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 3.486819 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GALT	disease_causing_automatic	0.998809032173999	simple_aae		affected	0	R201C	single base exchange	rs111033739		show file
GALT	disease_causing_automatic	0.998938266579421	simple_aae		affected	0	R92C	single base exchange	rs111033739		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.998809032173999 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM074212)
known disease mutation: rs25226 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:34648367C>TN/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.601C>T
cDNA.643C>T
g.10238C>T

AA changes

R201C Score: 180 explain score(s)

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

201

frameshift

known variant

Reference ID: rs111033739

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

known disease mutation: rs25226 (pathogenic for Galactosemia|Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase|not specified|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM074212)

known disease mutation at this position, please check HGMD for details (HGMD ID CM074212)
known disease mutation at this position, please check HGMD for details (HGMD ID CM074212)

regulatory features

H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.37	1
	1.881	1
(flanking)	1.087	0.997

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 marginally increased	10240	wt: 0.3591 / mu: 0.4355 (marginal change - not scored)	wt: CTGCCAGATATTGCCCAGCGTGAGGAGCGATCTCAGCAGGC mu: CTGCCAGATATTGCCCAGTGTGAGGAGCGATCTCAGCAGGC	gcgt\|GAGG
Donor increased	10242	wt: 0.38 / mu: 0.55	wt: GCGTGAGGAGCGATC mu: GTGTGAGGAGCGATC	GTGA\|ggag
Donor increased	10231	wt: 0.41 / mu: 0.96	wt: GATATTGCCCAGCGT mu: GATATTGCCCAGTGT	TATT\|gccc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

201

mutated

not conserved

201

Ptroglodytes

all identical

ENSPTRG00000020886

201

Mmulatta

all identical

ENSMMUG00000020789

201

Fcatus

all identical

ENSFCAG00000016304

201

Mmusculus

all identical

ENSMUSG00000036073

182

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000016445

186

Drerio

not conserved

ENSDARG00000069543

186

Dmelanogaster

not conserved

FBgn0263200

180

Celegans

all conserved

ZK1058.3

182

Xtropicalis

not conserved

ENSXETG00000013206

164

LVII

protein features

start (aa)	end (aa)	feature	details
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

601

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

643

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

10238

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

34648367

original gDNA sequence snippet

TCCTGCCAGATATTGCCCAGCGTGAGGAGCGATCTCAGCAG

altered gDNA sequence snippet

TCCTGCCAGATATTGCCCAGTGTGAGGAGCGATCTCAGCAG

original cDNA sequence snippet

TCCTGCCAGATATTGCCCAGCGTGAGGAGCGATCTCAGCAG

altered cDNA sequence snippet

TCCTGCCAGATATTGCCCAGTGTGAGGAGCGATCTCAGCAG

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

speed

0.33 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: 0.998938266579421 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM074212)
known disease mutation: rs25226 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:34648367C>TN/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

CDS

DNA changes

c.274C>T
cDNA.545C>T
g.10238C>T

AA changes

R92C Score: 180 explain score(s)

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

frameshift

known variant

Reference ID: rs111033739

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

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.37	1
	1.881	1
(flanking)	1.087	0.997

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 marginally increased	10240	wt: 0.3591 / mu: 0.4355 (marginal change - not scored)	wt: CTGCCAGATATTGCCCAGCGTGAGGAGCGATCTCAGCAGGC mu: CTGCCAGATATTGCCCAGTGTGAGGAGCGATCTCAGCAGGC	gcgt\|GAGG
Donor increased	10242	wt: 0.38 / mu: 0.55	wt: GCGTGAGGAGCGATC mu: GTGTGAGGAGCGATC	GTGA\|ggag
Donor increased	10231	wt: 0.41 / mu: 0.96	wt: GATATTGCCCAGCGT mu: GATATTGCCCAGTGT	TATT\|gccc

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

201

Mmulatta

all identical

ENSMMUG00000020789

201

Fcatus

all identical

ENSFCAG00000016304

201

Mmusculus

all identical

ENSMUSG00000036073

182

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000016445

186

Drerio

not conserved

ENSDARG00000069543

186

Dmelanogaster

not conserved

FBgn0263200

180

Celegans

all conserved

ZK1058.3

182

Xtropicalis

no alignment

ENSXETG00000013206

n/a

protein features

start (aa)	end (aa)	feature	details
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

813 / 813

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

271 / 271

position of stopcodon in wt / mu cDNA

1084 / 1084

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

274

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

545

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

10238

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

34648367

original gDNA sequence snippet

TCCTGCCAGATATTGCCCAGCGTGAGGAGCGATCTCAGCAG

altered gDNA sequence snippet

TCCTGCCAGATATTGCCCAGTGTGAGGAGCGATCTCAGCAG

original cDNA sequence snippet

TCCTGCCAGATATTGCCCAGCGTGAGGAGCGATCTCAGCAG

altered cDNA sequence snippet

TCCTGCCAGATATTGCCCAGTGTGAGGAGCGATCTCAGCAG

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

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

speed

1.16 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems