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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000305850
Querying Taster for transcript #2: ENST00000439957
Querying Taster for transcript #3: ENST00000393335
Querying Taster for transcript #4: ENST00000428963
MT speed 0 s - this script 6.369401 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CENPN	polymorphism_automatic	3.08117590529511e-05	simple_aae		affected		E268K	single base exchange	rs2549887		show file
CENPN	polymorphism_automatic	3.08117590529511e-05	simple_aae		affected		E288K	single base exchange	rs2549887		show file
CENPN	polymorphism_automatic	3.08117590529511e-05	simple_aae		affected		E288K	single base exchange	rs2549887		show file
CENPN	polymorphism_automatic	3.08117590529511e-05	simple_aae		affected		E254K	single base exchange	rs2549887		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999969188240947 (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)

chr16:81061827G>AN/A show variant in all transcripts IGV

HGNC symbol

CENPN

Ensembl transcript ID

ENST00000439957

Genbank transcript ID

NM_001270473

UniProt peptide

Q96H22

alteration type

single base exchange

alteration region

CDS

DNA changes

c.802G>A
cDNA.883G>A
g.21725G>A

AA changes

E268K Score: 56 explain score(s)

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

268

frameshift

known variant

Reference ID: rs2549887

database	homozygous (A/A)	heterozygous	allele carriers
1000G	988	1015	2003
ExAC	31537	-30307	1230

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.554	0.049
	-0.188	0.049
(flanking)	2.647	0.987

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	21718	wt: 0.7264 / mu: 0.7385 (marginal change - not scored)	wt: TTGGCTGAGAGGGAA mu: TTGGCTGAGAGGAAA	GGCT\|gaga
Donor gained	21720	0.31	mu: GGCTGAGAGGAAAGA	CTGA\|gagg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

268

mutated

all conserved

268

Ptroglodytes

all identical

ENSPTRG00000008383

288

Mmulatta

all identical

ENSMMUG00000013082

288

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000031756

286

Ggallus

all conserved

ENSGALG00000013494

283

Trubripes

no homologue

Drerio

all identical

ENSDARG00000043640

279

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000000170

284

protein features

start (aa)	end (aa)	feature	details
282	282	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

960 / 960

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

320 / 320

position of stopcodon in wt / mu cDNA

1041 / 1041

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

82 / 82

chromosome

strand

last intron/exon boundary

959

theoretical NMD boundary in CDS

827

length of CDS

960

coding sequence (CDS) position

802

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

883

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

21725

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

81061827

original gDNA sequence snippet

GGAGCATCTTGGCTGAGAGGGAAGAACCCCTCCGATGCCTA

altered gDNA sequence snippet

GGAGCATCTTGGCTGAGAGGAAAGAACCCCTCCGATGCCTA

original cDNA sequence snippet

GGAGCATCTTGGCTGAGAGGGAAGAACCCCTCCGATGCCTA

altered cDNA sequence snippet

GGAGCATCTTGGCTGAGAGGAAAGAACCCCTCCGATGCCTA

wildtype AA sequence

MDETVAEFIK RTILKIPMNE LTTILKAWDF LSENQLQTVN FRQRKESVVQ HLIHLCEEKR
ASISDAALLD IICEDVDLFD MKQFKNSFKK ILQRALKNVT VSFRETEENA VWIRIAWGTQ
YTKPNQYKPT YVVYYSQTPY AFTSSSMLRR NTPLLGQALT IASKHHQIVK MDLRSRYLDS
LKAIVFKQYN QTFETHNSTT PLQERSLGLD INMDSRIIHE NIVEKERVQR ITQETFGDYP
QPQLEFAQYK LETKFKSGLN GSILAEREEP LRCLIKFSSP HLLEALKSLA PAGIADAPLS
PLLTCIPNKR MNYFKIRDK*

mutated AA sequence

MDETVAEFIK RTILKIPMNE LTTILKAWDF LSENQLQTVN FRQRKESVVQ HLIHLCEEKR
ASISDAALLD IICEDVDLFD MKQFKNSFKK ILQRALKNVT VSFRETEENA VWIRIAWGTQ
YTKPNQYKPT YVVYYSQTPY AFTSSSMLRR NTPLLGQALT IASKHHQIVK MDLRSRYLDS
LKAIVFKQYN QTFETHNSTT PLQERSLGLD INMDSRIIHE NIVEKERVQR ITQETFGDYP
QPQLEFAQYK LETKFKSGLN GSILAERKEP LRCLIKFSSP HLLEALKSLA PAGIADAPLS
PLLTCIPNKR MNYFKIRDK*

speed

1.35 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: 0.999969188240947 (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)

chr16:81061827G>AN/A show variant in all transcripts IGV

HGNC symbol

CENPN

Ensembl transcript ID

ENST00000305850

Genbank transcript ID

NM_001100624

UniProt peptide

Q96H22

alteration type

single base exchange

alteration region

CDS

DNA changes

c.862G>A
cDNA.1652G>A
g.21725G>A

AA changes

E288K Score: 56 explain score(s)

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

288

frameshift

known variant

Reference ID: rs2549887

database	homozygous (A/A)	heterozygous	allele carriers
1000G	988	1015	2003
ExAC	31537	-30307	1230

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.554	0.049
	-0.188	0.049
(flanking)	2.647	0.987

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	21718	wt: 0.7264 / mu: 0.7385 (marginal change - not scored)	wt: TTGGCTGAGAGGGAA mu: TTGGCTGAGAGGAAA	GGCT\|gaga
Donor gained	21720	0.31	mu: GGCTGAGAGGAAAGA	CTGA\|gagg

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

ENSPTRG00000008383

288

Mmulatta

all identical

ENSMMUG00000013082

288

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000031756

286

Ggallus

all conserved

ENSGALG00000013494

283

Trubripes

no homologue

Drerio

all identical

ENSDARG00000043640

278

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000000170

284

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1020 / 1020

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

340 / 340

position of stopcodon in wt / mu cDNA

1810 / 1810

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

791 / 791

chromosome

strand

last intron/exon boundary

1728

theoretical NMD boundary in CDS

887

length of CDS

1020

coding sequence (CDS) position

862

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

1652

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

21725

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

81061827

original gDNA sequence snippet

GGAGCATCTTGGCTGAGAGGGAAGAACCCCTCCGATGCCTA

altered gDNA sequence snippet

GGAGCATCTTGGCTGAGAGGAAAGAACCCCTCCGATGCCTA

original cDNA sequence snippet

GGAGCATCTTGGCTGAGAGGGAAGAACCCCTCCGATGCCTA

altered cDNA sequence snippet

GGAGCATCTTGGCTGAGAGGAAAGAACCCCTCCGATGCCTA

wildtype AA sequence

MDETVAEFIK RTILKIPMNE LTTILKAWDF LSENQLQTVN FRQRKESVVQ HLIHLCEEKR
ASISDAALLD IIYMQFHQHQ KVWEVFQMSK GPGEDVDLFD MKQFKNSFKK ILQRALKNVT
VSFRETEENA VWIRIAWGTQ YTKPNQYKPT YVVYYSQTPY AFTSSSMLRR NTPLLGQALT
IASKHHQIVK MDLRSRYLDS LKAIVFKQYN QTFETHNSTT PLQERSLGLD INMDSRIIHE
NIVEKERVQR ITQETFGDYP QPQLEFAQYK LETKFKSGLN GSILAEREEP LRCLIKFSSP
HLLEALKSLA PAGIADAPLS PLLTCIPNKR MNYFKIRDK*

mutated AA sequence

MDETVAEFIK RTILKIPMNE LTTILKAWDF LSENQLQTVN FRQRKESVVQ HLIHLCEEKR
ASISDAALLD IIYMQFHQHQ KVWEVFQMSK GPGEDVDLFD MKQFKNSFKK ILQRALKNVT
VSFRETEENA VWIRIAWGTQ YTKPNQYKPT YVVYYSQTPY AFTSSSMLRR NTPLLGQALT
IASKHHQIVK MDLRSRYLDS LKAIVFKQYN QTFETHNSTT PLQERSLGLD INMDSRIIHE
NIVEKERVQR ITQETFGDYP QPQLEFAQYK LETKFKSGLN GSILAERKEP LRCLIKFSSP
HLLEALKSLA PAGIADAPLS PLLTCIPNKR MNYFKIRDK*

speed

1.26 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999969188240947 (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)

chr16:81061827G>AN/A show variant in all transcripts IGV

HGNC symbol

CENPN

Ensembl transcript ID

ENST00000393335

Genbank transcript ID

NM_001100625

UniProt peptide

Q96H22

alteration type

single base exchange

alteration region

CDS

DNA changes

c.862G>A
cDNA.936G>A
g.21725G>A

AA changes

E288K Score: 56 explain score(s)

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

288

frameshift

known variant

Reference ID: rs2549887

database	homozygous (A/A)	heterozygous	allele carriers
1000G	988	1015	2003
ExAC	31537	-30307	1230

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.554	0.049
	-0.188	0.049
(flanking)	2.647	0.987

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	21718	wt: 0.7264 / mu: 0.7385 (marginal change - not scored)	wt: TTGGCTGAGAGGGAA mu: TTGGCTGAGAGGAAA	GGCT\|gaga
Donor gained	21720	0.31	mu: GGCTGAGAGGAAAGA	CTGA\|gagg

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

ENSPTRG00000008383

288

Mmulatta

all identical

ENSMMUG00000013082

288

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000031756

286

Ggallus

all conserved

ENSGALG00000013494

283

Trubripes

no homologue

Drerio

all identical

ENSDARG00000043640

278

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000000170

284

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1062 / 1062

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

354 / 354

position of stopcodon in wt / mu cDNA

1136 / 1136

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

75 / 75

chromosome

strand

last intron/exon boundary

1012

theoretical NMD boundary in CDS

887

length of CDS

1062

coding sequence (CDS) position

862

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

936

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

21725

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

81061827

original gDNA sequence snippet

GGAGCATCTTGGCTGAGAGGGAAGAACCCCTCCGATGCCTA

altered gDNA sequence snippet

GGAGCATCTTGGCTGAGAGGAAAGAACCCCTCCGATGCCTA

original cDNA sequence snippet

GGAGCATCTTGGCTGAGAGGGAAGAACCCCTCCGATGCCTA

altered cDNA sequence snippet

GGAGCATCTTGGCTGAGAGGAAAGAACCCCTCCGATGCCTA

wildtype AA sequence

mutated AA sequence

MDETVAEFIK RTILKIPMNE LTTILKAWDF LSENQLQTVN FRQRKESVVQ HLIHLCEEKR
ASISDAALLD IIYMQFHQHQ KVWEVFQMSK GPGEDVDLFD MKQFKNSFKK ILQRALKNVT
VSFRETEENA VWIRIAWGTQ YTKPNQYKPT YVVYYSQTPY AFTSSSMLRR NTPLLGQALT
IASKHHQIVK MDLRSRYLDS LKAIVFKQYN QTFETHNSTT PLQERSLGLD INMDSRIIHE
NIVEKERVQR ITQETFGDYP QPQLEFAQYK LETKFKSGLN GSILAERKEP LRCLIKFSSP
HLLEALKSLA PAALVCRIQK LLCYSGSHSQ GTQDPSSWQK DLYLLFVPLY PRC*

speed

1.41 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999969188240947 (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)

chr16:81061827G>AN/A show variant in all transcripts IGV

HGNC symbol

CENPN

Ensembl transcript ID

ENST00000428963

Genbank transcript ID

N/A

UniProt peptide

Q96H22

alteration type

single base exchange

alteration region

CDS

DNA changes

c.760G>A
cDNA.804G>A
g.21725G>A

AA changes

E254K Score: 56 explain score(s)

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

254

frameshift

known variant

Reference ID: rs2549887

database	homozygous (A/A)	heterozygous	allele carriers
1000G	988	1015	2003
ExAC	31537	-30307	1230

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.554	0.049
	-0.188	0.049
(flanking)	2.647	0.987

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	21718	wt: 0.7264 / mu: 0.7385 (marginal change - not scored)	wt: TTGGCTGAGAGGGAA mu: TTGGCTGAGAGGAAA	GGCT\|gaga
Donor gained	21720	0.31	mu: GGCTGAGAGGAAAGA	CTGA\|gagg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

254

mutated

all conserved

254

Ptroglodytes

all identical

ENSPTRG00000008383

288

Mmulatta

all identical

ENSMMUG00000013082

288

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000031756

286

Ggallus

all conserved

ENSGALG00000013494

283

Trubripes

no homologue

Drerio

all identical

ENSDARG00000043640

282

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000000170

284

protein features

start (aa)	end (aa)	feature	details
282	282	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

918 / 918

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

306 / 306

position of stopcodon in wt / mu cDNA

962 / 962

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

45 / 45

chromosome

strand

last intron/exon boundary

880

theoretical NMD boundary in CDS

785

length of CDS

918

coding sequence (CDS) position

760

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

804

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

21725

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

81061827

original gDNA sequence snippet

GGAGCATCTTGGCTGAGAGGGAAGAACCCCTCCGATGCCTA

altered gDNA sequence snippet

GGAGCATCTTGGCTGAGAGGAAAGAACCCCTCCGATGCCTA

original cDNA sequence snippet

GGAGCATCTTGGCTGAGAGGGAAGAACCCCTCCGATGCCTA

altered cDNA sequence snippet

GGAGCATCTTGGCTGAGAGGAAAGAACCCCTCCGATGCCTA

wildtype AA sequence

MDETVAEFIK RTILKIPMNE LTTILKAWDF LSENQLQTVN FRQRKESVVQ HLIHLCEEKR
ASISDAALLD IIYMQFHQHQ KVWEVFQMSK GPGEDVDLFD MKQFKNSFKK ILQRALKNVT
VSFRETEENA VWIRIAWGTQ YTKPNQYKPT YVVYYSQTPY AFTSSSMLRR NTPLLGQTFE
THNSTTPLQE RSLGLDINMD SRIIHENIVE KERVQRITQE TFGDYPQPQL EFAQYKLETK
FKSGLNGSIL AEREEPLRCL IKFSSPHLLE ALKSLAPAGI ADAPLSPLLT CIPNKRMNYF
KIRDK*

mutated AA sequence

MDETVAEFIK RTILKIPMNE LTTILKAWDF LSENQLQTVN FRQRKESVVQ HLIHLCEEKR
ASISDAALLD IIYMQFHQHQ KVWEVFQMSK GPGEDVDLFD MKQFKNSFKK ILQRALKNVT
VSFRETEENA VWIRIAWGTQ YTKPNQYKPT YVVYYSQTPY AFTSSSMLRR NTPLLGQTFE
THNSTTPLQE RSLGLDINMD SRIIHENIVE KERVQRITQE TFGDYPQPQL EFAQYKLETK
FKSGLNGSIL AERKEPLRCL IKFSSPHLLE ALKSLAPAGI ADAPLSPLLT CIPNKRMNYF
KIRDK*

speed

1.32 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems