MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000283684
Querying Taster for transcript #2: ENST00000536015
MT speed 0 s - this script 3.526062 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ATP8B1	disease_causing_automatic	0.999999999842674	simple_aae		affected	0	R867C	single base exchange	rs121909103		show file
ATP8B1	disease_causing_automatic	0.999999999842674	simple_aae		affected	0	R867C	single base exchange	rs121909103		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999842674 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM051851)
known disease mutation: rs7272 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr18:55328514G>AN/A show variant in all transcripts IGV

HGNC symbol

ATP8B1

Ensembl transcript ID

ENST00000283684

Genbank transcript ID

N/A

UniProt peptide

O43520

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2599C>T
cDNA.2599C>T
g.141820C>T

AA changes

R867C Score: 180 explain score(s)

position(s) of altered AA
if AA alteration in CDS

867

frameshift

known variant

Reference ID: rs121909103

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation: rs7272 (pathogenic for Cholestasis of pregnancy) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM051851)

known disease mutation at this position, please check HGMD for details (HGMD ID CM051851)
known disease mutation at this position, please check HGMD for details (HGMD ID CM051851)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	6.097	1
	2.593	1
(flanking)	3.356	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Acc increased	141824	wt: 0.36 / mu: 0.47	wt: CGCAGTCATCTGCTGCCGCGTCACCCCCAAGCAGAAGGCCA mu: CGCAGTCATCTGCTGCTGCGTCACCCCCAAGCAGAAGGCCA	gcgt\|CACC
Acc marginally increased	141822	wt: 0.8813 / mu: 0.9247 (marginal change - not scored)	wt: AGCGCAGTCATCTGCTGCCGCGTCACCCCCAAGCAGAAGGC mu: AGCGCAGTCATCTGCTGCTGCGTCACCCCCAAGCAGAAGGC	ccgc\|GTCA

distance from splice site

109

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

867

mutated

not conserved

867

Ptroglodytes

all identical

ENSPTRG00000010048

834

Mmulatta

all identical

ENSMMUG00000019976

866

Fcatus

all identical

ENSFCAG00000014301

804

Mmusculus

all identical

ENSMUSG00000039529

867

Ggallus

all identical

ENSGALG00000003253

871

Trubripes

no homologue

Drerio

all identical

ENSDARG00000060980

858

Dmelanogaster

not conserved

FBgn0037989

1247

Celegans

all identical

H06H21.10

825

Xtropicalis

all identical

ENSXETG00000020878

686

protein features

start (aa)	end (aa)	feature	details
412	949	TOPO_DOM	Cytoplasmic (Potential).	lost
893	893	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
897	897	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
950	970	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
971	982	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
983	1002	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1003	1032	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1016	1016	CONFLICT	P -> L (in Ref. 4; AAH03534).	might get lost (downstream of altered splice site)
1033	1054	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1055	1068	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
1069	1091	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1092	1097	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1098	1118	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1119	1138	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
1139	1163	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1164	1251	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1217	1217	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3756 / 3756

position (AA) of stopcodon in wt / mu AA sequence

1252 / 1252

position of stopcodon in wt / mu cDNA

3756 / 3756

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

strand

-1

last intron/exon boundary

3532

theoretical NMD boundary in CDS

3481

length of CDS

3756

coding sequence (CDS) position

2599

cDNA position
(for ins/del: last normal base / first normal base)

2599

gDNA position
(for ins/del: last normal base / first normal base)

141820

chromosomal position
(for ins/del: last normal base / first normal base)

55328514

original gDNA sequence snippet

GCAGCGCAGTCATCTGCTGCCGCGTCACCCCCAAGCAGAAG

altered gDNA sequence snippet

GCAGCGCAGTCATCTGCTGCTGCGTCACCCCCAAGCAGAAG

original cDNA sequence snippet

GCAGCGCAGTCATCTGCTGCCGCGTCACCCCCAAGCAGAAG

altered cDNA sequence snippet

GCAGCGCAGTCATCTGCTGCTGCGTCACCCCCAAGCAGAAG

wildtype AA sequence

MSTERDSETT FDEDSQPNDE VVPYSDDETE DELDDQGSAV EPEQNRVNRE AEENREPFRK
ECTWQVKAND RKYHEQPHFM NTKFLCIKES KYANNAIKTY KYNAFTFIPM NLFEQFKRAA
NLYFLALLIL QAVPQISTLA WYTTLVPLLV VLGVTAIKDL VDDVARHKMD KEINNRTCEV
IKDGRFKVAK WKEIQVGDVI RLKKNDFVPA DILLLSSSEP NSLCYVETAE LDGETNLKFK
MSLEITDQYL QREDTLATFD GFIECEEPNN RLDKFTGTLF WRNTSFPLDA DKILLRGCVI
RNTDFCHGLV IFAGADTKIM KNSGKTRFKR TKIDYLMNYM VYTIFVVLIL LSAGLAIGHA
YWEAQVGNSS WYLYDGEDDT PSYRGFLIFW GYIIVLNTMV PISLYVSVEV IRLGQSHFIN
WDLQMYYAEK DTPAKARTTT LNEQLGQIHY IFSDKTGTLT QNIMTFKKCC INGQIYGDHR
DASQHNHNKI EQVDFSWNTY ADGKLAFYDH YLIEQIQSGK EPEVRQFFFL LAVCHTVMVD
RTDGQLNYQA ASPDEGALVN AARNFGFAFL ARTQNTITIS ELGTERTYNV LAILDFNSDR
KRMSIIVRTP EGNIKLYCKG ADTVIYERLH RMNPTKQETQ DALDIFANET LRTLCLCYKE
IEEKEFTEWN KKFMAASVAS TNRDEALDKV YEEIEKDLIL LGATAIEDKL QDGVPETISK
LAKADIKIWV LTGDKKETAE NIGFACELLT EDTTICYGED INSLLHARME NQRNRGGVYA
KFAPPVQESF FPPGGNRALI ITGSWLNEIL LEKKTKRNKI LKLKFPRTEE ERRMRTQSKR
RLEAKKEQRQ KNFVDLACEC SAVICCRVTP KQKAMVVDLV KRYKKAITLA IGDGANDVNM
IKTAHIGVGI SGQEGMQAVM SSDYSFAQFR YLQRLLLVHG RWSYIRMCKF LRYFFYKNFA
FTLVHFWYSF FNGYSAQTAY EDWFITLYNV LYTSLPVLLM GLLDQDVSDK LSLRFPGLYI
VGQRDLLFNY KRFFVSLLHG VLTSMILFFI PLGAYLQTVG QDGEAPSDYQ SFAVTIASAL
VITVNFQIGL DTSYWTFVNA FSIFGSIALY FGIMFDFHSA GIHVLFPSAF QFTGTASNAL
RQPYIWLTII LAVAVCLLPV VAIRFLSMTI WPSESDKIQK HRKRLKAEEQ WQRRQQVFRR
GVSTRRSAYA FSHQRGYADL ISSGRSIRKK RSPLDAIVAD GTAEYRRTGD S*

