mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.983878537466475 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM057090)
known disease mutation at this position (HGMD CM980840)
known disease mutation: rs4323 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:155206086G>CN/A show variant in all transcripts IGV

HGNC symbol

GBA

Ensembl transcript ID

ENST00000536770

Genbank transcript ID

N/A

UniProt peptide

P04062

alteration type

single base exchange

alteration region

CDS

DNA changes

c.835C>G
cDNA.949C>G
g.8568C>G

AA changes

R279G Score: 125 explain score(s)

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

279

frameshift

known variant

Reference ID: rs121908308
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs4323 (pathogenic for Subacute neuronopathic Gaucher's disease) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980840)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980840)
known disease mutation at this position, please check HGMD for details (HGMD ID CM057090)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980840)
known disease mutation at this position, please check HGMD for details (HGMD ID CM057090)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980840)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.382	1
	2.439	1
(flanking)	1.043	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 gained	8562	0.58	mu: AGCAGAGTGTGGGGC	CAGA\|gtgt

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

279

mutated

not conserved

279

Ptroglodytes

all identical

ENSPTRG00000001416

392

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000028048

371

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000010884

378

Drerio

all identical

ENSDARG00000076058

374

Dmelanogaster

not conserved

FBgn0051148

418

Celegans

all conserved

Y4C6B.6

373

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
275	279	HELIX		lost
284	286	STRAND		might get lost (downstream of altered splice site)
292	301	HELIX		might get lost (downstream of altered splice site)
303	308	HELIX		might get lost (downstream of altered splice site)
309	309	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
311	314	TURN		might get lost (downstream of altered splice site)
315	323	STRAND		might get lost (downstream of altered splice site)
324	326	HELIX		might get lost (downstream of altered splice site)
329	335	HELIX		might get lost (downstream of altered splice site)
338	341	HELIX		might get lost (downstream of altered splice site)
346	352	STRAND		might get lost (downstream of altered splice site)
354	356	HELIX		might get lost (downstream of altered splice site)
359	369	HELIX		might get lost (downstream of altered splice site)
373	381	STRAND		might get lost (downstream of altered splice site)
379	379	ACT_SITE	Nucleophile.	might get lost (downstream of altered splice site)
379	379	MUTAGEN	E->G: Decreases activity 1000-fold.	might get lost (downstream of altered splice site)
386	388	STRAND		might get lost (downstream of altered splice site)
396	411	HELIX		might get lost (downstream of altered splice site)
414	424	STRAND		might get lost (downstream of altered splice site)
426	428	STRAND		might get lost (downstream of altered splice site)
440	444	STRAND		might get lost (downstream of altered splice site)
445	447	HELIX		might get lost (downstream of altered splice site)
449	452	STRAND		might get lost (downstream of altered splice site)
454	463	HELIX		might get lost (downstream of altered splice site)
470	470	CONFLICT	S -> I (in Ref. 15; AA sequence).	might get lost (downstream of altered splice site)
471	479	STRAND		might get lost (downstream of altered splice site)
482	489	STRAND		might get lost (downstream of altered splice site)
495	501	STRAND		might get lost (downstream of altered splice site)
501	501	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
503	505	STRAND		might get lost (downstream of altered splice site)
507	513	STRAND		might get lost (downstream of altered splice site)
514	516	TURN		might get lost (downstream of altered splice site)
517	523	STRAND		might get lost (downstream of altered splice site)
527	533	STRAND		might get lost (downstream of altered splice site)
534	534	CONFLICT	R -> H (in Ref. 1; AAA35873).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1272 / 1272

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

424 / 424

position of stopcodon in wt / mu cDNA

1386 / 1386

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

115 / 115

chromosome

strand

-1

last intron/exon boundary

1281

theoretical NMD boundary in CDS

1116

length of CDS

1272

coding sequence (CDS) position

835

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

949

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

8568

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

155206086

original gDNA sequence snippet

AGTTCTGGGAGCAGAGTGTGCGGCTAGGCTCCTGGGATCGA

altered gDNA sequence snippet

AGTTCTGGGAGCAGAGTGTGGGGCTAGGCTCCTGGGATCGA

original cDNA sequence snippet

AGTTCTGGGAGCAGAGTGTGCGGCTAGGCTCCTGGGATCGA

altered cDNA sequence snippet

AGTTCTGGGAGCAGAGTGTGGGGCTAGGCTCCTGGGATCGA

wildtype AA sequence

MEFSSPSREE CPKPLSRVSI MAGSLTGLLL LQAVSWASGI GYNIIRVPMA SCDFSIRTYT
YADTPDDFQL HNFSLPEEDT KLKIPLIHRA LQLAQRPVSL LASPWTSPTW LKTNGAVNGK
GSLKGQPGDI YHQTWARYFV KFLDAYAEHK LQFWAVTAEN EPSAGLLSGY PFQCLGFTPE
HQRDFIARDL GPTLANSTHH NVRLLMLDDQ RLLLPHWAKV VLTDPEAAKY VHGIAVHWYL
DFLAPAKATL GETHRLFPNT MLFASEACVG SKFWEQSVRL GSWDRGMQYS HSIITNLLYH
VVGWTDWNLA LNPEGGPNWV RNFVDSPIIV DITKDTFYKQ PMFYHLGHFS KFIPEGSQRV
GLVASQKNDL DAVALMHPDG SAVVVVLNRS SKDVPLTIKD PAVGFLETIS PGYSIHTYLW
RRQ*

mutated AA sequence

MEFSSPSREE CPKPLSRVSI MAGSLTGLLL LQAVSWASGI GYNIIRVPMA SCDFSIRTYT
YADTPDDFQL HNFSLPEEDT KLKIPLIHRA LQLAQRPVSL LASPWTSPTW LKTNGAVNGK
GSLKGQPGDI YHQTWARYFV KFLDAYAEHK LQFWAVTAEN EPSAGLLSGY PFQCLGFTPE
HQRDFIARDL GPTLANSTHH NVRLLMLDDQ RLLLPHWAKV VLTDPEAAKY VHGIAVHWYL
DFLAPAKATL GETHRLFPNT MLFASEACVG SKFWEQSVGL GSWDRGMQYS HSIITNLLYH
VVGWTDWNLA LNPEGGPNWV RNFVDSPIIV DITKDTFYKQ PMFYHLGHFS KFIPEGSQRV
GLVASQKNDL DAVALMHPDG SAVVVVLNRS SKDVPLTIKD PAVGFLETIS PGYSIHTYLW
RRQ*

speed

0.13 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