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: ENST00000378842
Querying Taster for transcript #2: ENST00000450095
MT speed 0 s - this script 4.012051 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GALT	disease_causing_automatic	6.77962102707338e-06	simple_aae		affected	0	T23A	single base exchange	rs111033635		show file
GALT	disease_causing_automatic	0.972932873431959	without_aae		affected	0		single base exchange	rs111033635		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 6.77962102707338e-06 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM013716)
known disease mutation: rs25118 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:34646768A>GN/A show variant in all transcripts IGV

HGNC symbol

GALT

Ensembl transcript ID

ENST00000378842

Genbank transcript ID

NM_000155

UniProt peptide

P07902

alteration type

single base exchange

alteration region

CDS

DNA changes

c.67A>G
cDNA.109A>G
g.8639A>G

AA changes

T23A Score: 58 explain score(s)

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

frameshift

known variant

Reference ID: rs111033635
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs25118 (pathogenic for Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM013716)

known disease mutation at this position, please check HGMD for details (HGMD ID CM013716)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013716)

regulatory features

Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
CTCF, Transcription Factor, CCCTC-binding factor
Cfos, Transcription Factor, Cfos TF binding
Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
H2AZ, Histone, Histone 2A variant Z
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K5ac, Histone, Histone 4 Lysine 5 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Tcf12, Transcription Factor, Tcf12 Transcription Factor Binding
USF1, Transcription Factor, USF1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.411	0
	-1.889	0
(flanking)	1.167	0.833

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
Acc gained	8646	0.31	mu: CGCCGCAGCAGCAGCCTTCCGGGCAAACGGTAACTGCACCG	tccg\|GGCA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000020886

Mmulatta

all identical

ENSMMUG00000020789

Fcatus

not conserved

ENSFCAG00000016304

Mmusculus

all identical

ENSMUSG00000036073

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000016445

Drerio

all identical

ENSDARG00000069543

Dmelanogaster

no alignment

FBgn0263200

n/a

Celegans

no alignment

ZK1058.3

n/a

Xtropicalis

no alignment

ENSXETG00000013206

n/a

protein features

start (aa)	end (aa)	feature	details
75	75	METAL	Zinc (Potential).	might get lost (downstream of altered splice site)
184	184	METAL	Zinc (Potential).	might get lost (downstream of altered splice site)
186	186	ACT_SITE	Tele-UMP-histidine intermediate (By similarity).	might get lost (downstream of altered splice site)
202	202	METAL	Iron (Potential).	might get lost (downstream of altered splice site)
258	259	CONFLICT	RR -> VG (in Ref. 1; AAC83409).	might get lost (downstream of altered splice site)
301	301	METAL	Iron (Potential).	might get lost (downstream of altered splice site)
319	319	METAL	Iron (Potential).	might get lost (downstream of altered splice site)
321	321	METAL	Iron (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1140 / 1140

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

380 / 380

position of stopcodon in wt / mu cDNA

1182 / 1182

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

43 / 43

chromosome

strand

last intron/exon boundary

1102

theoretical NMD boundary in CDS

1009

length of CDS

1140

coding sequence (CDS) position

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

109

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

8639

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

34646768

original gDNA sequence snippet

AGGCGGACGCCGCAGCAGCAACCTTCCGGGCAAACGGTAAC

altered gDNA sequence snippet

AGGCGGACGCCGCAGCAGCAGCCTTCCGGGCAAACGGTAAC

original cDNA sequence snippet

AGGCGGACGCCGCAGCAGCAACCTTCCGGGCAAACGACCAT

altered cDNA sequence snippet

AGGCGGACGCCGCAGCAGCAGCCTTCCGGGCAAACGACCAT

wildtype AA sequence

MSRSGTDPQQ RQQASEADAA AATFRANDHQ HIRYNPLQDE WVLVSAHRMK RPWQGQVEPQ
LLKTVPRHDP LNPLCPGAIR ANGEVNPQYD STFLFDNDFP ALQPDAPSPG PSDHPLFQAK
SARGVCKVMC FHPWSDVTLP LMSVPEIRAV VDAWASVTEE LGAQYPWVQI FENKGAMMGC
SNPHPHCQVW ASSFLPDIAQ REERSQQAYK SQHGEPLLME YSRQELLRKE RLVLTSEHWL
VLVPFWATWP YQTLLLPRRH VRRLPELTPA ERDDLASIMK KLLTKYDNLF ETSFPYSMGW
HGAPTGSEAG ANWNHWQLHA HYYPPLLRSA TVRKFMVGYE MLAQAQRDLT PEQAAERLRA
LPEVHYHLGQ KDRETATIA*

mutated AA sequence

MSRSGTDPQQ RQQASEADAA AAAFRANDHQ HIRYNPLQDE WVLVSAHRMK RPWQGQVEPQ
LLKTVPRHDP LNPLCPGAIR ANGEVNPQYD STFLFDNDFP ALQPDAPSPG PSDHPLFQAK
SARGVCKVMC FHPWSDVTLP LMSVPEIRAV VDAWASVTEE LGAQYPWVQI FENKGAMMGC
SNPHPHCQVW ASSFLPDIAQ REERSQQAYK SQHGEPLLME YSRQELLRKE RLVLTSEHWL
VLVPFWATWP YQTLLLPRRH VRRLPELTPA ERDDLASIMK KLLTKYDNLF ETSFPYSMGW
HGAPTGSEAG ANWNHWQLHA HYYPPLLRSA TVRKFMVGYE MLAQAQRDLT PEQAAERLRA
LPEVHYHLGQ KDRETATIA*

speed

1.65 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: without_aae, prob: 0.972932873431959 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM013716)
known disease mutation: rs25118 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:34646768A>GN/A show variant in all transcripts IGV

HGNC symbol

GALT

Ensembl transcript ID

ENST00000450095

Genbank transcript ID

NM_001258332

UniProt peptide

P07902

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.136A>G
g.8639A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.411	0
	-1.889	0
(flanking)	1.167	0.833

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

splice sites

splice site change before start ATG (at aa -42) |

effect	gDNA position	score	detection sequence	exon-intron border
Acc gained	8646	0.31	mu: CGCCGCAGCAGCAGCCTTCCGGGCAAACGGTAACTGCACCG	tccg\|GGCA

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
75	75	METAL	Zinc (Potential).	might get lost (downstream of altered splice site)
184	184	METAL	Zinc (Potential).	might get lost (downstream of altered splice site)
186	186	ACT_SITE	Tele-UMP-histidine intermediate (By similarity).	might get lost (downstream of altered splice site)
202	202	METAL	Iron (Potential).	might get lost (downstream of altered splice site)
258	259	CONFLICT	RR -> VG (in Ref. 1; AAC83409).	might get lost (downstream of altered splice site)
301	301	METAL	Iron (Potential).	might get lost (downstream of altered splice site)
319	319	METAL	Iron (Potential).	might get lost (downstream of altered splice site)
321	321	METAL	Iron (Potential).	might get lost (downstream of altered splice site)

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

N/A

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

N/A

position of start ATG in wt / mu cDNA

272 / 272

chromosome

strand

last intron/exon boundary

1004

theoretical NMD boundary in CDS

682

length of CDS

813

coding sequence (CDS) position

N/A

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

136

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

8639

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

34646768

original gDNA sequence snippet

AGGCGGACGCCGCAGCAGCAACCTTCCGGGCAAACGGTAAC

altered gDNA sequence snippet

AGGCGGACGCCGCAGCAGCAGCCTTCCGGGCAAACGGTAAC

original cDNA sequence snippet

AGGCGGACGCCGCAGCAGCAACCTTCCGGGCAAACGACCAT

altered cDNA sequence snippet

AGGCGGACGCCGCAGCAGCAGCCTTCCGGGCAAACGACCAT

wildtype AA sequence

MTLSTLCVLG PSEPTESKVM CFHPWSDVTL PLMSVPEIRA VVDAWASVTE ELGAQYPWVQ
IFENKGAMMG CSNPHPHCQV WASSFLPDIA QREERSQQAY KSQHGEPLLM EYSRQELLRK
ERLVLTSEHW LVLVPFWATW PYQTLLLPRR HVRRLPELTP AERDDLASIM KKLLTKYDNL
FETSFPYSMG WHGAPTGSEA GANWNHWQLH AHYYPPLLRS ATVRKFMVGY EMLAQAQRDL
TPEQAAERLR ALPEVHYHLG QKDRETATIA *

mutated AA sequence

N/A

speed

0.36 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems