserved  T27A3.1  232---LADKDKKERMISMEKEEMGA
Xtropicalis  all identical  ENSXETG00000012489  321SSLMLDCVEQFSEASRHVALLAE
protein features
start (aa)end (aa)featuredetails 
106461DOMAINHAP1 N-terminal.lost
261601COMPBIASGlu-rich.lost
573573CONFLICTP -> L (in Ref. 3; BAB13952).might get lost (downstream of altered splice site)
579579CONFLICTM -> V (in Ref. 1; AAC39861).might get lost (downstream of altered splice site)
611611CONFLICTA -> T (in Ref. 7; AAC50297).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1809 / 1809
position (AA) of stopcodon in wt / mu AA sequence 603 / 603
position of stopcodon in wt / mu cDNA 1819 / 1819
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 11 / 11
chromosome 17
strand -1
last intron/exon boundary 1366
theoretical NMD boundary in CDS 1305
length of CDS 1809
coding sequence (CDS) position 1094
cDNA position
(for ins/del: last normal base / first normal base)		 1104
gDNA position
(for ins/del: last normal base / first normal base)		 6314
chromosomal position
(for ins/del: last normal base / first normal base)		 39884583
original gDNA sequence snippet CTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGATGG
altered gDNA sequence snippet CTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGATGG
original cDNA sequence snippet GGAGTGTGTGGAGCAGTTTTCGGAGGCCAGCCAACAGATGG
altered cDNA sequence snippet GGAGTGTGTGGAGCAGTTTTTGGAGGCCAGCCAACAGATGG
wildtype AA sequence MRPKRLGRCC AGSRLGPGDP AALTCAPSPS ASPAPEPSAQ PQARGTGQRV GSRATSGSQF
LSEARTGARP ASEAGAKAGA RRPSAFSAIQ GDVRSMPDNS DAPWTRFVFQ GPFGSRATGR
GTGKAAGIWK TPAAYVGRRP GVSGPERAAF IRELEEALCP NLPPPVKKIT QEDVKVMLYL
LEEVCTAFLI QLLPPVWESV TYGMVLQRER DLNTAARIGQ SLVKQNSVLM EENSKLEALL
GSAKEEILYL RHQVNLRDEL LQLYSDSDEE DEDEEEEEEE KEAEEEQEEE EAEEDLQCAH
PCDAPKLISQ EALLHQHHCP QLEALQEKLR LLEEENHQLR EEASQLDTLE DEEQMLILEC
VEQFSEASQQ MAELSEVLVL RLENYERQQQ EVARLQAQVL KLQQRCRMET LPGFQETLAE
ELRTSLRRMI SDPVYFMERN YEMPRGDTSS LRYDFRYSED REQVRGFEAE EGLMLAADIM
RGEDFTPAEE FVPQEELGAA KKVPAEEGVM EEAELVSEET EGWEEVELEL DEATRMNVVT
SALEASGLGP SHLDMNYVLQ QLANWQDAHY RRQLRWKMLQ KGECPHGALP AASRTSCRSS
CR*
mutated AA sequence MRPKRLGRCC AGSRLGPGDP AALTCAPSPS ASPAPEPSAQ PQARGTGQRV GSRATSGSQF
LSEARTGARP ASEAGAKAGA RRPSAFSAIQ GDVRSMPDNS DAPWTRFVFQ GPFGSRATGR
GTGKAAGIWK TPAAYVGRRP GVSGPERAAF IRELEEALCP NLPPPVKKIT QEDVKVMLYL
LEEVCTAFLI QLLPPVWESV TYGMVLQRER DLNTAARIGQ SLVKQNSVLM EENSKLEALL
GSAKEEILYL RHQVNLRDEL LQLYSDSDEE DEDEEEEEEE KEAEEEQEEE EAEEDLQCAH
PCDAPKLISQ EALLHQHHCP QLEALQEKLR LLEEENHQLR EEASQLDTLE DEEQMLILEC
VEQFLEASQQ MAELSEVLVL RLENYERQQQ EVARLQAQVL KLQQRCRMET LPGFQETLAE
ELRTSLRRMI SDPVYFMERN YEMPRGDTSS LRYDFRYSED REQVRGFEAE EGLMLAADIM
RGEDFTPAEE FVPQEELGAA KKVPAEEGVM EEAELVSEET EGWEEVELEL DEATRMNVVT
SALEASGLGP SHLDMNYVLQ QLANWQDAHY RRQLRWKMLQ KGECPHGALP AASRTSCRSS
CR*
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
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.901957741900338 (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) chr17:39884583G>AN/A show variant in all transcripts   IGV
HGNC symbol HAP1
Ensembl transcript ID ENST00000310778
Genbank transcript ID N/A
UniProt peptide P54257
alteration type single base exchange
alteration region CDS
DNA changes c.1070C>T
cDNA.1080C>T
g.6314C>T
AA changes S357L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 357
frameshift no
known variant Reference ID: rs4796693
databasehomozygous (A/A)heterozygousallele carriers
1000G15667402306
ExAC---
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.6360.704
0.2680.718
(flanking)3.2770.748
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost6313.5sequence motif lost- wt: ccca|GCGG
 mu: ccca.GTGG
Acc marginally increased6313wt: 0.9164 / mu: 0.9182 (marginal change - not scored)wt: CCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGATG
mu: CCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGATG		 ccag|CGGA
Acc marginally increased6312wt: 0.9947 / mu: 0.9967 (marginal change - not scored)wt: ACCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGAT
mu: ACCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGAT		 ccca|GCGG
Acc increased6304wt: 0.26 / mu: 0.37wt: CAGGGCTGACCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGC
mu: CAGGGCTGACCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGC		 ctgc|CCTC
Acc marginally increased6307wt: 0.4322 / mu: 0.4417 (marginal change - not scored)wt: GGCTGACCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAA
mu: GGCTGACCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAA		 ccct|CCCC
Acc marginally increased6316wt: 0.8703 / mu: 0.8861 (marginal change - not scored)wt: GTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGATGGCT
mu: GTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGATGGCT		 gcgg|AGGC
Donor marginally increased6312wt: 0.9986 / mu: 0.9987 (marginal change - not scored)wt: TCCCCAGCGGAGGCC
mu: TCCCCAGTGGAGGCC		 CCCA|gcgg
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      357QMLILECVEQFSEASQQMAELSEV
mutated  not conserved    357QMLILECVEQFLEAS
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  not conserved  ENSFCAG00000002132  346XXXEASQQMAELSE
Mmusculus  all identical  ENSMUSG00000006930  310FSEASQQMAELSE
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000074508  203QRLMMVCVDELTSANKQVVSLSE
Dmelanogaster  all conserved  FBgn0262872  415RQLMADISAQLNDANSQYDNLSL
Celegans  not conserved  T27A3.1  232---LADKDKKERMISMEKEEMGA
Xtropicalis  all identical  ENSXETG00000012489  322SSLMLDCVEQFSEASRHVAL
protein features
start (aa)end (aa)featuredetails 
106461DOMAINHAP1 N-terminal.lost
261601COMPBIASGlu-rich.lost
573573CONFLICTP -> L (in Ref. 3; BAB13952).might get lost (downstream of altered splice site)
579579CONFLICTM -> V (in Ref. 1; AAC39861).might get lost (downstream of altered splice site)
611611CONFLICTA -> T (in Ref. 7; AAC50297).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2016 / 2016
position (AA) of stopcodon in wt / mu AA sequence 672 / 672
position of stopcodon in wt / mu cDNA 2026 / 2026
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 11 / 11
chromosome 17
strand -1
last intron/exon boundary 1573
theoretical NMD boundary in CDS 1512
length of CDS 2016
coding sequence (CDS) position 1070
cDNA position
(for ins/del: last normal base / first normal base)		 1080
gDNA position
(for ins/del: last normal base / first normal base)		 6314
chromosomal position
(for ins/del: last normal base / first normal base)		 39884583
original gDNA sequence snippet CTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGATGG
altered gDNA sequence snippet CTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGATGG
original cDNA sequence snippet GGAGTGTGTGGAGCAGTTTTCGGAGGCCAGCCAACAGATGG
altered cDNA sequence snippet GGAGTGTGTGGAGCAGTTTTTGGAGGCCAGCCAACAGATGG
wildtype AA sequence MRPKRLGRCC AGSRLGPGDP AALTCAPSPS ASPAPEPSAQ PQARGTGQRV GSRATSGSQF
LSEARTGARP ASEAGAKAGA RRPSAFSAIQ GDVRSMPDNS DAPWTRFVFQ GPFGSRATGR
GTGKAAGIWK TPAAYVGRRP GVSGPERAAF IRELEEALCP NLPPPVKKIT QEDVKVMLYL
LEELLPPVWE SVTYGMVLQR ERDLNTAARI GQSLVKQNSV LMEENSKLEA LLGSAKEEIL
YLRHQVNLRD ELLQLYSDSD EEDEDEEEEE EEKEAEEEQE EEEAEEDLQC AHPCDAPKLI
SQEALLHQHH CPQLEALQEK LRLLEEENHQ LREEASQLDT LEDEEQMLIL ECVEQFSEAS
QQMAELSEVL VLRLENYERQ QQEVARLQAQ VLKLQQRCRM YGAETEKLQK QLASEKEIQM
QLQEESVWVG SQLQDLREKY MDCGGMLIEM QEEVKTLRQQ PPVSTGSATH YPYSVPLETL
PGFQETLAEE LRTSLRRMIS DPVYFMERNY EMPRGDTSSL RYDFRYSEDR EQVRGFEAEE
GLMLAADIMR GEDFTPAEEF VPQEELGAAK KVPAEEGVME EAELVSEETE GWEEVELELD
EATRMNVVTS ALEASGLGPS HLDMNYVLQQ LANWQDAHYR RQLRWKMLQK GECPHGALPA
ASRTSCRSSC R*
mutated AA sequence MRPKRLGRCC AGSRLGPGDP AALTCAPSPS ASPAPEPSAQ PQARGTGQRV GSRATSGSQF
LSEARTGARP ASEAGAKAGA RRPSAFSAIQ GDVRSMPDNS DAPWTRFVFQ GPFGSRATGR
GTGKAAGIWK TPAAYVGRRP GVSGPERAAF IRELEEALCP NLPPPVKKIT QEDVKVMLYL
LEELLPPVWE SVTYGMVLQR ERDLNTAARI GQSLVKQNSV LMEENSKLEA LLGSAKEEIL
YLRHQVNLRD ELLQLYSDSD EEDEDEEEEE EEKEAEEEQE EEEAEEDLQC AHPCDAPKLI
SQEALLHQHH CPQLEALQEK LRLLEEENHQ LREEASQLDT LEDEEQMLIL ECVEQFLEAS
QQMAELSEVL VLRLENYERQ QQEVARLQAQ VLKLQQRCRM YGAETEKLQK QLASEKEIQM
QLQEESVWVG SQLQDLREKY MDCGGMLIEM QEEVKTLRQQ PPVSTGSATH YPYSVPLETL
PGFQETLAEE LRTSLRRMIS DPVYFMERNY EMPRGDTSSL RYDFRYSEDR EQVRGFEAEE
GLMLAADIMR GEDFTPAEEF VPQEELGAAK KVPAEEGVME EAELVSEETE GWEEVELELD
EATRMNVVTS ALEASGLGPS HLDMNYVLQQ LANWQDAHYR RQLRWKMLQK GECPHGALPA
ASRTSCRSSC R*
speed 0.77 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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Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 1.47470574893592e-06 (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) chr17:39884583G>AN/A show variant in all transcripts   IGV
HGNC symbol JUP
Ensembl transcript ID ENST00000540235
Genbank transcript ID N/A
UniProt peptide P14923
alteration type single base exchange
alteration region intron
DNA changes g.58601C>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs4796693
databasehomozygous (A/A)heterozygousallele carriers
1000G15667402306
ExAC---
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.6360.704
0.2680.718
(flanking)3.2770.748
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased58594wt: 0.4322 / mu: 0.4417 (marginal change - not scored)wt: GGCTGACCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAA
mu: GGCTGACCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAA		 ccct|CCCC
Acc marginally increased58599wt: 0.9947 / mu: 0.9967 (marginal change - not scored)wt: ACCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGAT
mu: ACCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGAT		 ccca|GCGG
Acc marginally increased58603wt: 0.8703 / mu: 0.8861 (marginal change - not scored)wt: GTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGATGGCT
mu: GTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGATGGCT		 gcgg|AGGC
Acc marginally increased58600wt: 0.9164 / mu: 0.9182 (marginal change - not scored)wt: CCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGATG
mu: CCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGATG		 ccag|CGGA
Acc increased58591wt: 0.26 / mu: 0.37wt: CAGGGCTGACCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGC
mu: CAGGGCTGACCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGC		 ctgc|CCTC
Donor marginally increased58599wt: 0.9986 / mu: 0.9987 (marginal change - not scored)wt: TCCCCAGCGGAGGCC
mu: TCCCCAGTGGAGGCC		 CCCA|gcgg
distance from splice site 39048
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
300308HELIXmight get lost (downstream of altered splice site)
311321HELIXmight get lost (downstream of altered splice site)
325338HELIXmight get lost (downstream of altered splice site)
342381REPEATARM 4.might get lost (downstream of altered splice site)
344350HELIXmight get lost (downstream of altered splice site)
353358HELIXmight get lost (downstream of altered splice site)
359362HELIXmight get lost (downstream of altered splice site)
366380HELIXmight get lost (downstream of altered splice site)
383420REPEATARM 5.might get lost (downstream of altered splice site)
390397HELIXmight get lost (downstream of altered splice site)
398401TURNmight get lost (downstream of altered splice site)
405418HELIXmight get lost (downstream of altered splice site)
419421TURNmight get lost (downstream of altered splice site)
423429HELIXmight get lost (downstream of altered splice site)
423464REPEATARM 6.might get lost (downstream of altered splice site)
430433TURNmight get lost (downstream of altered splice site)
434445HELIXmight get lost (downstream of altered splice site)
449462HELIXmight get lost (downstream of altered splice site)
464466STRANDmight get lost (downstream of altered splice site)
469477HELIXmight get lost (downstream of altered splice site)
470510REPEATARM 7.might get lost (downstream of altered splice site)
478480TURNmight get lost (downstream of altered splice site)
481487HELIXmight get lost (downstream of altered splice site)
488490HELIXmight get lost (downstream of altered splice site)
495508HELIXmight get lost (downstream of altered splice site)
512514HELIXmight get lost (downstream of altered splice site)
512551REPEATARM 8.might get lost (downstream of altered splice site)
515520HELIXmight get lost (downstream of altered splice site)
523543HELIXmight get lost (downstream of altered splice site)
556570HELIXmight get lost (downstream of altered splice site)
574582HELIXmight get lost (downstream of altered splice site)
574613REPEATARM 9.might get lost (downstream of altered splice site)
586592HELIXmight get lost (downstream of altered splice site)
598611HELIXmight get lost (downstream of altered splice site)
615623HELIXmight get lost (downstream of altered splice site)
624626TURNmight get lost (downstream of altered splice site)
627633HELIXmight get lost (downstream of altered splice site)
639651HELIXmight get lost (downstream of altered splice site)
660660MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
662667HELIXmight get lost (downstream of altered splice site)
665665MOD_RESPhosphoserine.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 1 / 1
chromosome 17
strand -1
last intron/exon boundary 1682
theoretical NMD boundary in CDS 1631
length of CDS 1776
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)		 58601
chromosomal position
(for ins/del: last normal base / first normal base)		 39884583
original gDNA sequence snippet CTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGATGG
altered gDNA sequence snippet CTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGATGG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MEVMNLMEQP IKVTEWQQTY TYDSGIHSGA NTCVPSVSSK GIMEEDEACG RQYTLKKTTT
YTQGVPPSQG DLEYQMSTTA RAKRVREAMC PGVSGEDSSL LLATQVEGQA TNLQRLAEPS
QLLKSAIVHL INYQDDAELA TRALPELTKL LNDEDPVVVT KAAMIVNQLS KKEASRRALM
GSPQLVAAVV RTMQNTSDLD TARCTTSILH NLSHHREGLL AIFKSGGIPA LVRMLSSPVE
SVLFYAITTL HNLLLYQEGA KMAVRLADGL QKMVPLLNKN NPKFLAITTD CLQLLAYGNQ
ESKILTATVD NANILLQIDN ARLAADDFRT KFETEQALRL SVEADINGLR RVLDELTLAR
ADLEMQIENL KEELAYLKKN HEEEMNALRG QVGGEINVEM DAAPGVDLSR ILNEMRDQYE
KMAEKNRKDA EDWFFSKTEE LNREVATNSE LVQSGKSEIS ELRRTMQALE IELQSQLSMK
ASLEGNLAET ENRYCVQLSQ IQGLIGSVEE QLAQLRCEME QQNQEYKILL DVKTRLEQEI
ATYRRLLEGE DAHLTQYKKE PVTTRQVRTI VEEVQDGKVI SSREQVHQTT R*
mutated AA sequence N/A
speed 0.87 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