MutationTaster - study a chromosomal position

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: ENST00000281182
Querying Taster for transcript #2: ENST00000374752
Querying Taster for transcript #3: ENST00000543332
Querying Taster for transcript #4: ENST00000537423
MT speed 0 s - this script 5.768522 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ACAD8	disease_causing	0.999999914663548	simple_aae		affected		R203W	single base exchange	rs121908420		show file
ACAD8	disease_causing	0.999999914663548	simple_aae		affected		R253W	single base exchange	rs121908420		show file
ACAD8	disease_causing	0.999999936582879	simple_aae		affected		R330W	single base exchange	rs121908420		show file
ACAD8	disease_causing	1	without_aae		affected			single base exchange	rs121908420		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999914663548 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs5357 (probable pathogenic)
known disease mutation at this position (HGMD CM063826)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:134131680C>TN/A show variant in all transcripts IGV

HGNC symbol

ACAD8

Ensembl transcript ID

ENST00000374752

Genbank transcript ID

N/A

UniProt peptide

Q9UKU7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.607C>T
cDNA.647C>T
g.8292C>T

AA changes

R203W Score: 101 explain score(s)

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

203

frameshift

known variant

Reference ID: rs121908420

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

known as potential disease variant: rs5357 (probable pathogenic for Deficiency of isobutyryl-CoA dehydrogenase|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM063826)

known disease mutation at this position, please check HGMD for details (HGMD ID CM063826)
known disease mutation at this position, please check HGMD for details (HGMD ID CM063826)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-4.642	0
	1.74	0.938
(flanking)	6.185	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
Donor gained	8285	0.89	mu: CTGGTGGCCGCGTGG	GGTG\|gccg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

203

mutated

not conserved

203

Ptroglodytes

all identical

ENSPTRG00000004496

330

Mmulatta

all identical

ENSMMUG00000007107

330

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000031969

328

Ggallus

all identical

ENSGALG00000001557

327

Trubripes

no homologue

Drerio

all identical

ENSDARG00000042658

332

Dmelanogaster

no homologue

Celegans

all identical

F28A10.6

318

Xtropicalis

all identical

ENSXETG00000008327

331

protein features

start (aa)	end (aa)	feature	details
199	211	STRAND		lost
210	210	CONFLICT	P -> L (in Ref. 4; AAH01964).	might get lost (downstream of altered splice site)
212	214	HELIX		might get lost (downstream of altered splice site)
215	221	STRAND		might get lost (downstream of altered splice site)
227	229	STRAND		might get lost (downstream of altered splice site)
235	237	STRAND		might get lost (downstream of altered splice site)
243	254	STRAND		might get lost (downstream of altered splice site)
255	257	HELIX		might get lost (downstream of altered splice site)
258	261	STRAND		might get lost (downstream of altered splice site)
265	301	HELIX		might get lost (downstream of altered splice site)
274	277	REGION	Substrate binding.	might get lost (downstream of altered splice site)
302	302	BINDING	FAD; shared with dimeric partner.	might get lost (downstream of altered splice site)
309	311	HELIX		might get lost (downstream of altered splice site)
312	313	NP_BIND	FAD; shared with dimeric partner.	might get lost (downstream of altered splice site)
313	341	HELIX		might get lost (downstream of altered splice site)
347	372	HELIX		might get lost (downstream of altered splice site)
371	375	NP_BIND	FAD; shared with dimeric partner.	might get lost (downstream of altered splice site)
373	378	HELIX		might get lost (downstream of altered splice site)
384	393	HELIX		might get lost (downstream of altered splice site)
394	396	TURN		might get lost (downstream of altered splice site)
397	399	STRAND		might get lost (downstream of altered splice site)
398	398	ACT_SITE	Proton acceptor.	might get lost (downstream of altered splice site)
399	399	BINDING	Substrate; via amide nitrogen.	might get lost (downstream of altered splice site)
400	402	NP_BIND	FAD.	might get lost (downstream of altered splice site)
401	414	HELIX		might get lost (downstream of altered splice site)
410	410	BINDING	Substrate.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

867 / 867

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

289 / 289

position of stopcodon in wt / mu cDNA

907 / 907

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

41 / 41

chromosome

strand

last intron/exon boundary

855

theoretical NMD boundary in CDS

764

length of CDS

867

coding sequence (CDS) position

607

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

647

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

8292

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

134131680

original gDNA sequence snippet

CAACAAGGCTGGTGGCCGCGCGGCTGATGGTCCGCAATGCA

altered gDNA sequence snippet

CAACAAGGCTGGTGGCCGCGTGGCTGATGGTCCGCAATGCA

original cDNA sequence snippet

CAACAAGGCTGGTGGCCGCGCGGCTGATGGTCCGCAATGCA

altered cDNA sequence snippet

CAACAAGGCTGGTGGCCGCGTGGCTGATGGTCCGCAATGCA

wildtype AA sequence

MLWSGCRRFG ARLGCLPGGL RVLVQTGHRS LTSCIDRSGS DAASLLTSAK KQGDHYILNG
SKAFISGAGE SDIYVVMCRT GGPGPKGISC IVVEKGTPGL SFGKKEKKVG WNSQPTRAVI
FEDCAVPVAN RIGSEGQGFL IAVRGLNGGR INIASCSLGA AHASVILTRD HLNVRKQFGE
PLASNQYLQF TLADMATRLV AARLMVRNAA VALQEERKDA VALCSMAKLF ATDECFAICN
QALQMHGGYG YLKDYAVQQY VRDSRVHQIL EGSNEVMRIL ISRSLLQE*

mutated AA sequence

MLWSGCRRFG ARLGCLPGGL RVLVQTGHRS LTSCIDRSGS DAASLLTSAK KQGDHYILNG
SKAFISGAGE SDIYVVMCRT GGPGPKGISC IVVEKGTPGL SFGKKEKKVG WNSQPTRAVI
FEDCAVPVAN RIGSEGQGFL IAVRGLNGGR INIASCSLGA AHASVILTRD HLNVRKQFGE
PLASNQYLQF TLADMATRLV AAWLMVRNAA VALQEERKDA VALCSMAKLF ATDECFAICN
QALQMHGGYG YLKDYAVQQY VRDSRVHQIL EGSNEVMRIL ISRSLLQE*

speed

1.19 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: 0.999999914663548 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs5357 (probable pathogenic)
known disease mutation at this position (HGMD CM063826)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:134131680C>TN/A show variant in all transcripts IGV

HGNC symbol

ACAD8

Ensembl transcript ID

ENST00000537423

Genbank transcript ID

N/A

UniProt peptide

Q9UKU7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.757C>T
cDNA.940C>T
g.8292C>T

AA changes

R253W Score: 101 explain score(s)

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

253

frameshift

known variant

Reference ID: rs121908420

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

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-4.642	0
	1.74	0.938
(flanking)	6.185	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
Donor gained	8285	0.89	mu: CTGGTGGCCGCGTGG	GGTG\|gccg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

253

mutated

not conserved

253

Ptroglodytes

all identical

ENSPTRG00000004496

330

Mmulatta

all identical

ENSMMUG00000007107

330

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000031969

328

Ggallus

all identical

ENSGALG00000001557

327

Trubripes

no homologue

Drerio

all identical

ENSDARG00000042658

332

Dmelanogaster

no homologue

Celegans

all identical

F28A10.6

318

Xtropicalis

all identical

ENSXETG00000008327

331

protein features

start (aa)	end (aa)	feature	details
243	254	STRAND		lost
255	257	HELIX		might get lost (downstream of altered splice site)
258	261	STRAND		might get lost (downstream of altered splice site)
265	301	HELIX		might get lost (downstream of altered splice site)
274	277	REGION	Substrate binding.	might get lost (downstream of altered splice site)
302	302	BINDING	FAD; shared with dimeric partner.	might get lost (downstream of altered splice site)
309	311	HELIX		might get lost (downstream of altered splice site)
312	313	NP_BIND	FAD; shared with dimeric partner.	might get lost (downstream of altered splice site)
313	341	HELIX		might get lost (downstream of altered splice site)
347	372	HELIX		might get lost (downstream of altered splice site)
371	375	NP_BIND	FAD; shared with dimeric partner.	might get lost (downstream of altered splice site)
373	378	HELIX		might get lost (downstream of altered splice site)
384	393	HELIX		might get lost (downstream of altered splice site)
394	396	TURN		might get lost (downstream of altered splice site)
397	399	STRAND		might get lost (downstream of altered splice site)
398	398	ACT_SITE	Proton acceptor.	might get lost (downstream of altered splice site)
399	399	BINDING	Substrate; via amide nitrogen.	might get lost (downstream of altered splice site)
400	402	NP_BIND	FAD.	might get lost (downstream of altered splice site)
401	414	HELIX		might get lost (downstream of altered splice site)
410	410	BINDING	Substrate.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1074 / 1074

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

358 / 358

position of stopcodon in wt / mu cDNA

1257 / 1257

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

184 / 184

chromosome

strand

last intron/exon boundary

1148

theoretical NMD boundary in CDS

914

length of CDS

1074

coding sequence (CDS) position

757

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

940

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

8292

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

134131680

original gDNA sequence snippet

CAACAAGGCTGGTGGCCGCGCGGCTGATGGTCCGCAATGCA

altered gDNA sequence snippet

CAACAAGGCTGGTGGCCGCGTGGCTGATGGTCCGCAATGCA

original cDNA sequence snippet

CAACAAGGCTGGTGGCCGCGCGGCTGATGGTCCGCAATGCA

altered cDNA sequence snippet

CAACAAGGCTGGTGGCCGCGTGGCTGATGGTCCGCAATGCA

wildtype AA sequence

MRKAAQLGFG GVYIQTDVGG SGLSRLDTSV IFEALATGCT STTAYISIHN MCAWMIDSFG
NEEQRHKFCP PLCTMEKFAS YCLTEPGSGS DAASLLTSAK KQGDHYILNG SKAFISGAGE
SDIYVVMCRT GGPGPKGISC IVVEKGTPGL SFGKKEKKVG WNSQPTRAVI FEDCAVPVAN
RIGSEGQGFL IAVRGLNGGR INIASCSLGA AHASVILTRD HLNVRKQFGE PLASNQYLQF
TLADMATRLV AARLMVRNAA VALQEERKDA VALCSMAKLF ATDECFAICN QALQMHGGYG
YLKDYAVQQY VRDSRVHQIL EELFWQGPGV QSRSFVPFGG PQIALLLPFS SGDLREG*

mutated AA sequence

MRKAAQLGFG GVYIQTDVGG SGLSRLDTSV IFEALATGCT STTAYISIHN MCAWMIDSFG
NEEQRHKFCP PLCTMEKFAS YCLTEPGSGS DAASLLTSAK KQGDHYILNG SKAFISGAGE
SDIYVVMCRT GGPGPKGISC IVVEKGTPGL SFGKKEKKVG WNSQPTRAVI FEDCAVPVAN
RIGSEGQGFL IAVRGLNGGR INIASCSLGA AHASVILTRD HLNVRKQFGE PLASNQYLQF
TLADMATRLV AAWLMVRNAA VALQEERKDA VALCSMAKLF ATDECFAICN QALQMHGGYG
YLKDYAVQQY VRDSRVHQIL EELFWQGPGV QSRSFVPFGG PQIALLLPFS SGDLREG*

speed

1.29 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999936582879 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs5357 (probable pathogenic)
known disease mutation at this position (HGMD CM063826)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:134131680C>TN/A show variant in all transcripts IGV

HGNC symbol

ACAD8

Ensembl transcript ID

ENST00000281182

Genbank transcript ID

NM_014384

UniProt peptide

Q9UKU7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.988C>T
cDNA.1094C>T
g.8292C>T

AA changes

R330W Score: 101 explain score(s)

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

330

frameshift

known variant

Reference ID: rs121908420

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

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-4.642	0
	1.74	0.938
(flanking)	6.185	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
Donor gained	8285	0.89	mu: CTGGTGGCCGCGTGG	GGTG\|gccg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

330

mutated

not conserved

330

Ptroglodytes

all identical

ENSPTRG00000004496

330

Mmulatta

all identical

ENSMMUG00000007107

330

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000031969

328

Ggallus

all identical

ENSGALG00000001557

327

Trubripes

no homologue

Drerio

all identical

ENSDARG00000042658

332

Dmelanogaster

no homologue

Celegans

all identical

F28A10.6

318

Xtropicalis

all identical

ENSXETG00000008327

331

protein features

start (aa)	end (aa)	feature	details
313	341	HELIX		lost
347	372	HELIX		might get lost (downstream of altered splice site)
371	375	NP_BIND	FAD; shared with dimeric partner.	might get lost (downstream of altered splice site)
373	378	HELIX		might get lost (downstream of altered splice site)
384	393	HELIX		might get lost (downstream of altered splice site)
394	396	TURN		might get lost (downstream of altered splice site)
397	399	STRAND		might get lost (downstream of altered splice site)
398	398	ACT_SITE	Proton acceptor.	might get lost (downstream of altered splice site)
399	399	BINDING	Substrate; via amide nitrogen.	might get lost (downstream of altered splice site)
400	402	NP_BIND	FAD.	might get lost (downstream of altered splice site)
401	414	HELIX		might get lost (downstream of altered splice site)
410	410	BINDING	Substrate.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1248 / 1248

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

416 / 416

position of stopcodon in wt / mu cDNA

1354 / 1354

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

107 / 107

chromosome

strand

last intron/exon boundary

1302

theoretical NMD boundary in CDS

1145

length of CDS

1248

coding sequence (CDS) position

988

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

1094

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

8292

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

134131680

original gDNA sequence snippet

CAACAAGGCTGGTGGCCGCGCGGCTGATGGTCCGCAATGCA

altered gDNA sequence snippet

CAACAAGGCTGGTGGCCGCGTGGCTGATGGTCCGCAATGCA

original cDNA sequence snippet

CAACAAGGCTGGTGGCCGCGCGGCTGATGGTCCGCAATGCA

altered cDNA sequence snippet

CAACAAGGCTGGTGGCCGCGTGGCTGATGGTCCGCAATGCA

wildtype AA sequence

MLWSGCRRFG ARLGCLPGGL RVLVQTGHRS LTSCIDPSMG LNEEQKEFQK VAFDFAAREM
APNMAEWDQK ELFPVDVMRK AAQLGFGGVY IQTDVGGSGL SRLDTSVIFE ALATGCTSTT
AYISIHNMCA WMIDSFGNEE QRHKFCPPLC TMEKFASYCL TEPGSGSDAA SLLTSAKKQG
DHYILNGSKA FISGAGESDI YVVMCRTGGP GPKGISCIVV EKGTPGLSFG KKEKKVGWNS
QPTRAVIFED CAVPVANRIG SEGQGFLIAV RGLNGGRINI ASCSLGAAHA SVILTRDHLN
VRKQFGEPLA SNQYLQFTLA DMATRLVAAR LMVRNAAVAL QEERKDAVAL CSMAKLFATD
ECFAICNQAL QMHGGYGYLK DYAVQQYVRD SRVHQILEGS NEVMRILISR SLLQE*

mutated AA sequence

MLWSGCRRFG ARLGCLPGGL RVLVQTGHRS LTSCIDPSMG LNEEQKEFQK VAFDFAAREM
APNMAEWDQK ELFPVDVMRK AAQLGFGGVY IQTDVGGSGL SRLDTSVIFE ALATGCTSTT
AYISIHNMCA WMIDSFGNEE QRHKFCPPLC TMEKFASYCL TEPGSGSDAA SLLTSAKKQG
DHYILNGSKA FISGAGESDI YVVMCRTGGP GPKGISCIVV EKGTPGLSFG KKEKKVGWNS
QPTRAVIFED CAVPVANRIG SEGQGFLIAV RGLNGGRINI ASCSLGAAHA SVILTRDHLN
VRKQFGEPLA SNQYLQFTLA DMATRLVAAW LMVRNAAVAL QEERKDAVAL CSMAKLFATD
ECFAICNQAL QMHGGYGYLK DYAVQQYVRD SRVHQILEGS NEVMRILISR SLLQE*

speed

1.06 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (explain)

Summary

known as potential disease variant: rs5357 (probable pathogenic)
known disease mutation at this position (HGMD CM063826)
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:134131680C>TN/A show variant in all transcripts IGV

HGNC symbol

ACAD8

Ensembl transcript ID

ENST00000543332

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

3'UTR

DNA changes

cDNA.992C>T
g.8292C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121908420

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

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-4.642	0
	1.74	0.938
(flanking)	6.185	1

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

splice sites

splice site change occurs after stopcodon (at aa 272)

effect	gDNA position	score	detection sequence	exon-intron border
Donor gained	8285	0.89	mu: CTGGTGGCCGCGTGG	GGTG\|gccg

distance from splice site

105

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

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

signal is predicted to be ok

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

168 / 168

chromosome

strand

last intron/exon boundary

1097

theoretical NMD boundary in CDS

879

length of CDS

681

coding sequence (CDS) position

N/A

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

992

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

8292

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

134131680

original gDNA sequence snippet

CAACAAGGCTGGTGGCCGCGCGGCTGATGGTCCGCAATGCA

altered gDNA sequence snippet

CAACAAGGCTGGTGGCCGCGTGGCTGATGGTCCGCAATGCA

original cDNA sequence snippet

CAACAAGGCTGGTGGCCGCGCGGCTGATGGTCCGCAATGCA

altered cDNA sequence snippet

CAACAAGGCTGGTGGCCGCGTGGCTGATGGTCCGCAATGCA

wildtype AA sequence

MKSRKNFKKW PLTLLPERWL QIWQSGTRSM CAWMIDSFGN EEQRHKFCPP LCTMEKFASY
CLTEPGSGSD AASLLTSAKK QGDHYILNGS KAFISGAGES DIYVVMCRTG GPGPKGISCI
VVEKGTPGLS FGKKEKKVGW NSQPTRAVIF EDCAVPVANR IGSEGQGFLI AVRGLNGGRI
NIASCSLGAA HASVILTRDH LNVRKQFGEP LASNQKKQET LKLWIT*

mutated AA sequence

N/A

speed

1.27 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems