mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999791904194 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM960692)
known disease mutation: rs4296 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:155209730C>TN/A show variant in all transcripts IGV

HGNC symbol

GBA

Ensembl transcript ID

ENST00000427500

Genbank transcript ID

NM_001171812

UniProt peptide

P04062

alteration type

single base exchange

alteration region

CDS

DNA changes

c.254G>A
cDNA.417G>A
g.4924G>A

AA changes

G85E Score: 98 explain score(s)

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

frameshift

known variant

Reference ID: rs77829017

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

known disease mutation: rs4296 (pathogenic for Gaucher's disease, type 1|Gaucher disease) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960692)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960692)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960692)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.337	0.843
	4.243	0.995
(flanking)	4.243	0.995

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 marginally increased	4917	wt: 0.9183 / mu: 0.9459 (marginal change - not scored)	wt: GTACACGCAGTGGGC mu: GTACACGCAGTGAGC	ACAC\|gcag
Donor marginally increased	4924	wt: 0.9316 / mu: 0.9975 (marginal change - not scored)	wt: CAGTGGGCGACGGAT mu: CAGTGAGCGACGGAT	GTGG\|gcga
Donor increased	4920	wt: 0.37 / mu: 0.90	wt: CACGCAGTGGGCGAC mu: CACGCAGTGAGCGAC	CGCA\|gtgg
Donor gained	4928	0.33	mu: GAGCGACGGATGGAG	GCGA\|cgga

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

ENSPTRG00000001416

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000028048

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000010884

Drerio

all identical

ENSDARG00000076058

Dmelanogaster

all identical

FBgn0051148

Celegans

all identical

Y4C6B.6

SELKHTTSSTAKTKVYVNTTQSFQPVMGFGAAFTDAAGINMK

PQTMQ

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
88	94	STRAND		might get lost (downstream of altered splice site)
96	98	STRAND		might get lost (downstream of altered splice site)
98	98	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
103	116	STRAND		might get lost (downstream of altered splice site)
119	123	STRAND		might get lost (downstream of altered splice site)
126	133	HELIX		might get lost (downstream of altered splice site)
137	148	HELIX		might get lost (downstream of altered splice site)
150	153	TURN		might get lost (downstream of altered splice site)
157	163	STRAND		might get lost (downstream of altered splice site)
166	170	STRAND		might get lost (downstream of altered splice site)
177	179	STRAND		might get lost (downstream of altered splice site)
185	185	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
190	193	HELIX		might get lost (downstream of altered splice site)
196	206	HELIX		might get lost (downstream of altered splice site)
212	218	STRAND		might get lost (downstream of altered splice site)
222	224	HELIX		might get lost (downstream of altered splice site)
225	227	STRAND		might get lost (downstream of altered splice site)
227	227	CONFLICT	N -> R (in Ref. 5; BAA02546).	might get lost (downstream of altered splice site)
229	233	STRAND		might get lost (downstream of altered splice site)
235	238	STRAND		might get lost (downstream of altered splice site)
243	261	HELIX		might get lost (downstream of altered splice site)
267	271	STRAND		might get lost (downstream of altered splice site)
274	274	ACT_SITE	Proton donor.	might get lost (downstream of altered splice site)
275	279	HELIX		might get lost (downstream of altered splice site)
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

1464 / 1464

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

488 / 488

position of stopcodon in wt / mu cDNA

1627 / 1627

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

164 / 164

chromosome

strand

-1

last intron/exon boundary

1522

theoretical NMD boundary in CDS

1308

length of CDS

1464

coding sequence (CDS) position

254

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

417

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

4924

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

155209730

original gDNA sequence snippet

CTATGAGAGTACACGCAGTGGGCGACGGATGGAGCTGAGTA

altered gDNA sequence snippet

CTATGAGAGTACACGCAGTGAGCGACGGATGGAGCTGAGTA

original cDNA sequence snippet

CTATGAGAGTACACGCAGTGGGCGACGGATGGAGCTGAGTA

altered cDNA sequence snippet

CTATGAGAGTACACGCAGTGAGCGACGGATGGAGCTGAGTA

wildtype AA sequence

MEFSSPSREE CPKPLSRVSI MAGSLTGLLL LQAVSWASGA RPCIPKSFGY SSVVCVCNAT
YCDSFDPPTF PALGTFSRYE STRSGRRMEL SMGPIQANHT GTGIGYNIIR VPMASCDFSI
RTYTYADTPD DFQLHNFSLP EEDTKLKIPL IHRALQLAQR PVSLLASPWT SPTWLKTNGA
VNGKGSLKGQ PGDIYHQTWA RYFVKFLDAY AEHKLQFWAV TAENEPSAGL LSGYPFQCLG
FTPEHQRDFI ARDLGPTLAN STHHNVRLLM LDDQRLLLPH WAKVVLTDPE AAKYVHGIAV
HWYLDFLAPA KATLGETHRL FPNTMLFASE ACVGSKFWEQ SVRLGSWDRG MQYSHSIITN
LLYHVVGWTD WNLALNPEGG PNWVRNFVDS PIIVDITKDT FYKQPMFYHL GHFSKFIPEG
SQRVGLVASQ KNDLDAVALM HPDGSAVVVV LNRSSKDVPL TIKDPAVGFL ETISPGYSIH
TYLWRRQ*

mutated AA sequence

MEFSSPSREE CPKPLSRVSI MAGSLTGLLL LQAVSWASGA RPCIPKSFGY SSVVCVCNAT
YCDSFDPPTF PALGTFSRYE STRSERRMEL SMGPIQANHT GTGIGYNIIR VPMASCDFSI
RTYTYADTPD DFQLHNFSLP EEDTKLKIPL IHRALQLAQR PVSLLASPWT SPTWLKTNGA
VNGKGSLKGQ PGDIYHQTWA RYFVKFLDAY AEHKLQFWAV TAENEPSAGL LSGYPFQCLG
FTPEHQRDFI ARDLGPTLAN STHHNVRLLM LDDQRLLLPH WAKVVLTDPE AAKYVHGIAV
HWYLDFLAPA KATLGETHRL FPNTMLFASE ACVGSKFWEQ SVRLGSWDRG MQYSHSIITN
LLYHVVGWTD WNLALNPEGG PNWVRNFVDS PIIVDITKDT FYKQPMFYHL GHFSKFIPEG
SQRVGLVASQ KNDLDAVALM HPDGSAVVVV LNRSSKDVPL TIKDPAVGFL ETISPGYSIH
TYLWRRQ*

speed

1.13 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