MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 4 transcript(s)...
Querying Taster for transcript #1: ENST00000348931
Querying Taster for transcript #2: ENST00000583811
Querying Taster for transcript #3: ENST00000584588
Querying Taster for transcript #4: ENST00000377940
MT speed 0 s - this script 3.660204 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ZPBP2	polymorphism_automatic	1.24497503695142e-06	simple_aae				S173I	single base exchange	rs11557467		show file
ZPBP2	polymorphism_automatic	1.24497503695142e-06	simple_aae				S151I	single base exchange	rs11557467		show file
ZPBP2	polymorphism_automatic	0.027485216136822	without_aae					single base exchange	rs11557467		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999998755024963 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM1111300)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:38028634G>TN/A show variant in all transcripts IGV

HGNC symbol

ZPBP2

Ensembl transcript ID

ENST00000348931

Genbank transcript ID

NM_199321

UniProt peptide

Q6X784

alteration type

single base exchange

alteration region

CDS

DNA changes

c.518G>T
cDNA.709G>T
g.4218G>T

AA changes

S173I Score: 142 explain score(s)

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

173

frameshift

known variant

Reference ID: rs11557467

database	homozygous (T/T)	heterozygous	allele carriers
1000G	377	1147	1524
ExAC	12562	7643	20205

known disease mutation at this position, please check HGMD for details (HGMD ID CM1111300)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.667	0.462
	1.016	0.43
(flanking)	-0.181	0.306

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

108

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

173

mutated

not conserved

173

Ptroglodytes

all identical

ENSPTRG00000009105

173

Mmulatta

all conserved

ENSMMUG00000017341

172

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000017195

172

Ggallus

all identical

ENSGALG00000013484

196

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1017 / 1017

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

339 / 339

position of stopcodon in wt / mu cDNA

1208 / 1208

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

192 / 192

chromosome

strand

last intron/exon boundary

1081

theoretical NMD boundary in CDS

839

length of CDS

1017

coding sequence (CDS) position

518

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

709

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

4218

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

38028634

original gDNA sequence snippet

GCTGAAGAAAATCTTGGATAGTCTAATTTCTGATTTGTCAT

altered gDNA sequence snippet

GCTGAAGAAAATCTTGGATATTCTAATTTCTGATTTGTCAT

original cDNA sequence snippet

GCTGAAGAAAATCTTGGATAGTCTAATTTCTGATTTGTCAT

altered cDNA sequence snippet

GCTGAAGAAAATCTTGGATATTCTAATTTCTGATTTGTCAT

wildtype AA sequence

MMRTCVLLSA VLWCLTGVQC PRFTLFNKKG FIYGKTGQPD KIYVELHQNS PVLICMDFKL
SKKEIVDPTY LWIGPNEKTL TGNNRINITE TGQLMVKDFL EPLSGLYTCT LSYKTVKAET
QEEKTVKKRY DFMVFAYREP DYSYQMAVRF TTRSCIGRYN DVFFRVLKKI LDSLISDLSC
HVIEPSYKCH SVEIPEHGLI HELFIAFQVN PFAPGWKGAC NGSVDCEDTT NHNILQARDR
IEDFFRSQAY IFYHNFNKTL PAMHFVDHSL QVVRLDSCRP GFGKNERLHS NCASCCVVCS
PATFSPDVNV TCQTCVSVLT YGAKSCPQTS NKNQQYED*

mutated AA sequence

MMRTCVLLSA VLWCLTGVQC PRFTLFNKKG FIYGKTGQPD KIYVELHQNS PVLICMDFKL
SKKEIVDPTY LWIGPNEKTL TGNNRINITE TGQLMVKDFL EPLSGLYTCT LSYKTVKAET
QEEKTVKKRY DFMVFAYREP DYSYQMAVRF TTRSCIGRYN DVFFRVLKKI LDILISDLSC
HVIEPSYKCH SVEIPEHGLI HELFIAFQVN PFAPGWKGAC NGSVDCEDTT NHNILQARDR
IEDFFRSQAY IFYHNFNKTL PAMHFVDHSL QVVRLDSCRP GFGKNERLHS NCASCCVVCS
PATFSPDVNV TCQTCVSVLT YGAKSCPQTS NKNQQYED*

speed

0.52 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: 0.999998755024963 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM1111300)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:38028634G>TN/A show variant in all transcripts IGV

HGNC symbol

ZPBP2

Ensembl transcript ID

ENST00000377940

Genbank transcript ID

NM_198844

UniProt peptide

Q6X784

alteration type

single base exchange

alteration region

CDS

DNA changes

c.452G>T
cDNA.591G>T
g.4218G>T

AA changes

S151I Score: 142 explain score(s)

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

151

frameshift

known variant

Reference ID: rs11557467

database	homozygous (T/T)	heterozygous	allele carriers
1000G	377	1147	1524
ExAC	12562	7643	20205

known disease mutation at this position, please check HGMD for details (HGMD ID CM1111300)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.667	0.462
	1.016	0.43
(flanking)	-0.181	0.306

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

108

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

151

mutated

not conserved

151

Ptroglodytes

all identical

ENSPTRG00000009105

173

Mmulatta

all conserved

ENSMMUG00000017341

172

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000017195

172

Ggallus

all identical

ENSGALG00000013484

196

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

951 / 951

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

317 / 317

position of stopcodon in wt / mu cDNA

1090 / 1090

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

140 / 140

chromosome

strand

last intron/exon boundary

963

theoretical NMD boundary in CDS

773

length of CDS

951

coding sequence (CDS) position

452

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

591

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

4218

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

38028634

original gDNA sequence snippet

GCTGAAGAAAATCTTGGATAGTCTAATTTCTGATTTGTCAT

altered gDNA sequence snippet

GCTGAAGAAAATCTTGGATATTCTAATTTCTGATTTGTCAT

original cDNA sequence snippet

GCTGAAGAAAATCTTGGATAGTCTAATTTCTGATTTGTCAT

altered cDNA sequence snippet

GCTGAAGAAAATCTTGGATATTCTAATTTCTGATTTGTCAT

wildtype AA sequence

MMRTCVLLSA VLWCLTGDKI YVELHQNSPV LICMDFKLSK KEIVDPTYLW IGPNEKTLTG
NNRINITETG QLMVKDFLEP LSGLYTCTLS YKTVKAETQE EKTVKKRYDF MVFAYREPDY
SYQMAVRFTT RSCIGRYNDV FFRVLKKILD SLISDLSCHV IEPSYKCHSV EIPEHGLIHE
LFIAFQVNPF APGWKGACNG SVDCEDTTNH NILQARDRIE DFFRSQAYIF YHNFNKTLPA
MHFVDHSLQV VRLDSCRPGF GKNERLHSNC ASCCVVCSPA TFSPDVNVTC QTCVSVLTYG
AKSCPQTSNK NQQYED*

mutated AA sequence

MMRTCVLLSA VLWCLTGDKI YVELHQNSPV LICMDFKLSK KEIVDPTYLW IGPNEKTLTG
NNRINITETG QLMVKDFLEP LSGLYTCTLS YKTVKAETQE EKTVKKRYDF MVFAYREPDY
SYQMAVRFTT RSCIGRYNDV FFRVLKKILD ILISDLSCHV IEPSYKCHSV EIPEHGLIHE
LFIAFQVNPF APGWKGACNG SVDCEDTTNH NILQARDRIE DFFRSQAYIF YHNFNKTLPA
MHFVDHSLQV VRLDSCRPGF GKNERLHSNC ASCCVVCSPA TFSPDVNVTC QTCVSVLTYG
AKSCPQTSNK NQQYED*

speed

0.50 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.972514783863178 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM1111300)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:38028634G>TN/A show variant in all transcripts IGV

HGNC symbol

ZPBP2

Ensembl transcript ID

ENST00000584588

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.4218G>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs11557467

database	homozygous (T/T)	heterozygous	allele carriers
1000G	377	1147	1524
ExAC	12562	7643	20205

known disease mutation at this position, please check HGMD for details (HGMD ID CM1111300)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.667	0.462
	1.016	0.43
(flanking)	-0.181	0.306

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

663

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

140 / 140

chromosome

strand

last intron/exon boundary

810

theoretical NMD boundary in CDS

620

length of CDS

798

coding sequence (CDS) position

N/A

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

N/A

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

4218

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

38028634

original gDNA sequence snippet

GCTGAAGAAAATCTTGGATAGTCTAATTTCTGATTTGTCAT

altered gDNA sequence snippet

GCTGAAGAAAATCTTGGATATTCTAATTTCTGATTTGTCAT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MMRTCVLLSA VLWCLTGVQC PRFTLFNKKG FIYGKTGQPD KIYVELHQNS PVLICMDFKL
SKKEIVDPTY LWIGPNEKTL TGNNRINITE TGQLMVKDFL EPLSGLYTCT LSYKTVKAET
QEEKTVKKRY DFMVFVNPFA PGWKGACNGS VDCEDTTNHN ILQARDRIED FFRSQAYIFY
HNFNKTLPAM HFVDHSLQVV RLDSCRPGFG KNERLHSNCA SCCVVCSPAT FSPDVNVTCQ
TCVSVLTYGA KSCPQTSNKN QQYED*

mutated AA sequence

N/A

speed

0.74 s

Problems

annotation problem

The chosen transcript ENST00000583811 on chromosome 17 has no correct in-frame stop codon (TGA, TAA or TAG) annotated
This is likely to cause a false prediction. You should choose another transcript.

back to results table