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 3.239434 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
BCKDHA	disease_causing_automatic	0.999999999150751	simple_aae		affected	0	F412C	single base exchange	rs137852872		show file
BCKDHA	disease_causing_automatic	0.999999999239049	simple_aae		affected	0	F409C	single base exchange	rs137852872		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999150751 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM950136)
known disease mutation: rs2378 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:41930401T>GN/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.1235T>G
cDNA.1240T>G
g.27037T>G

AA changes

F412C Score: 205 explain score(s)

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

412

frameshift

known variant

Reference ID: rs137852872
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs2378 (pathogenic for Maple syrup urine disease type 1A|MAPLE SYRUP URINE DISEASE, INTERMEDIATE, TYPE IA) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950136)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950136)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950136)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.721	1
	4.721	1
(flanking)	2.114	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 marginally increased	27039	wt: 0.8077 / mu: 0.8766 (marginal change - not scored)	wt: TCTTCTCAGACGTGT mu: TCTGCTCAGACGTGT	TTCT\|caga
Donor gained	27036	0.46	mu: TACTCTGCTCAGACG	CTCT\|gctc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

412

mutated

not conserved

412

Ptroglodytes

all identical

ENSPTRG00000011025

409

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000060376

410

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000009706

410

Drerio

all identical

ENSDARG00000040555

410

Dmelanogaster

all identical

FBgn0037709

403

Celegans

all identical

Y39E4A.3

393

Xtropicalis

all identical

ENSXETG00000018753

372

protein features

start (aa)	end (aa)	feature	details
409	411	TURN		might get lost (downstream of altered splice site)
412	415	STRAND		lost
418	434	HELIX		might get lost (downstream of altered splice site)
435	437	HELIX		might get lost (downstream of altered splice site)
440	442	HELIX		might get lost (downstream of altered splice site)

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

1235

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

1240

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

27037

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

41930401

original gDNA sequence snippet

ACCCAACCCCAACCTACTCTTCTCAGACGTGTATCAGGAGA

altered gDNA sequence snippet

ACCCAACCCCAACCTACTCTGCTCAGACGTGTATCAGGAGA

original cDNA sequence snippet

ACCCAACCCCAACCTACTCTTCTCAGACGTGTATCAGGAGA

altered cDNA sequence snippet

ACCCAACCCCAACCTACTCTGCTCAGACGTGTATCAGGAGA

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

speed

0.88 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: 0.999999999239049 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM950136)
known disease mutation: rs2378 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:41930401T>GN/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.1226T>G
cDNA.1594T>G
g.27037T>G

AA changes

F409C Score: 205 explain score(s)

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

409

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.721	1
	4.721	1
(flanking)	2.114	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 marginally increased	27039	wt: 0.8077 / mu: 0.8766 (marginal change - not scored)	wt: TCTTCTCAGACGTGT mu: TCTGCTCAGACGTGT	TTCT\|caga
Donor gained	27036	0.46	mu: TACTCTGCTCAGACG	CTCT\|gctc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

409

mutated

not conserved

409

Ptroglodytes

all identical

ENSPTRG00000011025

409

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000060376

410

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000009706

410

Drerio

all identical

ENSDARG00000040555

410

Dmelanogaster

all identical

FBgn0037709

403

Celegans

all identical

Y39E4A.3

393

Xtropicalis

all identical

ENSXETG00000018753

372

protein features

start (aa)	end (aa)	feature	details
405	408	HELIX		might get lost (downstream of altered splice site)
409	411	TURN		lost
412	415	STRAND		might get lost (downstream of altered splice site)
418	434	HELIX		might get lost (downstream of altered splice site)
435	437	HELIX		might get lost (downstream of altered splice site)
440	442	HELIX		might get lost (downstream of altered splice site)

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

1226

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

1594

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

27037

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

41930401

original gDNA sequence snippet

ACCCAACCCCAACCTACTCTTCTCAGACGTGTATCAGGAGA

altered gDNA sequence snippet

ACCCAACCCCAACCTACTCTGCTCAGACGTGTATCAGGAGA

original cDNA sequence snippet

ACCCAACCCCAACCTACTCTTCTCAGACGTGTATCAGGAGA

altered cDNA sequence snippet

ACCCAACCCCAACCTACTCTGCTCAGACGTGTATCAGGAGA

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

speed

0.38 s

Problems

data problem

No NCBI gene ID found for this transcript

back to results table