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 3.431923 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ATP8B1	disease_causing_automatic	0.999999263046101	simple_aae			0	L288S	single base exchange	rs121909099		show file
ATP8B1	disease_causing_automatic	0.999999263046101	simple_aae			0	L288S	single base exchange	rs121909099		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999263046101 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM980759)
known disease mutation: rs7264 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr18:55362480A>GN/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.863T>C
cDNA.863T>C
g.107854T>C

AA changes

L288S Score: 145 explain score(s)

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

288

frameshift

known variant

Reference ID: rs121909099
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs7264 (pathogenic for Cholestasis, progressive familial intrahepatic 1) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980759)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980759)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980759)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.363	1
	5.037	1
(flanking)	0.815	0.99

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 marginally increased	107855	wt: 0.3280 / mu: 0.3437 (marginal change - not scored)	wt: AGAAACACAAGTTTTCCTTTGGATGCTGATAAAATTTTGTT mu: AGAAACACAAGTTTTCCTTCGGATGCTGATAAAATTTTGTT	tttg\|GATG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

288

mutated

not conserved

288

Ptroglodytes

all identical

ENSPTRG00000010048

255

Mmulatta

all identical

ENSMMUG00000019976

287

Fcatus

all identical

ENSFCAG00000014301

225

Mmusculus

all identical

ENSMUSG00000039529

288

Ggallus

all identical

ENSGALG00000003253

288

Trubripes

no homologue

Drerio

all identical

ENSDARG00000060980

282

Dmelanogaster

all identical

FBgn0037989

405

Celegans

all conserved

H06H21.10

232

Xtropicalis

not conserved

ENSXETG00000020878

104

protein features

start (aa)	end (aa)	feature	details
157	340	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

863

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

863

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

107854

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

55362480

original gDNA sequence snippet

GAGAAACACAAGTTTTCCTTTGGATGCTGATAAAATTTTGT

altered gDNA sequence snippet

GAGAAACACAAGTTTTCCTTCGGATGCTGATAAAATTTTGT

original cDNA sequence snippet

GAGAAACACAAGTTTTCCTTTGGATGCTGATAAAATTTTGT

altered cDNA sequence snippet

GAGAAACACAAGTTTTCCTTCGGATGCTGATAAAATTTTGT

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 WRNTSFPSDA 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*

speed

0.58 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: 0.999999263046101 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM980759)
known disease mutation: rs7264 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr18:55362480A>GN/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.863T>C
cDNA.983T>C
g.107854T>C

AA changes

L288S Score: 145 explain score(s)

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

288

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.363	1
	5.037	1
(flanking)	0.815	0.99

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 marginally increased	107855	wt: 0.3280 / mu: 0.3437 (marginal change - not scored)	wt: AGAAACACAAGTTTTCCTTTGGATGCTGATAAAATTTTGTT mu: AGAAACACAAGTTTTCCTTCGGATGCTGATAAAATTTTGTT	tttg\|GATG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

288

mutated

not conserved

288

Ptroglodytes

all identical

ENSPTRG00000010048

255

Mmulatta

all identical

ENSMMUG00000019976

287

Fcatus

all identical

ENSFCAG00000014301

225

Mmusculus

all identical

ENSMUSG00000039529

288

Ggallus

all identical

ENSGALG00000003253

288

Trubripes

no homologue

Drerio

all identical

ENSDARG00000060980

282

Dmelanogaster

all identical

FBgn0037989

405

Celegans

all conserved

H06H21.10

232

Xtropicalis

not conserved

ENSXETG00000020878

104

protein features

start (aa)	end (aa)	feature	details
157	340	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

863

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

983

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

107854

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

55362480

original gDNA sequence snippet

GAGAAACACAAGTTTTCCTTTGGATGCTGATAAAATTTTGT

altered gDNA sequence snippet

GAGAAACACAAGTTTTCCTTCGGATGCTGATAAAATTTTGT

original cDNA sequence snippet

GAGAAACACAAGTTTTCCTTTGGATGCTGATAAAATTTTGT

altered cDNA sequence snippet

GAGAAACACAAGTTTTCCTTCGGATGCTGATAAAATTTTGT

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 WRNTSFPSDA 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*

speed

0.91 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems