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: ENST00000523492
Querying Taster for transcript #2: ENST00000286234
MT speed 0 s - this script 3.15799 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
DEPTOR	polymorphism_automatic	0.999999997664144	simple_aae		affected		S288N	single base exchange	rs4871827		show file
DEPTOR	polymorphism_automatic	0.999999999649191	simple_aae		affected		S389N	single base exchange	rs4871827		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 2.33585551459644e-09 (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)

chr8:121061879G>AN/A show variant in all transcripts IGV

HGNC symbol

DEPTOR

Ensembl transcript ID

ENST00000523492

Genbank transcript ID

N/A

UniProt peptide

Q8TB45

alteration type

single base exchange

alteration region

CDS

DNA changes

c.863G>A
cDNA.993G>A
g.175923G>A

AA changes

S288N Score: 46 explain score(s)

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

288

frameshift

known variant

Reference ID: rs4871827

database	homozygous (A/A)	heterozygous	allele carriers
1000G	319	862	1181
ExAC	7088	18591	25679

regulatory features

H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H4K5ac, Histone, Histone 4 Lysine 5 Acetylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.162	1
	6.253	1
(flanking)	2.605	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 increased	175926	wt: 0.23 / mu: 0.26	wt: GAGCAATCTGATTCT mu: GAACAATCTGATTCT	GCAA\|tctg
Donor gained	175918	0.97	mu: CGGACCGTGAACAAT	GACC\|gtga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

288

mutated

all conserved

288

Ptroglodytes

all identical

ENSPTRG00000020537

389

Mmulatta

all identical

ENSMMUG00000002594

389

Fcatus

all identical

ENSFCAG00000010947

391

Mmusculus

all identical

ENSMUSG00000022419

389

Ggallus

all identical

ENSGALG00000016413

360

Trubripes

all identical

ENSTRUG00000012469

393

Drerio

all identical

ENSDARG00000040930

387

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000005764

349

protein features

start (aa)	end (aa)	feature	details
235	299	COMPBIAS	Ser-rich.	lost
287	287	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
293	293	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
297	297	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
298	298	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
299	299	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
330	407	DOMAIN	PDZ.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

927 / 927

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

309 / 309

position of stopcodon in wt / mu cDNA

1057 / 1057

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

131 / 131

chromosome

strand

last intron/exon boundary

929

theoretical NMD boundary in CDS

748

length of CDS

927

coding sequence (CDS) position

863

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

993

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

175923

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

121061879

original gDNA sequence snippet

TGTAGACTACCGGACCGTGAGCAATCTGATTCTGACGGGCC

altered gDNA sequence snippet

TGTAGACTACCGGACCGTGAACAATCTGATTCTGACGGGCC

original cDNA sequence snippet

TGTAGACTACCGGACCGTGAGCAATCTGATTCTGACGGGCC

altered cDNA sequence snippet

TGTAGACTACCGGACCGTGAACAATCTGATTCTGACGGGCC

wildtype AA sequence

MEEGGSTGSA GSDSSTSGSG GAQQRELERM AEVLVTGEQL RLMSPENTLL QPREEEGVKY
ERTFMASEFL DWLVQEGEAT TRKEAEQLCH RLMEHGIIQH VSNKHPFVDS NLLYQFRMNF
RRRRRLMELL NEKSPSSQET HDSPFCLRKQ SHDNRKSTSF MSVSPSKEIK IVSAVRRSSM
SSCGSSGYFS SSPTLSSSPP VLCNPKSVLK RPVTSEELLT PGAPYARKTF TIVGDAVGWG
FVVRGSKPCH IQAVDPSGPA AAAGMKVCQF VVSVNGLNVL HVDYRTVSNL ILTGPRTIVM
EVMEELEC*

mutated AA sequence

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
back to results table

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 3.50809196008404e-10 (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)

chr8:121061879G>AN/A show variant in all transcripts IGV

HGNC symbol

DEPTOR

Ensembl transcript ID

ENST00000286234

Genbank transcript ID

NM_022783

UniProt peptide

Q8TB45

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1166G>A
cDNA.1296G>A
g.175923G>A

AA changes

S389N Score: 46 explain score(s)

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

389

frameshift

known variant

Reference ID: rs4871827

database	homozygous (A/A)	heterozygous	allele carriers
1000G	319	862	1181
ExAC	7088	18591	25679

regulatory features

H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H4K5ac, Histone, Histone 4 Lysine 5 Acetylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.162	1
	6.253	1
(flanking)	2.605	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 increased	175926	wt: 0.23 / mu: 0.26	wt: GAGCAATCTGATTCT mu: GAACAATCTGATTCT	GCAA\|tctg
Donor gained	175918	0.97	mu: CGGACCGTGAACAAT	GACC\|gtga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

389

mutated

all conserved

389

Ptroglodytes

all identical

ENSPTRG00000020537

389

Mmulatta

all identical

ENSMMUG00000002594

389

Fcatus

all identical

ENSFCAG00000010947

391

Mmusculus

all identical

ENSMUSG00000022419

389

Ggallus

all identical

ENSGALG00000016413

360

Trubripes

all identical

ENSTRUG00000012469

393

Drerio

all identical

ENSDARG00000040930

387

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000005764

349

protein features

start (aa)	end (aa)	feature	details
330	407	DOMAIN	PDZ.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1230 / 1230

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

410 / 410

position of stopcodon in wt / mu cDNA

1360 / 1360

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

131 / 131

chromosome

strand

last intron/exon boundary

1232

theoretical NMD boundary in CDS

1051

length of CDS

1230

coding sequence (CDS) position

1166

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

1296

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

175923

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

121061879

original gDNA sequence snippet

TGTAGACTACCGGACCGTGAGCAATCTGATTCTGACGGGCC

altered gDNA sequence snippet

TGTAGACTACCGGACCGTGAACAATCTGATTCTGACGGGCC

original cDNA sequence snippet

TGTAGACTACCGGACCGTGAGCAATCTGATTCTGACGGGCC

altered cDNA sequence snippet

TGTAGACTACCGGACCGTGAACAATCTGATTCTGACGGGCC

wildtype AA sequence

MEEGGSTGSA GSDSSTSGSG GAQQRELERM AEVLVTGEQL RLRLHEEKVI KDRRHHLKTY
PNCFVAKELI DWLIEHKEAS DRETAIKLMQ KLADRGIIHH VCDEHKEFKD VKLFYRFRKD
DGTFPLDNEV KAFMRGQRLY EKLMSPENTL LQPREEEGVK YERTFMASEF LDWLVQEGEA
TTRKEAEQLC HRLMEHGIIQ HVSNKHPFVD SNLLYQFRMN FRRRRRLMEL LNEKSPSSQE
THDSPFCLRK QSHDNRKSTS FMSVSPSKEI KIVSAVRRSS MSSCGSSGYF SSSPTLSSSP
PVLCNPKSVL KRPVTSEELL TPGAPYARKT FTIVGDAVGW GFVVRGSKPC HIQAVDPSGP
AAAAGMKVCQ FVVSVNGLNV LHVDYRTVSN LILTGPRTIV MEVMEELEC*

mutated AA sequence

speed

1.07 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems