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: ENST00000258105
Querying Taster for transcript #2: ENST00000409710
MT speed 0 s - this script 3.225347 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
MRPL53	polymorphism_automatic	1.83070225645565e-11	simple_aae		affected		A4S	single base exchange	rs1047911		show file
MRPL53	polymorphism_automatic	2.31900054714629e-11	simple_aae		affected		A4S	single base exchange	rs1047911		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999981693 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:74699778C>AN/A show variant in all transcripts IGV

HGNC symbol

MRPL53

Ensembl transcript ID

ENST00000258105

Genbank transcript ID

NM_053050

UniProt peptide

Q96EL3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.10G>T
cDNA.672G>T
g.672G>T

AA changes

A4S Score: 99 explain score(s)

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

frameshift

known variant

Reference ID: rs1047911

database	homozygous (A/A)	heterozygous	allele carriers
1000G	874	840	1714
ExAC	7533	17410	24943

regulatory features

BCLAF1, Transcription Factor, BCLAF1 Transcription Factor Binding
Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
ETS1, Transcription Factor, ETS1 Transcription Factor Binding
Egr1, Transcription Factor, Egr1 Transcription Factor Binding
FOSL2, Transcription Factor, FOSL2 Transcription Factor Binding
Gabp, Transcription Factor, Gabp TF binding
H2AZ, Histone, Histone 2A variant Z
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 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
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K5ac, Histone, Histone 4 Lysine 5 Acetylation
H4K8ac, Histone, Histone 4 Lysine 8 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Jund, Transcription Factor, Jund TF binding
Max, Transcription Factor, Max TF binding
POU2F2, Transcription Factor, POU2F2 Transcription Factor Binding
PU1, Transcription Factor, PU1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
SIX5, Transcription Factor, SIX5 Transcription Factor Binding
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Tcf12, Transcription Factor, Tcf12 Transcription Factor Binding
Tr4, Transcription Factor, Tr4 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
p300, Transcription Factor, p300 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.956	0.066
	0.469	0.045
(flanking)	-0.262	0.024

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	681	wt: 0.31 / mu: 0.83	wt: CCATGGCAGCTGCCTTGGCTCGGCTTGGTCTGCGGCCTGTC mu: CCATGGCAGCTTCCTTGGCTCGGCTTGGTCTGCGGCCTGTC	gctc\|GGCT
Acc gained	682	0.45	mu: CATGGCAGCTTCCTTGGCTCGGCTTGGTCTGCGGCCTGTCA	ctcg\|GCTT
Acc gained	676	0.48	mu: GGTCACCATGGCAGCTTCCTTGGCTCGGCTTGGTCTGCGGC	cctt\|GGCT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000033835

Mmulatta

no homologue

Fcatus

all conserved

ENSFCAG00000007151

Mmusculus

all identical

ENSMUSG00000030037

Ggallus

all conserved

ENSGALG00000015761

Trubripes

no alignment

ENSTRUG00000014652

n/a

Drerio

not conserved

ENSDARG00000008920

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000027254

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

339 / 339

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

113 / 113

position of stopcodon in wt / mu cDNA

1001 / 1001

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

663 / 663

chromosome

strand

-1

last intron/exon boundary

868

theoretical NMD boundary in CDS

155

length of CDS

339

coding sequence (CDS) position

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

672

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

672

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

74699778

original gDNA sequence snippet

CGGAGGTCACCATGGCAGCTGCCTTGGCTCGGCTTGGTCTG

altered gDNA sequence snippet

CGGAGGTCACCATGGCAGCTTCCTTGGCTCGGCTTGGTCTG

original cDNA sequence snippet

CGGAGGTCACCATGGCAGCTGCCTTGGCTCGGCTTGGTCTG

altered cDNA sequence snippet

CGGAGGTCACCATGGCAGCTTCCTTGGCTCGGCTTGGTCTG

wildtype AA sequence

MAAALARLGL RPVKQVRVQF CPFEKNVEST RTFLQTVSSE KVRSTNLNCS VIADVRHDGS
EPCVDVLFGD GHRLIMRGAH LTALEMLTAF ASHIRARDAA GSGDKPGADT GR*

mutated AA sequence

MAASLARLGL RPVKQVRVQF CPFEKNVEST RTFLQTVSSE KVRSTNLNCS VIADVRHDGS
EPCVDVLFGD GHRLIMRGAH LTALEMLTAF ASHIRARDAA GSGDKPGADT GR*

speed

0.57 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: 0.99999999997681 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:74699778C>AN/A show variant in all transcripts IGV

HGNC symbol

MRPL53

Ensembl transcript ID

ENST00000409710

Genbank transcript ID

N/A

UniProt peptide

Q96EL3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.10G>T
cDNA.37G>T
g.672G>T

AA changes

A4S Score: 99 explain score(s)

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

frameshift

known variant

Reference ID: rs1047911

database	homozygous (A/A)	heterozygous	allele carriers
1000G	874	840	1714
ExAC	7533	17410	24943

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.956	0.066
	0.469	0.045
(flanking)	-0.262	0.024

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	681	wt: 0.31 / mu: 0.83	wt: CCATGGCAGCTGCCTTGGCTCGGCTTGGTCTGCGGCCTGTC mu: CCATGGCAGCTTCCTTGGCTCGGCTTGGTCTGCGGCCTGTC	gctc\|GGCT
Acc gained	682	0.45	mu: CATGGCAGCTTCCTTGGCTCGGCTTGGTCTGCGGCCTGTCA	ctcg\|GCTT
Acc gained	676	0.48	mu: GGTCACCATGGCAGCTTCCTTGGCTCGGCTTGGTCTGCGGC	cctt\|GGCT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000033835

Mmulatta

no homologue

Fcatus

all conserved

ENSFCAG00000007151

Mmusculus

all identical

ENSMUSG00000030037

Ggallus

no alignment

ENSGALG00000015761

n/a

Trubripes

no alignment

ENSTRUG00000014652

n/a

Drerio

not conserved

ENSDARG00000008920

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000027254

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

213 / 213

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

71 / 71

position of stopcodon in wt / mu cDNA

240 / 240

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

28 / 28

chromosome

strand

-1

last intron/exon boundary

120

theoretical NMD boundary in CDS

length of CDS

213

coding sequence (CDS) position

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

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

672

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

74699778

original gDNA sequence snippet

CGGAGGTCACCATGGCAGCTGCCTTGGCTCGGCTTGGTCTG

altered gDNA sequence snippet

CGGAGGTCACCATGGCAGCTTCCTTGGCTCGGCTTGGTCTG

original cDNA sequence snippet

CGGAGGTCACCATGGCAGCTGCCTTGGCTCGGCTTGGTCTG

altered cDNA sequence snippet

CGGAGGTCACCATGGCAGCTTCCTTGGCTCGGCTTGGTCTG

wildtype AA sequence

MAAALARLGL RPVKQVRVQF CPFEKNVEST RRRASPDYAR RSSHRSGNAH RLRLPHPGQG
RGGQRGQAGR *

mutated AA sequence

MAASLARLGL RPVKQVRVQF CPFEKNVEST RRRASPDYAR RSSHRSGNAH RLRLPHPGQG
RGGQRGQAGR *

speed

0.71 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems