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: ENST00000429644
Querying Taster for transcript #2: ENST00000489715
MT speed 0 s - this script 4.73149 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GBE1	disease_causing_automatic	0.999999999702729	simple_aae		affected	0	R515C	single base exchange	rs80338672		show file
GBE1	disease_causing_automatic	0.999999999702729	simple_aae		affected	0	R474C	single base exchange	rs80338672		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999702729 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM960706)
known disease mutation: rs2779 (pathogenic)
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:81627151G>AN/A show variant in all transcripts IGV

HGNC symbol

GBE1

Ensembl transcript ID

ENST00000429644

Genbank transcript ID

NM_000158

UniProt peptide

Q04446

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1543C>T
cDNA.2187C>T
g.184162C>T

AA changes

R515C Score: 180 explain score(s)

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

515

frameshift

known variant

Reference ID: rs80338672

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	6	6

known disease mutation: rs2779 (pathogenic for Glycogen storage disease, type IV|Inborn genetic diseases|Glycogen storage disease IV, classic hepatic) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960706)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960706)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960706)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.801	1
	5.801	1
(flanking)	1.722	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
Acc increased	184152	wt: 0.64 / mu: 0.76	wt: GTCCTGACTCCTTTTACTCCAGTTATTGATCGTGGAATACA mu: GTCCTGACTCCTTTTACTCCAGTTATTGATTGTGGAATACA	tcca\|GTTA
Acc increased	184166	wt: 0.34 / mu: 0.56	wt: TACTCCAGTTATTGATCGTGGAATACAGCTTCATAAAATGA mu: TACTCCAGTTATTGATTGTGGAATACAGCTTCATAAAATGA	gtgg\|AATA
Acc marginally increased	184162	wt: 0.2071 / mu: 0.2161 (marginal change - not scored)	wt: CTTTTACTCCAGTTATTGATCGTGGAATACAGCTTCATAAA mu: CTTTTACTCCAGTTATTGATTGTGGAATACAGCTTCATAAA	gatc\|GTGG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

515

mutated

not conserved

515

Ptroglodytes

all identical

ENSPTRG00000015119

515

Mmulatta

all identical

ENSMMUG00000015877

515

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000022707

515

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all identical

FBgn0053138

500

Celegans

all identical

T04A8.7

496

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2109 / 2109

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

703 / 703

position of stopcodon in wt / mu cDNA

2753 / 2753

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

645 / 645

chromosome

strand

-1

last intron/exon boundary

2697

theoretical NMD boundary in CDS

2002

length of CDS

2109

coding sequence (CDS) position

1543

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

2187

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

184162

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

81627151

original gDNA sequence snippet

CTTTTACTCCAGTTATTGATCGTGGAATACAGCTTCATAAA

altered gDNA sequence snippet

CTTTTACTCCAGTTATTGATTGTGGAATACAGCTTCATAAA

original cDNA sequence snippet

CTTTTACTCCAGTTATTGATCGTGGAATACAGCTTCATAAA

altered cDNA sequence snippet

CTTTTACTCCAGTTATTGATTGTGGAATACAGCTTCATAAA

wildtype AA sequence

MAAPMTPAAR PEDYEAALNA ALADVPELAR LLEIDPYLKP YAVDFQRRYK QFSQILKNIG
ENEGGIDKFS RGYESFGVHR CADGGLYCKE WAPGAEGVFL TGDFNGWNPF SYPYKKLDYG
KWELYIPPKQ NKSVLVPHGS KLKVVITSKS GEILYRISPW AKYVVREGDN VNYDWIHWDP
EHSYEFKHSR PKKPRSLRIY ESHVGISSHE GKVASYKHFT CNVLPRIKGL GYNCIQLMAI
MEHAYYASFG YQITSFFAAS SRYGTPEELQ ELVDTAHSMG IIVLLDVVHS HASKNSADGL
NMFDGTDSCY FHSGPRGTHD LWDSRLFAYS SWEILRFLLS NIRWWLEEYR FDGFRFDGVT
SMLYHHHGVG QGFSGDYSEY FGLQVDEDAL TYLMLANHLV HTLCPDSITI AEDVSGMPAL
CSPISQGGGG FDYRLAMAIP DKWIQLLKEF KDEDWNMGDI VYTLTNRRYL EKCIAYAESH
DQALVGDKSL AFWLMDAEMY TNMSVLTPFT PVIDRGIQLH KMIRLITHGL GGEGYLNFMG
NEFGHPEWLD FPRKGNNESY HYARRQFHLT DDDLLRYKFL NNFDRDMNRL EERYGWLAAP
QAYVSEKHEG NKIIAFERAG LLFIFNFHPS KSYTDYRVGT ALPGKFKIVL DSDAAEYGGH
QRLDHSTDFF SEAFEHNGRP YSLLVYIPSR VALILQNVDL PN*

mutated AA sequence

MAAPMTPAAR PEDYEAALNA ALADVPELAR LLEIDPYLKP YAVDFQRRYK QFSQILKNIG
ENEGGIDKFS RGYESFGVHR CADGGLYCKE WAPGAEGVFL TGDFNGWNPF SYPYKKLDYG
KWELYIPPKQ NKSVLVPHGS KLKVVITSKS GEILYRISPW AKYVVREGDN VNYDWIHWDP
EHSYEFKHSR PKKPRSLRIY ESHVGISSHE GKVASYKHFT CNVLPRIKGL GYNCIQLMAI
MEHAYYASFG YQITSFFAAS SRYGTPEELQ ELVDTAHSMG IIVLLDVVHS HASKNSADGL
NMFDGTDSCY FHSGPRGTHD LWDSRLFAYS SWEILRFLLS NIRWWLEEYR FDGFRFDGVT
SMLYHHHGVG QGFSGDYSEY FGLQVDEDAL TYLMLANHLV HTLCPDSITI AEDVSGMPAL
CSPISQGGGG FDYRLAMAIP DKWIQLLKEF KDEDWNMGDI VYTLTNRRYL EKCIAYAESH
DQALVGDKSL AFWLMDAEMY TNMSVLTPFT PVIDCGIQLH KMIRLITHGL GGEGYLNFMG
NEFGHPEWLD FPRKGNNESY HYARRQFHLT DDDLLRYKFL NNFDRDMNRL EERYGWLAAP
QAYVSEKHEG NKIIAFERAG LLFIFNFHPS KSYTDYRVGT ALPGKFKIVL DSDAAEYGGH
QRLDHSTDFF SEAFEHNGRP YSLLVYIPSR VALILQNVDL PN*

speed

1.38 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: 0.999999999702729 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM960706)
known disease mutation: rs2779 (pathogenic)
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:81627151G>AN/A show variant in all transcripts IGV

HGNC symbol

GBE1

Ensembl transcript ID

ENST00000489715

Genbank transcript ID

N/A

UniProt peptide

Q04446

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1420C>T
cDNA.1473C>T
g.184162C>T

AA changes

R474C Score: 180 explain score(s)

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

474

frameshift

known variant

Reference ID: rs80338672

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	6	6

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.801	1
	5.801	1
(flanking)	1.722	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
Acc increased	184152	wt: 0.64 / mu: 0.76	wt: GTCCTGACTCCTTTTACTCCAGTTATTGATCGTGGAATACA mu: GTCCTGACTCCTTTTACTCCAGTTATTGATTGTGGAATACA	tcca\|GTTA
Acc increased	184166	wt: 0.34 / mu: 0.56	wt: TACTCCAGTTATTGATCGTGGAATACAGCTTCATAAAATGA mu: TACTCCAGTTATTGATTGTGGAATACAGCTTCATAAAATGA	gtgg\|AATA
Acc marginally increased	184162	wt: 0.2071 / mu: 0.2161 (marginal change - not scored)	wt: CTTTTACTCCAGTTATTGATCGTGGAATACAGCTTCATAAA mu: CTTTTACTCCAGTTATTGATTGTGGAATACAGCTTCATAAA	gatc\|GTGG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

474

mutated

not conserved

474

Ptroglodytes

all identical

ENSPTRG00000015119

515

Mmulatta

all identical

ENSMMUG00000015877

515

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000022707

515

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all identical

FBgn0053138

500

Celegans

all identical

T04A8.7

496

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1986 / 1986

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

662 / 662

position of stopcodon in wt / mu cDNA

2039 / 2039

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

54 / 54

chromosome

strand

-1

last intron/exon boundary

1983

theoretical NMD boundary in CDS

1879

length of CDS

1986

coding sequence (CDS) position

1420

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

1473

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

184162

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

81627151

original gDNA sequence snippet

CTTTTACTCCAGTTATTGATCGTGGAATACAGCTTCATAAA

altered gDNA sequence snippet

CTTTTACTCCAGTTATTGATTGTGGAATACAGCTTCATAAA

original cDNA sequence snippet

CTTTTACTCCAGTTATTGATCGTGGAATACAGCTTCATAAA

altered cDNA sequence snippet

CTTTTACTCCAGTTATTGATTGTGGAATACAGCTTCATAAA

wildtype AA sequence

MNLAKVRYKQ FSQILKNIGE NEGGIDKFSR GYESFGVHRC ADGGLYCKEW APGAEGVFLT
GDFNGWNPFS YPYKKLDYGK WELYIPPKQN KSVLVPHGSK LKVVITSKSG EILYRISPWA
KYVVREGDNV NYDWIHWDPE HSYEFKHSRP KKPRSLRIYE SHVGISSHEG KVASYKHFTC
NVLPRIKGLG YNCIQLMAIM EHAYYASFGY QITSFFAASS RYGTPEELQE LVDTAHSMGI
IVLLDVVHSH ASKNSADGLN MFDGTDSCYF HSGPRGTHDL WDSRLFAYSS WEILRFLLSN
IRWWLEEYRF DGFRFDGVTS MLYHHHGVGQ GFSGDYSEYF GLQVDEDALT YLMLANHLVH
TLCPDSITIA EDVSGMPALC SPISQGGGGF DYRLAMAIPD KWIQLLKEFK DEDWNMGDIV
YTLTNRRYLE KCIAYAESHD QALVGDKSLA FWLMDAEMYT NMSVLTPFTP VIDRGIQLHK
MIRLITHGLG GEGYLNFMGN EFGHPEWLDF PRKGNNESYH YARRQFHLTD DDLLRYKFLN
NFDRDMNRLE ERYGWLAAPQ AYVSEKHEGN KIIAFERAGL LFIFNFHPSK SYTDYRVGTA
LPGKFKIVLD SDAAEYGGHQ RLDHSTDFFS EAFEHNGRPY SLLVYIPSRV ALILQNVDLP
N*

mutated AA sequence

MNLAKVRYKQ FSQILKNIGE NEGGIDKFSR GYESFGVHRC ADGGLYCKEW APGAEGVFLT
GDFNGWNPFS YPYKKLDYGK WELYIPPKQN KSVLVPHGSK LKVVITSKSG EILYRISPWA
KYVVREGDNV NYDWIHWDPE HSYEFKHSRP KKPRSLRIYE SHVGISSHEG KVASYKHFTC
NVLPRIKGLG YNCIQLMAIM EHAYYASFGY QITSFFAASS RYGTPEELQE LVDTAHSMGI
IVLLDVVHSH ASKNSADGLN MFDGTDSCYF HSGPRGTHDL WDSRLFAYSS WEILRFLLSN
IRWWLEEYRF DGFRFDGVTS MLYHHHGVGQ GFSGDYSEYF GLQVDEDALT YLMLANHLVH
TLCPDSITIA EDVSGMPALC SPISQGGGGF DYRLAMAIPD KWIQLLKEFK DEDWNMGDIV
YTLTNRRYLE KCIAYAESHD QALVGDKSLA FWLMDAEMYT NMSVLTPFTP VIDCGIQLHK
MIRLITHGLG GEGYLNFMGN EFGHPEWLDF PRKGNNESYH YARRQFHLTD DDLLRYKFLN
NFDRDMNRLE ERYGWLAAPQ AYVSEKHEGN KIIAFERAGL LFIFNFHPSK SYTDYRVGTA
LPGKFKIVLD SDAAEYGGHQ RLDHSTDFFS EAFEHNGRPY SLLVYIPSRV ALILQNVDLP
N*

speed

1.35 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems