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: ENST00000200453
MT speed 0 s - this script 2.968472 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PPP1R15A	polymorphism_automatic	5.99520433297585e-15	simple_aae		affected		R251P	single base exchange	rs557806		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999994 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:49377242G>CN/A show variant in all transcripts IGV

HGNC symbol

PPP1R15A

Ensembl transcript ID

ENST00000200453

Genbank transcript ID

NM_014330

UniProt peptide

O75807

alteration type

single base exchange

alteration region

CDS

DNA changes

c.752G>C
cDNA.1021G>C
g.1594G>C

AA changes

R251P Score: 103 explain score(s)

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

251

frameshift

known variant

Reference ID: rs557806

database	homozygous (C/C)	heterozygous	allele carriers
1000G	452	838	1290
ExAC	4089	17342	21431

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4ac, Histone, Histone 3 Lysine 4 Acetylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.329	0.002
	0.111	0.001
(flanking)	-1.537	0

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	1602	wt: 0.54 / mu: 0.83	wt: CCGTGTCCCCCCGATCTTCAGGCTCCGACCCCAGGTCCTGG mu: CCGTGTCCCCCCCATCTTCAGGCTCCGACCCCAGGTCCTGG	tcag\|GCTC
Acc increased	1601	wt: 0.59 / mu: 0.88	wt: TCCGTGTCCCCCCGATCTTCAGGCTCCGACCCCAGGTCCTG mu: TCCGTGTCCCCCCCATCTTCAGGCTCCGACCCCAGGTCCTG	ttca\|GGCT
Acc increased	1598	wt: 0.85 / mu: 0.97	wt: ACCTCCGTGTCCCCCCGATCTTCAGGCTCCGACCCCAGGTC mu: ACCTCCGTGTCCCCCCCATCTTCAGGCTCCGACCCCAGGTC	atct\|TCAG
Acc marginally increased	1595	wt: 0.4509 / mu: 0.5173 (marginal change - not scored)	wt: AAGACCTCCGTGTCCCCCCGATCTTCAGGCTCCGACCCCAG mu: AAGACCTCCGTGTCCCCCCCATCTTCAGGCTCCGACCCCAG	ccga\|TCTT
Acc marginally increased	1594	wt: 0.8089 / mu: 0.8290 (marginal change - not scored)	wt: GAAGACCTCCGTGTCCCCCCGATCTTCAGGCTCCGACCCCA mu: GAAGACCTCCGTGTCCCCCCCATCTTCAGGCTCCGACCCCA	cccg\|ATCT
Acc gained	1603	0.41	mu: CGTGTCCCCCCCATCTTCAGGCTCCGACCCCAGGTCCTGGG	cagg\|CTCC
Acc gained	1596	0.51	mu: AGACCTCCGTGTCCCCCCCATCTTCAGGCTCCGACCCCAGG	ccat\|CTTC
Acc gained	1600	0.60	mu: CTCCGTGTCCCCCCCATCTTCAGGCTCCGACCCCAGGTCCT	cttc\|AGGC
Acc gained	1599	0.67	mu: CCTCCGTGTCCCCCCCATCTTCAGGCTCCGACCCCAGGTCC	tctt\|CAGG

distance from splice site

761

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

251

mutated

not conserved

251

Ptroglodytes

not conserved

ENSPTRG00000011261

251

Mmulatta

not conserved

ENSMMUG00000009223

252

Fcatus

not conserved

ENSFCAG00000003345

243

Mmusculus

not conserved

ENSMUSG00000040435

232

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000069135

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000030234

345

SQVLH

protein features

start (aa)	end (aa)	feature	details
160	503	COMPBIAS	Glu-rich.	lost
262	262	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
264	264	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
297	297	CONFLICT	P -> L (in Ref. 2; CAG33540).	might get lost (downstream of altered splice site)
337	369	REPEAT	1.	might get lost (downstream of altered splice site)
337	510	REGION	4 X 34 AA approximate repeats.	might get lost (downstream of altered splice site)
337	510	REGION	Interaction with SMAD7.	might get lost (downstream of altered splice site)
384	417	REPEAT	2.	might get lost (downstream of altered splice site)
427	460	REPEAT	3.	might get lost (downstream of altered splice site)
477	510	REPEAT	4.	might get lost (downstream of altered splice site)
483	555	REGION	Interaction with MLL.	might get lost (downstream of altered splice site)
518	521	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
536	583	REGION	Interaction with SMARCB1.	might get lost (downstream of altered splice site)
555	558	MUTAGEN	KVRF->AAAA: Reduces interaction with SMARCB1.	might get lost (downstream of altered splice site)
556	558	MUTAGEN	VRF->ARA: Impairs PP1 activation.	might get lost (downstream of altered splice site)
612	612	MUTAGEN	R->K: Reduces PP1-binding; when associated with K-614.	might get lost (downstream of altered splice site)
614	614	MUTAGEN	R->K: Reduces PP1-binding; when associated with K-612.	might get lost (downstream of altered splice site)
618	618	MUTAGEN	R->D: Reduces PP1-binding.	might get lost (downstream of altered splice site)
661	666	COMPBIAS	Poly-Ala.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2025 / 2025

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

675 / 675

position of stopcodon in wt / mu cDNA

2294 / 2294

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

270 / 270

chromosome

strand

last intron/exon boundary

1935

theoretical NMD boundary in CDS

1615

length of CDS

2025

coding sequence (CDS) position

752

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

1021

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

1594

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

49377242

original gDNA sequence snippet

GAAGACCTCCGTGTCCCCCCGATCTTCAGGCTCCGACCCCA

altered gDNA sequence snippet

GAAGACCTCCGTGTCCCCCCCATCTTCAGGCTCCGACCCCA

original cDNA sequence snippet

GAAGACCTCCGTGTCCCCCCGATCTTCAGGCTCCGACCCCA

altered cDNA sequence snippet

GAAGACCTCCGTGTCCCCCCCATCTTCAGGCTCCGACCCCA

wildtype AA sequence

MAPGQAPHQA TPWRDAHPFF LLSPVMGLLS RAWSRLRGLG PLEPWLVEAV KGAALVEAGL
EGEARTPLAI PHTPWGRRPE EEAEDSGGPG EDRETLGLKT SSSLPEAWGL LDDDDGMYGE
REATSVPRGQ GSQFADGQRA PLSPSLLIRT LQGSDKNPGE EKAEEEGVAE EEGVNKFSYP
PSHRECCPAV EEEDDEEAVK KEAHRTSTSA LSPGSKPSTW VSCPGEEENQ ATEDKRTERS
KGARKTSVSP RSSGSDPRSW EYRSGEASEE KEEKAHKETG KGEAAPGPQS SAPAQRPQLK
SWWCQPSDEE EGEVKALGAA EKDGEAECPP CIPPPSAFLK AWVYWPGEDT EEEEDEEEDE
DSDSGSDEEE GEAEASSSTP ATGVFLKSWV YQPGEDTEEE EDEDSDTGSA EDEREAETSA
STPPASAFLK AWVYRPGEDT EEEEDEDVDS EDKEDDSEAA LGEAESDPHP SHPDQRAHFR
GWGYRPGKET EEEEAAEDWG EAEPCPFRVA IYVPGEKPPP PWAPPRLPLR LQRRLKRPET
PTHDPDPETP LKARKVRFSE KVTVHFLAVW AGPAQAARQG PWEQLARDRS RFARRITQAQ
EELSPCLTPA ARARAWARLR NPPLAPIPAL TQTLPSSSVP SSPVQTTPLS QAVATPSRSS
AAAAAALDLS GRRG*

mutated AA sequence

MAPGQAPHQA TPWRDAHPFF LLSPVMGLLS RAWSRLRGLG PLEPWLVEAV KGAALVEAGL
EGEARTPLAI PHTPWGRRPE EEAEDSGGPG EDRETLGLKT SSSLPEAWGL LDDDDGMYGE
REATSVPRGQ GSQFADGQRA PLSPSLLIRT LQGSDKNPGE EKAEEEGVAE EEGVNKFSYP
PSHRECCPAV EEEDDEEAVK KEAHRTSTSA LSPGSKPSTW VSCPGEEENQ ATEDKRTERS
KGARKTSVSP PSSGSDPRSW EYRSGEASEE KEEKAHKETG KGEAAPGPQS SAPAQRPQLK
SWWCQPSDEE EGEVKALGAA EKDGEAECPP CIPPPSAFLK AWVYWPGEDT EEEEDEEEDE
DSDSGSDEEE GEAEASSSTP ATGVFLKSWV YQPGEDTEEE EDEDSDTGSA EDEREAETSA
STPPASAFLK AWVYRPGEDT EEEEDEDVDS EDKEDDSEAA LGEAESDPHP SHPDQRAHFR
GWGYRPGKET EEEEAAEDWG EAEPCPFRVA IYVPGEKPPP PWAPPRLPLR LQRRLKRPET
PTHDPDPETP LKARKVRFSE KVTVHFLAVW AGPAQAARQG PWEQLARDRS RFARRITQAQ
EELSPCLTPA ARARAWARLR NPPLAPIPAL TQTLPSSSVP SSPVQTTPLS QAVATPSRSS
AAAAAALDLS GRRG*

speed

0.91 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
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MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

Problems