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 3.2043 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ACADS	disease_causing_automatic	0.999999999993975	simple_aae			0	R325W	single base exchange	rs121908006		show file
ACADS	disease_causing_automatic	0.999999999993975	simple_aae			0	R321W	single base exchange	rs121908006		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999993975 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM010007)
known disease mutation: rs3835 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:121176662C>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.973C>T
cDNA.1124C>T
g.13125C>T

AA changes

R325W Score: 101 explain score(s)

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

325

frameshift

known variant

Reference ID: rs121908006

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	3	3

known disease mutation: rs3835 (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 CM010007)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010007)
known disease mutation at this position, please check HGMD for details (HGMD ID CM010007)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.062	0.995
	5.505	1
(flanking)	5.505	1

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

325

mutated

not conserved

325

Ptroglodytes

all identical

ENSPTRG00000005547

325

Mmulatta

all identical

ENSMMUG00000020648

325

Fcatus

no alignment

ENSFCAG00000002402

n/a

Mmusculus

all identical

ENSMUSG00000029545

325

Ggallus

all identical

ENSGALG00000007072

329

Trubripes

all identical

ENSTRUG00000018610

325

Drerio

all identical

ENSDARG00000030781

337

Dmelanogaster

all identical

FBgn0038742

318

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000012275

322

protein features

start (aa)	end (aa)	feature	details
308	336	HELIX		lost

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

973

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

1124

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

13125

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

121176662

original gDNA sequence snippet

CCCTGGCCCTGGAGAGTGCCCGGCTGCTGACCTGGCGCGCT

altered gDNA sequence snippet

CCCTGGCCCTGGAGAGTGCCTGGCTGCTGACCTGGCGCGCT

original cDNA sequence snippet

CCCTGGCCCTGGAGAGTGCCCGGCTGCTGACCTGGCGCGCT

altered cDNA sequence snippet

CCCTGGCCCTGGAGAGTGCCTGGCTGCTGACCTGGCGCGCT

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 LESAWLLTWR AAMLKDNKKP FIKEAAMAKL AASEAATAIS
HQAIQILGGM GYVTEMPAER HYRDARITEI YEGTSEIQRL VIAGHLLRSY RS*

speed

0.63 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: 0.999999999993975 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM010007)
known disease mutation: rs3835 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:121176662C>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.961C>T
cDNA.986C>T
g.13125C>T

AA changes

R321W Score: 101 explain score(s)

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

321

frameshift

known variant

Reference ID: rs121908006

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	3	3

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.062	0.995
	5.505	1
(flanking)	5.505	1

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

321

mutated

not conserved

321

Ptroglodytes

all identical

ENSPTRG00000005547

325

Mmulatta

all identical

ENSMMUG00000020648

325

Fcatus

no alignment

ENSFCAG00000002402

n/a

Mmusculus

all identical

ENSMUSG00000029545

325

Ggallus

all identical

ENSGALG00000007072

329

Trubripes

all identical

ENSTRUG00000018610

325

Drerio

all identical

ENSDARG00000030781

337

Dmelanogaster

all identical

FBgn0038742

318

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000012275

322

protein features

start (aa)	end (aa)	feature	details
308	336	HELIX		lost

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

961

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

986

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

13125

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

121176662

original gDNA sequence snippet

CCCTGGCCCTGGAGAGTGCCCGGCTGCTGACCTGGCGCGCT

altered gDNA sequence snippet

CCCTGGCCCTGGAGAGTGCCTGGCTGCTGACCTGGCGCGCT

original cDNA sequence snippet

CCCTGGCCCTGGAGAGTGCCCGGCTGCTGACCTGGCGCGCT

altered cDNA sequence snippet

CCCTGGCCCTGGAGAGTGCCTGGCTGCTGACCTGGCGCGCT

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

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 WLLTWRAAML KDNKKPFIKE AAMAKLAASE AATAISHQAI
QILGGMGYVT EMPAERHYRD ARITEIYEGT SEIQRLVIAG HLLRSYRS*

speed

0.62 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems