MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000396094
Querying Taster for transcript #2: ENST00000510709
MT speed 0 s - this script 3.276332 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ODAM	polymorphism_automatic	7.32802707403835e-12	simple_aae		affected		I222T	single base exchange	rs3196714		show file
ODAM	polymorphism_automatic	7.32802707403835e-12	simple_aae		affected		I208T	single base exchange	rs3196714		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999992672 (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)

chr4:71068489T>CN/A show variant in all transcripts IGV

HGNC symbol

ODAM

Ensembl transcript ID

ENST00000396094

Genbank transcript ID

NM_017855

UniProt peptide

A1E959

alteration type

single base exchange

alteration region

CDS

DNA changes

c.665T>C
cDNA.713T>C
g.6277T>C

AA changes

I222T Score: 89 explain score(s)

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

222

frameshift

known variant

Reference ID: rs3196714

database	homozygous (C/C)	heterozygous	allele carriers
1000G	262	897	1159
ExAC	5781	21205	26986

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.721	0
	0.18	0
(flanking)	-0.543	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
Donor marginally increased	6274	wt: 0.8812 / mu: 0.9008 (marginal change - not scored)	wt: AGAAGAGATACCATA mu: AGAAGAGACACCATA	AAGA\|gata
Donor marginally increased	6269	wt: 0.9905 / mu: 0.9958 (marginal change - not scored)	wt: ACAGGAGAAGAGATA mu: ACAGGAGAAGAGACA	AGGA\|gaag
Donor increased	6272	wt: 0.55 / mu: 0.74	wt: GGAGAAGAGATACCA mu: GGAGAAGAGACACCA	AGAA\|gaga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

222

mutated

not conserved

222

Ptroglodytes

all identical

ENSPTRG00000016124

222

Mmulatta

all identical

ENSMMUG00000006029

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000009580

219

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000033018

n/a

protein features

start (aa)	end (aa)	feature	details
244	244	CARBOHYD	O-linked (GalNAc...) (Potential).	might get lost (downstream of altered splice site)
249	249	CARBOHYD	O-linked (GalNAc...) (Potential).	might get lost (downstream of altered splice site)
250	250	CARBOHYD	O-linked (GalNAc...) (Potential).	might get lost (downstream of altered splice site)
251	251	CARBOHYD	O-linked (GalNAc...) (Potential).	might get lost (downstream of altered splice site)
255	255	CARBOHYD	O-linked (GalNAc...) (Potential).	might get lost (downstream of altered splice site)
256	256	CARBOHYD	O-linked (GalNAc...) (Potential).	might get lost (downstream of altered splice site)
261	261	CARBOHYD	O-linked (GalNAc...) (Potential).	might get lost (downstream of altered splice site)
263	263	CARBOHYD	O-linked (GalNAc...) (Potential).	might get lost (downstream of altered splice site)
273	273	CARBOHYD	O-linked (GalNAc...) (Potential).	might get lost (downstream of altered splice site)
275	275	CARBOHYD	O-linked (GalNAc...) (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

840 / 840

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

280 / 280

position of stopcodon in wt / mu cDNA

888 / 888

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

49 / 49

chromosome

strand

last intron/exon boundary

918

theoretical NMD boundary in CDS

819

length of CDS

840

coding sequence (CDS) position

665

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

713

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

6277

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

71068489

original gDNA sequence snippet

GTAGTCAACAGGAGAAGAGATACCATATTTACAAAAAGAAG

altered gDNA sequence snippet

GTAGTCAACAGGAGAAGAGACACCATATTTACAAAAAGAAG

original cDNA sequence snippet

GATGTCAACAGGAGAAGAGATACCATATTTACAAAAAGAAG

altered cDNA sequence snippet

GATGTCAACAGGAGAAGAGACACCATATTTACAAAAAGAAG

wildtype AA sequence

MKIIILLGFL GATLSAPLIP QRLMSASNSN ELLLNLNNGQ LLPLQLQGPL NSWIPPFSGI
LQQQQQAQIP GLSQFSLSAL DQFAGLLPNQ IPLTGEASFA QGAQAGQVDP LQLQTPPQTQ
PGPSHVMPYV FSFKMPQEQG QMFQYYPVYM VLPWEQPQQT VPRSPQQTRQ QQYEEQIPFY
AQFGYIPQLA EPAISGGQQQ LAFDPQLGTA PEIAVMSTGE EIPYLQKEAI NFRHDSAGVF
MPSTSPKPST TNVFTSAVDQ TITPELPEEK DKTDSLREP*

mutated AA sequence

MKIIILLGFL GATLSAPLIP QRLMSASNSN ELLLNLNNGQ LLPLQLQGPL NSWIPPFSGI
LQQQQQAQIP GLSQFSLSAL DQFAGLLPNQ IPLTGEASFA QGAQAGQVDP LQLQTPPQTQ
PGPSHVMPYV FSFKMPQEQG QMFQYYPVYM VLPWEQPQQT VPRSPQQTRQ QQYEEQIPFY
AQFGYIPQLA EPAISGGQQQ LAFDPQLGTA PEIAVMSTGE ETPYLQKEAI NFRHDSAGVF
MPSTSPKPST TNVFTSAVDQ TITPELPEEK DKTDSLREP*

speed

1.08 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: 0.999999999992672 (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)

chr4:71068489T>CN/A show variant in all transcripts IGV

HGNC symbol

ODAM

Ensembl transcript ID

ENST00000510709

Genbank transcript ID

N/A

UniProt peptide

A1E959

alteration type

single base exchange

alteration region

CDS

DNA changes

c.623T>C
cDNA.642T>C
g.6277T>C

AA changes

I208T Score: 89 explain score(s)

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

208

frameshift

known variant

Reference ID: rs3196714

database	homozygous (C/C)	heterozygous	allele carriers
1000G	262	897	1159
ExAC	5781	21205	26986

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.721	0
	0.18	0
(flanking)	-0.543	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
Donor marginally increased	6274	wt: 0.8812 / mu: 0.9008 (marginal change - not scored)	wt: AGAAGAGATACCATA mu: AGAAGAGACACCATA	AAGA\|gata
Donor marginally increased	6269	wt: 0.9905 / mu: 0.9958 (marginal change - not scored)	wt: ACAGGAGAAGAGATA mu: ACAGGAGAAGAGACA	AGGA\|gaag
Donor increased	6272	wt: 0.55 / mu: 0.74	wt: GGAGAAGAGATACCA mu: GGAGAAGAGACACCA	AGAA\|gaga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

208

mutated

not conserved

208

Ptroglodytes

all identical

ENSPTRG00000016124

222

Mmulatta

all identical

ENSMMUG00000006029

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000009580

219

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000033018

n/a

protein features

start (aa)	end (aa)	feature	details
62	206	COMPBIAS	Gln-rich.	might get lost (downstream of altered splice site)
244	244	CARBOHYD	O-linked (GalNAc...) (Potential).	might get lost (downstream of altered splice site)
249	249	CARBOHYD	O-linked (GalNAc...) (Potential).	might get lost (downstream of altered splice site)
250	250	CARBOHYD	O-linked (GalNAc...) (Potential).	might get lost (downstream of altered splice site)
251	251	CARBOHYD	O-linked (GalNAc...) (Potential).	might get lost (downstream of altered splice site)
255	255	CARBOHYD	O-linked (GalNAc...) (Potential).	might get lost (downstream of altered splice site)
256	256	CARBOHYD	O-linked (GalNAc...) (Potential).	might get lost (downstream of altered splice site)
261	261	CARBOHYD	O-linked (GalNAc...) (Potential).	might get lost (downstream of altered splice site)
263	263	CARBOHYD	O-linked (GalNAc...) (Potential).	might get lost (downstream of altered splice site)
273	273	CARBOHYD	O-linked (GalNAc...) (Potential).	might get lost (downstream of altered splice site)
275	275	CARBOHYD	O-linked (GalNAc...) (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

798 / 798

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

266 / 266

position of stopcodon in wt / mu cDNA

817 / 817

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

20 / 20

chromosome

strand

last intron/exon boundary

847

theoretical NMD boundary in CDS

777

length of CDS

798

coding sequence (CDS) position

623

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

642

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

6277

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

71068489

original gDNA sequence snippet

GTAGTCAACAGGAGAAGAGATACCATATTTACAAAAAGAAG

altered gDNA sequence snippet

GTAGTCAACAGGAGAAGAGACACCATATTTACAAAAAGAAG

original cDNA sequence snippet

GATGTCAACAGGAGAAGAGATACCATATTTACAAAAAGAAG

altered cDNA sequence snippet

GATGTCAACAGGAGAAGAGACACCATATTTACAAAAAGAAG

wildtype AA sequence

MKIIILLGFL GATLSAPLLL NLNNGQLLPL QLQGPLNSWI PPFSGILQQQ QQAQIPGLSQ
FSLSALDQFA GLLPNQIPLT GEASFAQGAQ AGQVDPLQLQ TPPQTQPGPS HVMPYVFSFK
MPQEQGQMFQ YYPVYMVLPW EQPQQTVPRS PQQTRQQQYE EQIPFYAQFG YIPQLAEPAI
SGGQQQLAFD PQLGTAPEIA VMSTGEEIPY LQKEAINFRH DSAGVFMPST SPKPSTTNVF
TSAVDQTITP ELPEEKDKTD SLREP*

mutated AA sequence

MKIIILLGFL GATLSAPLLL NLNNGQLLPL QLQGPLNSWI PPFSGILQQQ QQAQIPGLSQ
FSLSALDQFA GLLPNQIPLT GEASFAQGAQ AGQVDPLQLQ TPPQTQPGPS HVMPYVFSFK
MPQEQGQMFQ YYPVYMVLPW EQPQQTVPRS PQQTRQQQYE EQIPFYAQFG YIPQLAEPAI
SGGQQQLAFD PQLGTAPEIA VMSTGEETPY LQKEAINFRH DSAGVFMPST SPKPSTTNVF
TSAVDQTITP ELPEEKDKTD SLREP*

speed

0.20 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems