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: ENST00000242592
Querying Taster for transcript #2: ENST00000411593
MT speed 0 s - this script 3.434272 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ACADS	disease_causing_automatic	0.999999987355624	simple_aae		affected	0	R376W	single base exchange	rs28940875		show file
ACADS	disease_causing_automatic	0.999999997925281	simple_aae		affected	0	R380W	single base exchange	rs28940875		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999987355624 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM010009)
known disease mutation: rs3837 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:121177150C>TN/A show variant in all transcripts IGV

HGNC symbol

ACADS

Ensembl transcript ID

ENST00000411593

Genbank transcript ID

N/A

UniProt peptide

P16219

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1126C>T
cDNA.1151C>T
g.13613C>T

AA changes

R376W Score: 101 explain score(s)

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

376

frameshift

known variant

Reference ID: rs28940875

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	6	6

known disease mutation: rs3837 (pathogenic for Deficiency of butyryl-CoA dehydrogenase|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM010009)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010009)
known disease mutation at this position, please check HGMD for details (HGMD ID CM010009)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.06	0.994
	1.775	1
(flanking)	5.558	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 increased	13609	wt: 0.24 / mu: 0.51	wt: CCGGCAGAGCGGCAC mu: CCGGCAGAGTGGCAC	GGCA\|gagc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

376

mutated

not conserved

376

Ptroglodytes

all identical

ENSPTRG00000005547

380

Mmulatta

all identical

ENSMMUG00000020648

380

Fcatus

all identical

ENSFCAG00000002402

310

Mmusculus

all identical

ENSMUSG00000029545

380

Ggallus

all identical

ENSGALG00000007072

384

Trubripes

all identical

ENSTRUG00000018610

380

Drerio

all identical

ENSDARG00000030781

392

Dmelanogaster

all identical

FBgn0038742

373

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000012275

377

protein features

start (aa)	end (aa)	feature	details
378	388	HELIX		might get lost (downstream of altered splice site)
389	392	TURN		might get lost (downstream of altered splice site)
392	392	ACT_SITE	Proton acceptor (By similarity).	might get lost (downstream of altered splice site)
393	393	BINDING	Substrate; via amide nitrogen.	might get lost (downstream of altered splice site)
394	396	NP_BIND	FAD.	might get lost (downstream of altered splice site)
395	411	HELIX		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1227 / 1227

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

409 / 409

position of stopcodon in wt / mu cDNA

1252 / 1252

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

26 / 26

chromosome

strand

last intron/exon boundary

1100

theoretical NMD boundary in CDS

1024

length of CDS

1227

coding sequence (CDS) position

1126

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

1151

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

13613

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

121177150

original gDNA sequence snippet

TGACAGAGATGCCGGCAGAGCGGCACTACCGCGACGCCCGC

altered gDNA sequence snippet

TGACAGAGATGCCGGCAGAGTGGCACTACCGCGACGCCCGC

original cDNA sequence snippet

TGACAGAGATGCCGGCAGAGCGGCACTACCGCGACGCCCGC

altered cDNA sequence snippet

TGACAGAGATGCCGGCAGAGTGGCACTACCGCGACGCCCGC

wildtype AA sequence

MAAALLARAS GPARRALCPR AWRQLHTIYQ SVELPETHQM LLQTCRDFAE KELFPIAAQV
DKEHLFPAAQ VKKMGGLGLL AMDVPEELGG AGLDYLAYAI AMEEISRGCA STGVIMSVNN
SLYLGPILKF GSKEQKQAWV TPFTSGDKIG CFALSEPGPS LLGPTGPIFA LGQVGCPCPS
SAATEACTFP RSRQRVSRPE LLREGISAFL VPMPTPGLTL GKKEDKLGIR GSSTANLIFE
DCRIPKDSIL GEPGMGFKIA MQTLDMGRIG IASQALGIAQ TALDCAVNYA ENRMAFGAPL
TKLQVIQFKL ADMALALESA RLLTWRAAML KDNKKPFIKE AAMAKLAASE AATAISHQAI
QILGGMGYVT EMPAERHYRD ARITEIYEGT SEIQRLVIAG HLLRSYRS*

mutated AA sequence

speed

0.59 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: 0.999999997925281 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM010009)
known disease mutation: rs3837 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:121177150C>TN/A show variant in all transcripts IGV

HGNC symbol

ACADS

Ensembl transcript ID

ENST00000242592

Genbank transcript ID

NM_000017

UniProt peptide

P16219

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1138C>T
cDNA.1289C>T
g.13613C>T

AA changes

R380W Score: 101 explain score(s)

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

380

frameshift

known variant

Reference ID: rs28940875

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	6	6

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.06	0.994
	1.775	1
(flanking)	5.558	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 increased	13609	wt: 0.24 / mu: 0.51	wt: CCGGCAGAGCGGCAC mu: CCGGCAGAGTGGCAC	GGCA\|gagc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

380

mutated

not conserved

380

Ptroglodytes

all identical

ENSPTRG00000005547

380

Mmulatta

all identical

ENSMMUG00000020648

380

Fcatus

all identical

ENSFCAG00000002402

310

Mmusculus

all identical

ENSMUSG00000029545

380

Ggallus

all identical

ENSGALG00000007072

384

Trubripes

all identical

ENSTRUG00000018610

380

Drerio

all identical

ENSDARG00000030781

392

Dmelanogaster

all identical

FBgn0038742

373

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000012275

377

protein features

start (aa)	end (aa)	feature	details
378	388	HELIX		lost
389	392	TURN		might get lost (downstream of altered splice site)
392	392	ACT_SITE	Proton acceptor (By similarity).	might get lost (downstream of altered splice site)
393	393	BINDING	Substrate; via amide nitrogen.	might get lost (downstream of altered splice site)
394	396	NP_BIND	FAD.	might get lost (downstream of altered splice site)
395	411	HELIX		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1239 / 1239

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

413 / 413

position of stopcodon in wt / mu cDNA

1390 / 1390

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

152 / 152

chromosome

strand

last intron/exon boundary

1238

theoretical NMD boundary in CDS

1036

length of CDS

1239

coding sequence (CDS) position

1138

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

1289

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

13613

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

121177150

original gDNA sequence snippet

TGACAGAGATGCCGGCAGAGCGGCACTACCGCGACGCCCGC

altered gDNA sequence snippet

TGACAGAGATGCCGGCAGAGTGGCACTACCGCGACGCCCGC

original cDNA sequence snippet

TGACAGAGATGCCGGCAGAGCGGCACTACCGCGACGCCCGC

altered cDNA sequence snippet

TGACAGAGATGCCGGCAGAGTGGCACTACCGCGACGCCCGC

wildtype AA sequence

MAAALLARAS GPARRALCPR AWRQLHTIYQ SVELPETHQM LLQTCRDFAE KELFPIAAQV
DKEHLFPAAQ VKKMGGLGLL AMDVPEELGG AGLDYLAYAI AMEEISRGCA STGVIMSVNN
SLYLGPILKF GSKEQKQAWV TPFTSGDKIG CFALSEPGNG SDAGAASTTA RAEGDSWVLN
GTKAWITNAW EASAAVVFAS TDRALQNKGI SAFLVPMPTP GLTLGKKEDK LGIRGSSTAN
LIFEDCRIPK DSILGEPGMG FKIAMQTLDM GRIGIASQAL GIAQTALDCA VNYAENRMAF
GAPLTKLQVI QFKLADMALA LESARLLTWR AAMLKDNKKP FIKEAAMAKL AASEAATAIS
HQAIQILGGM GYVTEMPAER HYRDARITEI YEGTSEIQRL VIAGHLLRSY RS*

mutated AA sequence

MAAALLARAS GPARRALCPR AWRQLHTIYQ SVELPETHQM LLQTCRDFAE KELFPIAAQV
DKEHLFPAAQ VKKMGGLGLL AMDVPEELGG AGLDYLAYAI AMEEISRGCA STGVIMSVNN
SLYLGPILKF GSKEQKQAWV TPFTSGDKIG CFALSEPGNG SDAGAASTTA RAEGDSWVLN
GTKAWITNAW EASAAVVFAS TDRALQNKGI SAFLVPMPTP GLTLGKKEDK LGIRGSSTAN
LIFEDCRIPK DSILGEPGMG FKIAMQTLDM GRIGIASQAL GIAQTALDCA VNYAENRMAF
GAPLTKLQVI QFKLADMALA LESARLLTWR AAMLKDNKKP FIKEAAMAKL AASEAATAIS
HQAIQILGGM GYVTEMPAEW HYRDARITEI YEGTSEIQRL VIAGHLLRSY RS*

speed

0.89 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems