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 2.610117 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GBE1	disease_causing_automatic	0.999935694678671	simple_aae		affected	0	F257L	single base exchange	rs137852887		show file
GBE1	disease_causing_automatic	0.999935694678671	simple_aae		affected	0	F216L	single base exchange	rs137852887		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999935694678671 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM960704)
known disease mutation: rs2780 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:81695554A>TN/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.771T>A
cDNA.1415T>A
g.115759T>A

AA changes

F257L Score: 22 explain score(s)

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

257

frameshift

known variant

Reference ID: rs137852887
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs2780 (pathogenic for Glycogen storage disease, type IV|Glycogen storage disease IV, classic hepatic|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960704)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960704)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960704)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.619	1
	3.121	1
(flanking)	4.656	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 decreased	115770	wt: 0.95 / mu: 0.81	wt: AAGCTTCTTTGCAGCTTCCAGGTAAAATCAGAGACTCATTG mu: AAGCTTCTTAGCAGCTTCCAGGTAAAATCAGAGACTCATTG	ccag\|GTAA
Donor gained	115759	0.38	mu: TTCTTAGCAGCTTCC	CTTA\|gcag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

257

mutated

not conserved

257

Ptroglodytes

all identical

ENSPTRG00000015119

257

Mmulatta

all identical

ENSMMUG00000015877

257

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000022707

257

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all conserved

FBgn0053138

242

Celegans

all identical

T04A8.7

238

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
357	357	ACT_SITE	Nucleophile (By similarity).	might get lost (downstream of altered splice site)
412	412	ACT_SITE	Proton donor (By similarity).	might get lost (downstream of altered splice site)

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

771

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

1415

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

115759

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

81695554

original gDNA sequence snippet

TACCAAATCACAAGCTTCTTTGCAGCTTCCAGGTAAAATCA

altered gDNA sequence snippet

TACCAAATCACAAGCTTCTTAGCAGCTTCCAGGTAAAATCA

original cDNA sequence snippet

TACCAAATCACAAGCTTCTTTGCAGCTTCCAGCCGTTATGG

altered cDNA sequence snippet

TACCAAATCACAAGCTTCTTAGCAGCTTCCAGCCGTTATGG

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 YQITSFLAAS 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*

speed

0.54 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: 0.999935694678671 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM960704)
known disease mutation: rs2780 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:81695554A>TN/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.648T>A
cDNA.701T>A
g.115759T>A

AA changes

F216L Score: 22 explain score(s)

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

216

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.619	1
	3.121	1
(flanking)	4.656	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 decreased	115770	wt: 0.95 / mu: 0.81	wt: AAGCTTCTTTGCAGCTTCCAGGTAAAATCAGAGACTCATTG mu: AAGCTTCTTAGCAGCTTCCAGGTAAAATCAGAGACTCATTG	ccag\|GTAA
Donor gained	115759	0.38	mu: TTCTTAGCAGCTTCC	CTTA\|gcag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

216

mutated

not conserved

216

Ptroglodytes

all identical

ENSPTRG00000015119

257

Mmulatta

all identical

ENSMMUG00000015877

257

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000022707

257

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all conserved

FBgn0053138

242

Celegans

all identical

T04A8.7

238

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
357	357	ACT_SITE	Nucleophile (By similarity).	might get lost (downstream of altered splice site)
412	412	ACT_SITE	Proton donor (By similarity).	might get lost (downstream of altered splice site)

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

648

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

701

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

115759

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

81695554

original gDNA sequence snippet

TACCAAATCACAAGCTTCTTTGCAGCTTCCAGGTAAAATCA

altered gDNA sequence snippet

TACCAAATCACAAGCTTCTTAGCAGCTTCCAGGTAAAATCA

original cDNA sequence snippet

TACCAAATCACAAGCTTCTTTGCAGCTTCCAGCCGTTATGG

altered cDNA sequence snippet

TACCAAATCACAAGCTTCTTAGCAGCTTCCAGCCGTTATGG

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 QITSFLAASS 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*

speed

0.57 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems