MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000389266
MT speed 0 s - this script 2.309162 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GARS1	disease_causing_automatic	1	simple_aae		affected	0	L183P	single base exchange	rs137852644		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM031185)
known disease mutation: rs9205 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr7:30640795T>CN/A show variant in all transcripts IGV

HGNC symbol

GARS1

Ensembl transcript ID

ENST00000389266

Genbank transcript ID

NM_002047

UniProt peptide

P41250

alteration type

single base exchange

alteration region

CDS

DNA changes

c.548T>C
cDNA.789T>C
g.6499T>C

AA changes

L183P Score: 98 explain score(s)

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

183

frameshift

known variant

Reference ID: rs137852644
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs9205 (pathogenic for Distal hereditary motor neuronopathy type 5|Charcot-Marie-Tooth disease|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM031185)

known disease mutation at this position, please check HGMD for details (HGMD ID CM031185)
known disease mutation at this position, please check HGMD for details (HGMD ID CM031185)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.801	1
	4.791	1
(flanking)	-0.084	0.983

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 increased	6491	wt: 0.23 / mu: 0.41	wt: GATTGCACCATGCTC mu: GATTGCACCATGCCC	TTGC\|acca
Donor marginally increased	6503	wt: 0.8593 / mu: 0.8616 (marginal change - not scored)	wt: CTCACCCCTGAGCCA mu: CCCACCCCTGAGCCA	CACC\|cctg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

183

mutated

not conserved

183

Ptroglodytes

all identical

ENSPTRG00000019042

183

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000011415

109

Mmusculus

all identical

ENSMUSG00000029777

173

Ggallus

all identical

ENSGALG00000005694

191

Trubripes

all identical

ENSTRUG00000017557

214

Drerio

all identical

ENSDARG00000059070

208

Dmelanogaster

all identical

FBgn0027088

215

Celegans

all identical

T10F2.1

193

Xtropicalis

all identical

ENSXETG00000018474

190

protein features

start (aa)	end (aa)	feature	details
182	185	STRAND		lost
186	191	HELIX		might get lost (downstream of altered splice site)
194	197	HELIX		might get lost (downstream of altered splice site)
199	208	STRAND		might get lost (downstream of altered splice site)
204	204	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
205	205	CONFLICT	D -> G (in Ref. 3; BAG51964).	might get lost (downstream of altered splice site)
211	213	STRAND		might get lost (downstream of altered splice site)
213	213	BINDING	Substrate.	might get lost (downstream of altered splice site)
214	227	HELIX		might get lost (downstream of altered splice site)
219	219	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
229	231	STRAND		might get lost (downstream of altered splice site)
233	243	HELIX		might get lost (downstream of altered splice site)
244	248	TURN		might get lost (downstream of altered splice site)
251	260	HELIX		might get lost (downstream of altered splice site)
266	268	STRAND		might get lost (downstream of altered splice site)
276	279	STRAND		might get lost (downstream of altered splice site)
283	285	STRAND		might get lost (downstream of altered splice site)
287	296	STRAND		might get lost (downstream of altered splice site)
298	300	STRAND		might get lost (downstream of altered splice site)
299	299	BINDING	Substrate.	might get lost (downstream of altered splice site)
301	305	HELIX		might get lost (downstream of altered splice site)
308	314	HELIX		might get lost (downstream of altered splice site)
315	317	TURN		might get lost (downstream of altered splice site)
321	330	STRAND		might get lost (downstream of altered splice site)
331	333	NP_BIND	ATP.	might get lost (downstream of altered splice site)
339	341	HELIX		might get lost (downstream of altered splice site)
341	346	NP_BIND	ATP.	might get lost (downstream of altered splice site)
344	355	STRAND		might get lost (downstream of altered splice site)
346	350	REGION	Substrate binding.	might get lost (downstream of altered splice site)
357	359	HELIX		might get lost (downstream of altered splice site)
365	367	HELIX		might get lost (downstream of altered splice site)
368	370	TURN		might get lost (downstream of altered splice site)
372	376	STRAND		might get lost (downstream of altered splice site)
378	382	HELIX		might get lost (downstream of altered splice site)
388	391	STRAND		might get lost (downstream of altered splice site)
392	397	HELIX		might get lost (downstream of altered splice site)
400	402	STRAND		might get lost (downstream of altered splice site)
404	420	HELIX		might get lost (downstream of altered splice site)
424	426	HELIX		might get lost (downstream of altered splice site)
427	431	STRAND		might get lost (downstream of altered splice site)
434	436	HELIX		might get lost (downstream of altered splice site)
435	435	BINDING	Substrate; via carbonyl oxygen.	might get lost (downstream of altered splice site)
442	451	STRAND		might get lost (downstream of altered splice site)
453	453	MOD_RES	Phosphotyrosine (By similarity).	might get lost (downstream of altered splice site)
454	462	STRAND		might get lost (downstream of altered splice site)
457	458	NP_BIND	ATP.	might get lost (downstream of altered splice site)
467	476	HELIX		might get lost (downstream of altered splice site)
482	484	STRAND		might get lost (downstream of altered splice site)
501	501	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
530	530	CONFLICT	M -> I (in Ref. 2; AAA86443).	might get lost (downstream of altered splice site)
562	564	STRAND		might get lost (downstream of altered splice site)
565	567	TURN		might get lost (downstream of altered splice site)
568	570	STRAND		might get lost (downstream of altered splice site)
573	580	STRAND		might get lost (downstream of altered splice site)
576	580	REGION	Substrate binding.	might get lost (downstream of altered splice site)
580	583	NP_BIND	ATP.	might get lost (downstream of altered splice site)
581	592	HELIX		might get lost (downstream of altered splice site)
593	595	STRAND		might get lost (downstream of altered splice site)
597	600	STRAND		might get lost (downstream of altered splice site)
603	605	STRAND		might get lost (downstream of altered splice site)
609	611	TURN		might get lost (downstream of altered splice site)
615	621	STRAND		might get lost (downstream of altered splice site)
625	627	TURN		might get lost (downstream of altered splice site)
628	640	HELIX		might get lost (downstream of altered splice site)
634	634	CONFLICT	L -> S (in Ref. 3; BAG51964).	might get lost (downstream of altered splice site)
635	635	MUTAGEN	S->L: Reduced activity.	might get lost (downstream of altered splice site)
645	647	STRAND		might get lost (downstream of altered splice site)
654	663	HELIX		might get lost (downstream of altered splice site)
668	672	STRAND		might get lost (downstream of altered splice site)
674	677	HELIX		might get lost (downstream of altered splice site)
679	681	STRAND		might get lost (downstream of altered splice site)
683	688	STRAND		might get lost (downstream of altered splice site)
689	691	TURN		might get lost (downstream of altered splice site)
694	698	STRAND		might get lost (downstream of altered splice site)
699	701	TURN		might get lost (downstream of altered splice site)
702	710	HELIX		might get lost (downstream of altered splice site)
716	722	HELIX		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2220 / 2220

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

740 / 740

position of stopcodon in wt / mu cDNA

2461 / 2461

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

242 / 242

chromosome

strand

last intron/exon boundary

2336

theoretical NMD boundary in CDS

2044

length of CDS

2220

coding sequence (CDS) position

548

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

789

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

6499

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

30640795

original gDNA sequence snippet

GGAGATCGATTGCACCATGCTCACCCCTGAGCCAGTTTTAA

altered gDNA sequence snippet

GGAGATCGATTGCACCATGCCCACCCCTGAGCCAGTTTTAA

original cDNA sequence snippet

GGAGATCGATTGCACCATGCTCACCCCTGAGCCAGTTTTAA

altered cDNA sequence snippet

GGAGATCGATTGCACCATGCCCACCCCTGAGCCAGTTTTAA

wildtype AA sequence

MPSPRPVLLR GARAALLLLL PPRLLARPSL LLRRSLSAAS CPPISLPAAA SRSSMDGAGA
EEVLAPLRLA VRQQGDLVRK LKEDKAPQVD VDKAVAELKA RKRVLEAKEL ALQPKDDIVD
RAKMEDTLKR RFFYDQAFAI YGGVSGLYDF GPVGCALKNN IIQTWRQHFI QEEQILEIDC
TMLTPEPVLK TSGHVDKFAD FMVKDVKNGE CFRADHLLKA HLQKLMSDKK CSVEKKSEME
SVLAQLDNYG QQELADLFVN YNVKSPITGN DLSPPVSFNL MFKTFIGPGG NMPGYLRPET
AQGIFLNFKR LLEFNQGKLP FAAAQIGNSF RNEISPRSGL IRVREFTMAE IEHFVDPSEK
DHPKFQNVAD LHLYLYSAKA QVSGQSARKM RLGDAVEQGV INNTVLGYFI GRIYLYLTKV
GISPDKLRFR QHMENEMAHY ACDCWDAESK TSYGWIEIVG CADRSCYDLS CHARATKVPL
VAEKPLKEPK TVNVVQFEPS KGAIGKAYKK DAKLVMEYLA ICDECYITEM EMLLNEKGEF
TIETEGKTFQ LTKDMINVKR FQKTLYVEEV VPNVIEPSFG LGRIMYTVFE HTFHVREGDE
QRTFFSFPAV VAPFKCSVLP LSQNQEFMPF VKELSEALTR HGVSHKVDDS SGSIGRRYAR
TDEIGVAFGV TIDFDTVNKT PHTATLRDRD SMRQIRAEIS ELPSIVQDLA NGNITWADVE
ARYPLFEGQE TGKKETIEE*

mutated AA sequence

MPSPRPVLLR GARAALLLLL PPRLLARPSL LLRRSLSAAS CPPISLPAAA SRSSMDGAGA
EEVLAPLRLA VRQQGDLVRK LKEDKAPQVD VDKAVAELKA RKRVLEAKEL ALQPKDDIVD
RAKMEDTLKR RFFYDQAFAI YGGVSGLYDF GPVGCALKNN IIQTWRQHFI QEEQILEIDC
TMPTPEPVLK TSGHVDKFAD FMVKDVKNGE CFRADHLLKA HLQKLMSDKK CSVEKKSEME
SVLAQLDNYG QQELADLFVN YNVKSPITGN DLSPPVSFNL MFKTFIGPGG NMPGYLRPET
AQGIFLNFKR LLEFNQGKLP FAAAQIGNSF RNEISPRSGL IRVREFTMAE IEHFVDPSEK
DHPKFQNVAD LHLYLYSAKA QVSGQSARKM RLGDAVEQGV INNTVLGYFI GRIYLYLTKV
GISPDKLRFR QHMENEMAHY ACDCWDAESK TSYGWIEIVG CADRSCYDLS CHARATKVPL
VAEKPLKEPK TVNVVQFEPS KGAIGKAYKK DAKLVMEYLA ICDECYITEM EMLLNEKGEF
TIETEGKTFQ LTKDMINVKR FQKTLYVEEV VPNVIEPSFG LGRIMYTVFE HTFHVREGDE
QRTFFSFPAV VAPFKCSVLP LSQNQEFMPF VKELSEALTR HGVSHKVDDS SGSIGRRYAR
TDEIGVAFGV TIDFDTVNKT PHTATLRDRD SMRQIRAEIS ELPSIVQDLA NGNITWADVE
ARYPLFEGQE TGKKETIEE*

speed

0.25 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

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

Problems