MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000540732
Querying Taster for transcript #2: ENST00000269980
Querying Taster for transcript #3: ENST00000457836
MT speed 0 s - this script 2.932771 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
BCKDHA	disease_causing	0.999996087897251	simple_aae				G227S	single base exchange	rs137852874		show file
BCKDHA	disease_causing	0.999999358091038	simple_aae				G249S	single base exchange	rs137852874		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999996087897251 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs2380 (probable pathogenic)
known disease mutation at this position (HGMD CM984176)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:41928167G>AN/A show variant in all transcripts IGV

HGNC symbol

BCKDHA

Ensembl transcript ID

ENST00000457836

Genbank transcript ID

N/A

UniProt peptide

P12694

alteration type

single base exchange

alteration region

CDS

DNA changes

c.679G>A
cDNA.684G>A
g.24803G>A

AA changes

G227S Score: 56 explain score(s)

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

227

frameshift

known variant

Reference ID: rs137852874

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

known as potential disease variant: rs2380 (probable pathogenic for Maple syrup urine disease|Maple syrup urine disease type 1A) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM984176)

known disease mutation at this position, please check HGMD for details (HGMD ID CM984176)
known disease mutation at this position, please check HGMD for details (HGMD ID CM984176)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.441	0.185
	5.495	1
(flanking)	3.724	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

227

mutated

not conserved

227

Ptroglodytes

all identical

ENSPTRG00000011025

249

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000060376

250

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000009706

250

Drerio

all identical

ENSDARG00000040555

250

Dmelanogaster

not conserved

FBgn0037709

242

Celegans

not conserved

Y39E4A.3

234

Xtropicalis

not conserved

ENSXETG00000018753

212

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1347 / 1347

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

449 / 449

position of stopcodon in wt / mu cDNA

1352 / 1352

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

6 / 6

chromosome

strand

last intron/exon boundary

1182

theoretical NMD boundary in CDS

1126

length of CDS

1347

coding sequence (CDS) position

679

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

684

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

24803

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

41928167

original gDNA sequence snippet

GTGAGGGGGACGCCCATGCCGGCTTCAACTTCGCTGCCACA

altered gDNA sequence snippet

GTGAGGGGGACGCCCATGCCAGCTTCAACTTCGCTGCCACA

original cDNA sequence snippet

GTGAGGGGGACGCCCATGCCGGCTTCAACTTCGCTGCCACA

altered cDNA sequence snippet

GTGAGGGGGACGCCCATGCCAGCTTCAACTTCGCTGCCACA

wildtype AA sequence

MAVAIAAARV WRLNRGLSQQ QQFSSLDDKP QFPGASAEFI DKLEFIQPNV ISGIPIYRVM
DRQGQIINPS EDPHLPKEKV LKLYKSMTLL NTMDRILYES QRQGRISFYM TNYGEEGTHV
GSAAALDNTD LVFGQYREAG VLMYRDYPLE LFMAQCYGNI SDLGKGRQMP VHYGCKERHF
VTISSPLATQ IPQAVGAAYA AKRANANRVV ICYFGEGAAS EGDAHAGFNF AATLECPIIF
FCRNNGYAIS TPTSEQYRGD GIAARGPGYG IMSIRVDGND VFAVYNATKE ARRRAVAENQ
PFLIEAMTYS SSPILPPDPH SREPTLTWGP LPLCRIGHHS TSDDSSAYRS VDEVNYWDKQ
DHPISRLRHY LLSQGWWDEE QEKAWRKQSR RKVMEAFEQA ERKPKPNPNL LFSDVYQEMP
AQLRKQQESL ARHLQTYGEH YPLDHFDK*

mutated AA sequence

MAVAIAAARV WRLNRGLSQQ QQFSSLDDKP QFPGASAEFI DKLEFIQPNV ISGIPIYRVM
DRQGQIINPS EDPHLPKEKV LKLYKSMTLL NTMDRILYES QRQGRISFYM TNYGEEGTHV
GSAAALDNTD LVFGQYREAG VLMYRDYPLE LFMAQCYGNI SDLGKGRQMP VHYGCKERHF
VTISSPLATQ IPQAVGAAYA AKRANANRVV ICYFGEGAAS EGDAHASFNF AATLECPIIF
FCRNNGYAIS TPTSEQYRGD GIAARGPGYG IMSIRVDGND VFAVYNATKE ARRRAVAENQ
PFLIEAMTYS SSPILPPDPH SREPTLTWGP LPLCRIGHHS TSDDSSAYRS VDEVNYWDKQ
DHPISRLRHY LLSQGWWDEE QEKAWRKQSR RKVMEAFEQA ERKPKPNPNL LFSDVYQEMP
AQLRKQQESL ARHLQTYGEH YPLDHFDK*

speed

0.26 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: 0.999999358091038 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs2380 (probable pathogenic)
known disease mutation at this position (HGMD CM984176)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:41928167G>AN/A show variant in all transcripts IGV

HGNC symbol

BCKDHA

Ensembl transcript ID

ENST00000269980

Genbank transcript ID

NM_000709

UniProt peptide

P12694

alteration type

single base exchange

alteration region

CDS

DNA changes

c.745G>A
cDNA.1113G>A
g.24803G>A

AA changes

G249S Score: 56 explain score(s)

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

249

frameshift

known variant

Reference ID: rs137852874

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

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.441	0.185
	5.495	1
(flanking)	3.724	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

249

mutated

not conserved

249

Ptroglodytes

all identical

ENSPTRG00000011025

249

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000060376

250

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000009706

250

Drerio

all identical

ENSDARG00000040555

250

Dmelanogaster

not conserved

FBgn0037709

242

Celegans

not conserved

Y39E4A.3

234

Xtropicalis

not conserved

ENSXETG00000018753

212

protein features

start (aa)	end (aa)	feature	details
244	255	HELIX		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1338 / 1338

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

446 / 446

position of stopcodon in wt / mu cDNA

1706 / 1706

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

369 / 369

chromosome

strand

last intron/exon boundary

1536

theoretical NMD boundary in CDS

1117

length of CDS

1338

coding sequence (CDS) position

745

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

1113

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

24803

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

41928167

original gDNA sequence snippet

GTGAGGGGGACGCCCATGCCGGCTTCAACTTCGCTGCCACA

altered gDNA sequence snippet

GTGAGGGGGACGCCCATGCCAGCTTCAACTTCGCTGCCACA

original cDNA sequence snippet

GTGAGGGGGACGCCCATGCCGGCTTCAACTTCGCTGCCACA

altered cDNA sequence snippet

GTGAGGGGGACGCCCATGCCAGCTTCAACTTCGCTGCCACA

wildtype AA sequence

MAVAIAAARV WRLNRGLSQA ALLLLRQPGA RGLARSHPPR QQQQFSSLDD KPQFPGASAE
FIDKLEFIQP NVISGIPIYR VMDRQGQIIN PSEDPHLPKE KVLKLYKSMT LLNTMDRILY
ESQRQGRISF YMTNYGEEGT HVGSAAALDN TDLVFGQYRE AGVLMYRDYP LELFMAQCYG
NISDLGKGRQ MPVHYGCKER HFVTISSPLA TQIPQAVGAA YAAKRANANR VVICYFGEGA
ASEGDAHAGF NFAATLECPI IFFCRNNGYA ISTPTSEQYR GDGIAARGPG YGIMSIRVDG
NDVFAVYNAT KEARRRAVAE NQPFLIEAMT YRIGHHSTSD DSSAYRSVDE VNYWDKQDHP
ISRLRHYLLS QGWWDEEQEK AWRKQSRRKV MEAFEQAERK PKPNPNLLFS DVYQEMPAQL
RKQQESLARH LQTYGEHYPL DHFDK*

mutated AA sequence

MAVAIAAARV WRLNRGLSQA ALLLLRQPGA RGLARSHPPR QQQQFSSLDD KPQFPGASAE
FIDKLEFIQP NVISGIPIYR VMDRQGQIIN PSEDPHLPKE KVLKLYKSMT LLNTMDRILY
ESQRQGRISF YMTNYGEEGT HVGSAAALDN TDLVFGQYRE AGVLMYRDYP LELFMAQCYG
NISDLGKGRQ MPVHYGCKER HFVTISSPLA TQIPQAVGAA YAAKRANANR VVICYFGEGA
ASEGDAHASF NFAATLECPI IFFCRNNGYA ISTPTSEQYR GDGIAARGPG YGIMSIRVDG
NDVFAVYNAT KEARRRAVAE NQPFLIEAMT YRIGHHSTSD DSSAYRSVDE VNYWDKQDHP
ISRLRHYLLS QGWWDEEQEK AWRKQSRRKV MEAFEQAERK PKPNPNLLFS DVYQEMPAQL
RKQQESLARH LQTYGEHYPL DHFDK*

speed

0.75 s

Problems

data problem

No NCBI gene ID found for this transcript

back to results table