mutated AA sequence

MSTERDSETT FDEDSQPNDE VVPYSDDETE DELDDQGSAV EPEQNRVNRE AEENREPFRK
ECTWQVKAND RKYHEQPHFM NTKFLCIKES KYANNAIKTY KYNAFTFIPM NLFEQFKRAA
NLYFLALLIL QAVPQISTLA WYTTLVPLLV VLGVTAIKDL VDDVARHKMD KEINNRTCEV
IKDGRFKVAK WKEIQVGDVI RLKKNDFVPA DILLLSSSEP NSLCYVETAE LDGETNLKFK
MSLEITDQYL QREDTLATFD GFIECEEPNN RLDKFTGTLF WRNTSFPLDA DKILLRGCVI
RNTDFCHGLV IFAGADTKIM KNSGKTRFKR TKIDYLMNYM VYTIFVVLIL LSAGLAIGHA
YWEAQVGNSS WYLYDGEDDT PSYRGFLIFW GYIIVLNTMV PISLYVSVEV IRLGQSHFIN
WDLQMYYAEK DTPAKARTTT LNEQLGQIHY IFSDKTGTLT QNIMTFKKCC INGQIYGDHR
DASQHNHNKI EQVDFSWNTY ADGKLAFYDH YLIEQIQSGK EPEVRQFFFL LAVCHTVMVD
RTDGQLNYQA ASPDEGALVN AARNFGFAFL ARTQNTITIS ELGTERTYNV LAILDFNSDR
KRMSIIVRTP EGNIKLYCKG ADTVIYERLH RMNPTKQETQ DALDIFANET LRTLCLCYKE
IEEKEFTEWN KKFMAASVAS TNRDEALDKV YEEIEKDLIL LGATAIEDKL QDGVPETISK
LAKADIKIWV LTGDKKETAE NIGFACELLT EDTTICYGED INSLLHARME NQRNRGGVYA
KFAPPVQESF FPPGGNRALI ITGSWLNEIL LEKKTKRNKI LKLKFPRTEE ERRMRTQSKR
RLEAKKEQRQ KNFVDLACEC SAVICCCVTP KQKAMVVDLV KRYKKAITLA IGDGANDVNM
IKTAHIGVGI SGQEGMQAVM SSDYSFAQFR YLQRLLLVHG RWSYIRMCKF LRYFFYKNFA
FTLVHFWYSF FNGYSAQTAY EDWFITLYNV LYTSLPVLLM GLLDQDVSDK LSLRFPGLYI
VGQRDLLFNY KRFFVSLLHG VLTSMILFFI PLGAYLQTVG QDGEAPSDYQ SFAVTIASAL
VITVNFQIGL DTSYWTFVNA FSIFGSIALY FGIMFDFHSA GIHVLFPSAF QFTGTASNAL
RQPYIWLTII LAVAVCLLPV VAIRFLSMTI WPSESDKIQK HRKRLKAEEQ WQRRQQVFRR
GVSTRRSAYA FSHQRGYADL ISSGRSIRKK RSPLDAIVAD GTAEYRRTGD S*

speed

0.83 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

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999842674 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM051851)
known disease mutation: rs7272 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr18:55328514G>AN/A show variant in all transcripts IGV

HGNC symbol

ATP8B1

Ensembl transcript ID

ENST00000536015

Genbank transcript ID

NM_005603

UniProt peptide

O43520

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2599C>T
cDNA.2719C>T
g.141820C>T

AA changes

R867C Score: 180 explain score(s)

position(s) of altered AA
if AA alteration in CDS

867

frameshift

known variant

Reference ID: rs121909103

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	6.097	1
	2.593	1
(flanking)	3.356	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Acc increased	141824	wt: 0.36 / mu: 0.47	wt: CGCAGTCATCTGCTGCCGCGTCACCCCCAAGCAGAAGGCCA mu: CGCAGTCATCTGCTGCTGCGTCACCCCCAAGCAGAAGGCCA	gcgt\|CACC
Acc marginally increased	141822	wt: 0.8813 / mu: 0.9247 (marginal change - not scored)	wt: AGCGCAGTCATCTGCTGCCGCGTCACCCCCAAGCAGAAGGC mu: AGCGCAGTCATCTGCTGCTGCGTCACCCCCAAGCAGAAGGC	ccgc\|GTCA

distance from splice site

109

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

867

mutated

not conserved

867

Ptroglodytes

all identical

ENSPTRG00000010048

834

Mmulatta

all identical

ENSMMUG00000019976

866

Fcatus

all identical

ENSFCAG00000014301

804

Mmusculus

all identical

ENSMUSG00000039529

867

Ggallus

all identical

ENSGALG00000003253

871

Trubripes

no homologue

Drerio

all identical

ENSDARG00000060980

858

Dmelanogaster

not conserved

FBgn0037989

1247

Celegans

all identical

H06H21.10

825

Xtropicalis

all identical

ENSXETG00000020878

686

protein features

start (aa)	end (aa)	feature	details
412	949	TOPO_DOM	Cytoplasmic (Potential).	lost
893	893	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
897	897	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
950	970	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
971	982	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
983	1002	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1003	1032	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1016	1016	CONFLICT	P -> L (in Ref. 4; AAH03534).	might get lost (downstream of altered splice site)
1033	1054	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1055	1068	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
1069	1091	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1092	1097	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1098	1118	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1119	1138	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
1139	1163	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1164	1251	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1217	1217	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3756 / 3756

position (AA) of stopcodon in wt / mu AA sequence

1252 / 1252

position of stopcodon in wt / mu cDNA

3876 / 3876

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

121 / 121

chromosome

strand

-1

last intron/exon boundary

3652

theoretical NMD boundary in CDS

3481

length of CDS

3756

coding sequence (CDS) position

2599

cDNA position
(for ins/del: last normal base / first normal base)

2719

gDNA position
(for ins/del: last normal base / first normal base)

141820

chromosomal position
(for ins/del: last normal base / first normal base)

55328514

original gDNA sequence snippet

GCAGCGCAGTCATCTGCTGCCGCGTCACCCCCAAGCAGAAG

altered gDNA sequence snippet

GCAGCGCAGTCATCTGCTGCTGCGTCACCCCCAAGCAGAAG

original cDNA sequence snippet

GCAGCGCAGTCATCTGCTGCCGCGTCACCCCCAAGCAGAAG

altered cDNA sequence snippet

GCAGCGCAGTCATCTGCTGCTGCGTCACCCCCAAGCAGAAG

wildtype AA sequence

mutated AA sequence

MSTERDSETT FDEDSQPNDE VVPYSDDETE DELDDQGSAV EPEQNRVNRE AEENREPFRK
ECTWQVKAND RKYHEQPHFM NTKFLCIKES KYANNAIKTY KYNAFTFIPM NLFEQFKRAA
NLYFLALLIL QAVPQISTLA WYTTLVPLLV VLGVTAIKDL VDDVARHKMD KEINNRTCEV
IKDGRFKVAK WKEIQVGDVI RLKKNDFVPA DILLLSSSEP NSLCYVETAE LDGETNLKFK
MSLEITDQYL QREDTLATFD GFIECEEPNN RLDKFTGTLF WRNTSFPLDA DKILLRGCVI
RNTDFCHGLV IFAGADTKIM KNSGKTRFKR TKIDYLMNYM VYTIFVVLIL LSAGLAIGHA
YWEAQVGNSS WYLYDGEDDT PSYRGFLIFW GYIIVLNTMV PISLYVSVEV IRLGQSHFIN
WDLQMYYAEK DTPAKARTTT LNEQLGQIHY IFSDKTGTLT QNIMTFKKCC INGQIYGDHR
DASQHNHNKI EQVDFSWNTY ADGKLAFYDH YLIEQIQSGK EPEVRQFFFL LAVCHTVMVD
RTDGQLNYQA ASPDEGALVN AARNFGFAFL ARTQNTITIS ELGTERTYNV LAILDFNSDR
KRMSIIVRTP EGNIKLYCKG ADTVIYERLH RMNPTKQETQ DALDIFANET LRTLCLCYKE
IEEKEFTEWN KKFMAASVAS TNRDEALDKV YEEIEKDLIL LGATAIEDKL QDGVPETISK
LAKADIKIWV LTGDKKETAE NIGFACELLT EDTTICYGED INSLLHARME NQRNRGGVYA
KFAPPVQESF FPPGGNRALI ITGSWLNEIL LEKKTKRNKI LKLKFPRTEE ERRMRTQSKR
RLEAKKEQRQ KNFVDLACEC SAVICCCVTP KQKAMVVDLV KRYKKAITLA IGDGANDVNM
IKTAHIGVGI SGQEGMQAVM SSDYSFAQFR YLQRLLLVHG RWSYIRMCKF LRYFFYKNFA
FTLVHFWYSF FNGYSAQTAY EDWFITLYNV LYTSLPVLLM GLLDQDVSDK LSLRFPGLYI
VGQRDLLFNY KRFFVSLLHG VLTSMILFFI PLGAYLQTVG QDGEAPSDYQ SFAVTIASAL
VITVNFQIGL DTSYWTFVNA FSIFGSIALY FGIMFDFHSA GIHVLFPSAF QFTGTASNAL
RQPYIWLTII LAVAVCLLPV VAIRFLSMTI WPSESDKIQK HRKRLKAEEQ WQRRQQVFRR
GVSTRRSAYA FSHQRGYADL ISSGRSIRKK RSPLDAIVAD GTAEYRRTGD S*

speed

0.60 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems