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 3.659901 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ATP8B1	disease_causing_automatic	0.999999999975042	simple_aae			0	D554N	single base exchange	rs121909101		show file
ATP8B1	disease_causing_automatic	0.999999999975042	simple_aae			0	D554N	single base exchange	rs121909101		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999975042 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM004386)
known disease mutation: rs7269 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr18:55342225C>TN/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.1660G>A
cDNA.1660G>A
g.128109G>A

AA changes

D554N Score: 23 explain score(s)

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

554

frameshift

known variant

Reference ID: rs121909101
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs7269 (pathogenic for Cholestasis, progressive familial intrahepatic 1|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM004386)

known disease mutation at this position, please check HGMD for details (HGMD ID CM004386)
known disease mutation at this position, please check HGMD for details (HGMD ID CM004386)

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
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.954	0.998
	5.999	0.998
(flanking)	-4.263	0.002

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
Donor marginally increased	128110	wt: 0.9087 / mu: 0.9338 (marginal change - not scored)	wt: TCCCGATGAAGGTGC mu: TCCCAATGAAGGTGC	CCGA\|tgaa
Donor marginally increased	128109	wt: 0.9746 / mu: 0.9821 (marginal change - not scored)	wt: CTCCCGATGAAGGTG mu: CTCCCAATGAAGGTG	CCCG\|atga
Donor marginally increased	128106	wt: 0.3785 / mu: 0.4363 (marginal change - not scored)	wt: CCTCTCCCGATGAAG mu: CCTCTCCCAATGAAG	TCTC\|ccga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

554

mutated

all conserved

554

Ptroglodytes

all identical

ENSPTRG00000010048

521

Mmulatta

all identical

ENSMMUG00000019976

553

Fcatus

all identical

ENSFCAG00000014301

491

Mmusculus

all identical

ENSMUSG00000039529

554

Ggallus

all identical

ENSGALG00000003253

556

Trubripes

no homologue

Drerio

all identical

ENSDARG00000060980

548

Dmelanogaster

all identical

FBgn0037989

913

Celegans

all identical

H06H21.10

512

Xtropicalis

all identical

ENSXETG00000020878

373

protein features

start (aa)	end (aa)	feature	details
412	949	TOPO_DOM	Cytoplasmic (Potential).	lost

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

1660

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

1660

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

128109

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

55342225

original gDNA sequence snippet

ACTACCAGGCAGCCTCTCCCGATGAAGGTGCCCTGGTAAAC

altered gDNA sequence snippet

ACTACCAGGCAGCCTCTCCCAATGAAGGTGCCCTGGTAAAC

original cDNA sequence snippet

ACTACCAGGCAGCCTCTCCCGATGAAGGTGCCCTGGTAAAC

altered cDNA sequence snippet

ACTACCAGGCAGCCTCTCCCAATGAAGGTGCCCTGGTAAAC

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 ASPNEGALVN 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*

speed

0.79 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: 0.999999999975042 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM004386)
known disease mutation: rs7269 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr18:55342225C>TN/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.1660G>A
cDNA.1780G>A
g.128109G>A

AA changes

D554N Score: 23 explain score(s)

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

554

frameshift

known variant

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.954	0.998
	5.999	0.998
(flanking)	-4.263	0.002

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
Donor marginally increased	128110	wt: 0.9087 / mu: 0.9338 (marginal change - not scored)	wt: TCCCGATGAAGGTGC mu: TCCCAATGAAGGTGC	CCGA\|tgaa
Donor marginally increased	128109	wt: 0.9746 / mu: 0.9821 (marginal change - not scored)	wt: CTCCCGATGAAGGTG mu: CTCCCAATGAAGGTG	CCCG\|atga
Donor marginally increased	128106	wt: 0.3785 / mu: 0.4363 (marginal change - not scored)	wt: CCTCTCCCGATGAAG mu: CCTCTCCCAATGAAG	TCTC\|ccga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

554

mutated

all conserved

554

Ptroglodytes

all identical

ENSPTRG00000010048

521

Mmulatta

all identical

ENSMMUG00000019976

553

Fcatus

all identical

ENSFCAG00000014301

491

Mmusculus

all identical

ENSMUSG00000039529

554

Ggallus

all identical

ENSGALG00000003253

556

Trubripes

no homologue

Drerio

all identical

ENSDARG00000060980

548

Dmelanogaster

all identical

FBgn0037989

913

Celegans

all identical

H06H21.10

512

Xtropicalis

all identical

ENSXETG00000020878

373

protein features

start (aa)	end (aa)	feature	details
412	949	TOPO_DOM	Cytoplasmic (Potential).	lost

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

1660

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

1780

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

128109

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

55342225

original gDNA sequence snippet

ACTACCAGGCAGCCTCTCCCGATGAAGGTGCCCTGGTAAAC

altered gDNA sequence snippet

ACTACCAGGCAGCCTCTCCCAATGAAGGTGCCCTGGTAAAC

original cDNA sequence snippet

ACTACCAGGCAGCCTCTCCCGATGAAGGTGCCCTGGTAAAC

altered cDNA sequence snippet

ACTACCAGGCAGCCTCTCCCAATGAAGGTGCCCTGGTAAAC

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 ASPNEGALVN 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*

speed

0.88 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems