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: ENST00000320129
Querying Taster for transcript #2: ENST00000519564
MT speed 0 s - this script 3.438634 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ZNF454	polymorphism_automatic	1.0991207943789e-14	simple_aae				D166A	single base exchange	rs12719860		show file
ZNF454	polymorphism_automatic	1.0991207943789e-14	simple_aae				D166A	single base exchange	rs12719860		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999989 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:178391902A>CN/A show variant in all transcripts IGV

HGNC symbol

ZNF454

Ensembl transcript ID

ENST00000320129

Genbank transcript ID

NM_001178090

UniProt peptide

Q8N9F8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.497A>C
cDNA.800A>C
g.23711A>C

AA changes

D166A Score: 126 explain score(s)

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

166

frameshift

known variant

Reference ID: rs12719860

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1076	1154	2230
ExAC	27389	-22011	5378

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.178	0
	-0.13	0
(flanking)	-0.375	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
Acc marginally increased	23706	wt: 0.6963 / mu: 0.7169 (marginal change - not scored)	wt: ACTATGAGCTCATCTCTTCACAGTGATCAAAGTCAGGGATT mu: ACTATGAGCTCATCTCTTCACAGTGCTCAAAGTCAGGGATT	tcac\|AGTG
Acc marginally increased	23708	wt: 0.5268 / mu: 0.5716 (marginal change - not scored)	wt: TATGAGCTCATCTCTTCACAGTGATCAAAGTCAGGGATTTC mu: TATGAGCTCATCTCTTCACAGTGCTCAAAGTCAGGGATTTC	acag\|TGAT
Acc marginally increased	23707	wt: 0.4029 / mu: 0.4371 (marginal change - not scored)	wt: CTATGAGCTCATCTCTTCACAGTGATCAAAGTCAGGGATTT mu: CTATGAGCTCATCTCTTCACAGTGCTCAAAGTCAGGGATTT	caca\|GTGA
Acc marginally increased	23704	wt: 0.2738 / mu: 0.2992 (marginal change - not scored)	wt: GCACTATGAGCTCATCTCTTCACAGTGATCAAAGTCAGGGA mu: GCACTATGAGCTCATCTCTTCACAGTGCTCAAAGTCAGGGA	cttc\|ACAG
Acc marginally increased	23705	wt: 0.3658 / mu: 0.3764 (marginal change - not scored)	wt: CACTATGAGCTCATCTCTTCACAGTGATCAAAGTCAGGGAT mu: CACTATGAGCTCATCTCTTCACAGTGCTCAAAGTCAGGGAT	ttca\|CAGT

distance from splice site

247

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

166

mutated

not conserved

166

Ptroglodytes

not conserved

ENSPTRG00000017611

164

Mmulatta

not conserved

ENSMMUG00000008980

166

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000048728

181

Ggallus

no homologue

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

1569 / 1569

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

523 / 523

position of stopcodon in wt / mu cDNA

1872 / 1872

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

304 / 304

chromosome

strand

last intron/exon boundary

554

theoretical NMD boundary in CDS

200

length of CDS

1569

coding sequence (CDS) position

497

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

800

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

23711

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

178391902

original gDNA sequence snippet

GAGCTCATCTCTTCACAGTGATCAAAGTCAGGGATTTCAAC

altered gDNA sequence snippet

GAGCTCATCTCTTCACAGTGCTCAAAGTCAGGGATTTCAAC

original cDNA sequence snippet

GAGCTCATCTCTTCACAGTGATCAAAGTCAGGGATTTCAAC

altered cDNA sequence snippet

GAGCTCATCTCTTCACAGTGCTCAAAGTCAGGGATTTCAAC

wildtype AA sequence

MAVSHLPTMV QESVTFKDVA ILFTQEEWGQ LSPAQRALYR DVMLENYSNL VSLGLLGPKP
DTFSQLEKRE VWMPEDTPGG FCLDWMTMPA SKKSTVKAEI PEEELDQWTI KERFSSSSHW
KCASLLEWQC GGQEISLQRV VLTHPNTPSQ ECDESGSTMS SSLHSDQSQG FQPSKNAFEC
SECGKVFSKS STLNKHQKIH NEKNANQKIH IKEKRYECRE CGKAFHQSTH LIHHQRIHTG
EKPYECKECG KAFSVSSSLT YHQKIHTGEK PFECNLCGKA FIRNIHLAHH HRIHTGEKPF
KCNICEKAFV CRAHLTKHQN IHSGEKPYKC NECGKAFNQS TSFLQHQRIH TGEKPFECNE
CGKAFRVNSS LTEHQRIHTG EKPYKCNECG KAFRDNSSFA RHRKIHTGEK PYRCGLCEKA
FRDQSALAQH QRIHTGEKPY TCNICEKAFS DHSALTQHKR IHTREKPYKC KICEKAFIRS
THLTQHQRIH TGEKPYKCNK CGKAFNQTAN LIQHQRHHIG EK*

mutated AA sequence

MAVSHLPTMV QESVTFKDVA ILFTQEEWGQ LSPAQRALYR DVMLENYSNL VSLGLLGPKP
DTFSQLEKRE VWMPEDTPGG FCLDWMTMPA SKKSTVKAEI PEEELDQWTI KERFSSSSHW
KCASLLEWQC GGQEISLQRV VLTHPNTPSQ ECDESGSTMS SSLHSAQSQG FQPSKNAFEC
SECGKVFSKS STLNKHQKIH NEKNANQKIH IKEKRYECRE CGKAFHQSTH LIHHQRIHTG
EKPYECKECG KAFSVSSSLT YHQKIHTGEK PFECNLCGKA FIRNIHLAHH HRIHTGEKPF
KCNICEKAFV CRAHLTKHQN IHSGEKPYKC NECGKAFNQS TSFLQHQRIH TGEKPFECNE
CGKAFRVNSS LTEHQRIHTG EKPYKCNECG KAFRDNSSFA RHRKIHTGEK PYRCGLCEKA
FRDQSALAQH QRIHTGEKPY TCNICEKAFS DHSALTQHKR IHTREKPYKC KICEKAFIRS
THLTQHQRIH TGEKPYKCNK CGKAFNQTAN LIQHQRHHIG EK*

speed

0.81 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: 0.999999999999989 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr5:178391902A>CN/A show variant in all transcripts IGV

HGNC symbol

ZNF454

Ensembl transcript ID

ENST00000519564

Genbank transcript ID

NM_001178089

UniProt peptide

Q8N9F8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.497A>C
cDNA.826A>C
g.23711A>C

AA changes

D166A Score: 126 explain score(s)

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

166

frameshift

known variant

Reference ID: rs12719860

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1076	1154	2230
ExAC	27389	-22011	5378

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.178	0
	-0.13	0
(flanking)	-0.375	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
Acc marginally increased	23706	wt: 0.6963 / mu: 0.7169 (marginal change - not scored)	wt: ACTATGAGCTCATCTCTTCACAGTGATCAAAGTCAGGGATT mu: ACTATGAGCTCATCTCTTCACAGTGCTCAAAGTCAGGGATT	tcac\|AGTG
Acc marginally increased	23708	wt: 0.5268 / mu: 0.5716 (marginal change - not scored)	wt: TATGAGCTCATCTCTTCACAGTGATCAAAGTCAGGGATTTC mu: TATGAGCTCATCTCTTCACAGTGCTCAAAGTCAGGGATTTC	acag\|TGAT
Acc marginally increased	23707	wt: 0.4029 / mu: 0.4371 (marginal change - not scored)	wt: CTATGAGCTCATCTCTTCACAGTGATCAAAGTCAGGGATTT mu: CTATGAGCTCATCTCTTCACAGTGCTCAAAGTCAGGGATTT	caca\|GTGA
Acc marginally increased	23704	wt: 0.2738 / mu: 0.2992 (marginal change - not scored)	wt: GCACTATGAGCTCATCTCTTCACAGTGATCAAAGTCAGGGA mu: GCACTATGAGCTCATCTCTTCACAGTGCTCAAAGTCAGGGA	cttc\|ACAG
Acc marginally increased	23705	wt: 0.3658 / mu: 0.3764 (marginal change - not scored)	wt: CACTATGAGCTCATCTCTTCACAGTGATCAAAGTCAGGGAT mu: CACTATGAGCTCATCTCTTCACAGTGCTCAAAGTCAGGGAT	ttca\|CAGT

distance from splice site

247

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

166

mutated

not conserved

166

Ptroglodytes

not conserved

ENSPTRG00000017611

164

Mmulatta

not conserved

ENSMMUG00000008980

166

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000048728

181

Ggallus

no homologue

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

1569 / 1569

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

523 / 523

position of stopcodon in wt / mu cDNA

1898 / 1898

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

330 / 330

chromosome

strand

last intron/exon boundary

580

theoretical NMD boundary in CDS

200

length of CDS

1569

coding sequence (CDS) position

497

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

826

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

23711

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

178391902

original gDNA sequence snippet

GAGCTCATCTCTTCACAGTGATCAAAGTCAGGGATTTCAAC

altered gDNA sequence snippet

GAGCTCATCTCTTCACAGTGCTCAAAGTCAGGGATTTCAAC

original cDNA sequence snippet

GAGCTCATCTCTTCACAGTGATCAAAGTCAGGGATTTCAAC

altered cDNA sequence snippet

GAGCTCATCTCTTCACAGTGCTCAAAGTCAGGGATTTCAAC

wildtype AA sequence

mutated AA sequence

MAVSHLPTMV QESVTFKDVA ILFTQEEWGQ LSPAQRALYR DVMLENYSNL VSLGLLGPKP
DTFSQLEKRE VWMPEDTPGG FCLDWMTMPA SKKSTVKAEI PEEELDQWTI KERFSSSSHW
KCASLLEWQC GGQEISLQRV VLTHPNTPSQ ECDESGSTMS SSLHSAQSQG FQPSKNAFEC
SECGKVFSKS STLNKHQKIH NEKNANQKIH IKEKRYECRE CGKAFHQSTH LIHHQRIHTG
EKPYECKECG KAFSVSSSLT YHQKIHTGEK PFECNLCGKA FIRNIHLAHH HRIHTGEKPF
KCNICEKAFV CRAHLTKHQN IHSGEKPYKC NECGKAFNQS TSFLQHQRIH TGEKPFECNE
CGKAFRVNSS LTEHQRIHTG EKPYKCNECG KAFRDNSSFA RHRKIHTGEK PYRCGLCEKA
FRDQSALAQH QRIHTGEKPY TCNICEKAFS DHSALTQHKR IHTREKPYKC KICEKAFIRS
THLTQHQRIH TGEKPYKCNK CGKAFNQTAN LIQHQRHHIG EK*

speed

0.63 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems