MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000296091
Querying Taster for transcript #2: ENST00000436624
Querying Taster for transcript #3: ENST00000449836
MT speed 0 s - this script 3.918745 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ZNF502	polymorphism_automatic	5.10557017896485e-06	simple_aae				E243A	single base exchange	rs7640654		show file
ZNF502	polymorphism_automatic	5.10557017896485e-06	simple_aae				E243A	single base exchange	rs7640654		show file
ZNF502	polymorphism_automatic	5.10557017896485e-06	simple_aae				E243A	single base exchange	rs7640654		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999994894429821 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:44763037A>CN/A show variant in all transcripts IGV

HGNC symbol

ZNF502

Ensembl transcript ID

ENST00000296091

Genbank transcript ID

NM_001134440

UniProt peptide

Q8TBZ5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.728A>C
cDNA.984A>C
g.8903A>C

AA changes

E243A Score: 107 explain score(s)

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

243

frameshift

known variant

Reference ID: rs7640654

database	homozygous (C/C)	heterozygous	allele carriers
1000G	861	975	1836
ExAC	18120	-3473	14647

regulatory features

Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation
H4K20me3, Histone, Histone 4 Lysine 20 Tri-Methylation
ZNF274, Transcription Factor, ZNF274 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.357	0.102
	0.987	0.395
(flanking)	0.207	0.481

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	8896	wt: 0.9945 / mu: 0.9959 (marginal change - not scored)	wt: ATAAATGCAATGAAT mu: ATAAATGCAATGCAT	AAAT\|gcaa

distance from splice site

673

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

243

mutated

not conserved

243

Ptroglodytes

all identical

ENSPTRG00000022973

243

Mmulatta

all identical

ENSMMUG00000009542

243

Fcatus

all identical

ENSFCAG00000004663

241

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
239	261	ZN_FING	C2H2-type 4.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1635 / 1635

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

545 / 545

position of stopcodon in wt / mu cDNA

1891 / 1891

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

257 / 257

chromosome

strand

last intron/exon boundary

312

theoretical NMD boundary in CDS

length of CDS

1635

coding sequence (CDS) position

728

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

984

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

8903

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

44763037

original gDNA sequence snippet

GAAACCTTATAAATGCAATGAATGTGGGAATTCCTTCCGCA

altered gDNA sequence snippet

GAAACCTTATAAATGCAATGCATGTGGGAATTCCTTCCGCA

original cDNA sequence snippet

GAAACCTTATAAATGCAATGAATGTGGGAATTCCTTCCGCA

altered cDNA sequence snippet

GAAACCTTATAAATGCAATGCATGTGGGAATTCCTTCCGCA

wildtype AA sequence

MLNMQGAEER DIRRETCPGW VNKNKPALEQ DVCKIDSSGI VVKRFQEDEY QDSTFEEKYA
CEGMKENSPR EIAESCLFQE GGFGRITFIH KEAPPEIISQ GYNFEKSLLL TSSLVTRLRV
STEESLHQWE TSNIQTNDIS DQSKCPTLCT QKKSWKCNEC GKTFTQSSSL TQHQRTHTGE
RPYTCEECGK AFSRSSFLVQ HQRIHTGVKP YGCEQCGKTF RCRSFLTQHQ RIHTGEKPYK
CNECGNSFRN HSHLTEHQRI HTGEKPYKCN RCGKAFNQNT HLIHHQRIHT GEKPYICSEC
GSSFRKHSNL TQHQRIHTGE KPHKCDECGK TFQTKANLSQ HQRIHSGEKP YKCKECGKAF
CQSPSLIKHQ RIHTGEKPYK CKECGKAFTQ STPLTKHQRI HTGERPYKCS ECGKAFIQSI
CLIRHQRSHT GEKPYKCNEC GKGFNQNTCL TQHMRIHTGE KPYKCKECGK AFAHSSSLTE
HHRTHTGEKL YKCSECEKTF RKYAHLSEHY RIHTGEKPYE CIECGKFFRH SSVLFRHQKL
HSGD*

mutated AA sequence

MLNMQGAEER DIRRETCPGW VNKNKPALEQ DVCKIDSSGI VVKRFQEDEY QDSTFEEKYA
CEGMKENSPR EIAESCLFQE GGFGRITFIH KEAPPEIISQ GYNFEKSLLL TSSLVTRLRV
STEESLHQWE TSNIQTNDIS DQSKCPTLCT QKKSWKCNEC GKTFTQSSSL TQHQRTHTGE
RPYTCEECGK AFSRSSFLVQ HQRIHTGVKP YGCEQCGKTF RCRSFLTQHQ RIHTGEKPYK
CNACGNSFRN HSHLTEHQRI HTGEKPYKCN RCGKAFNQNT HLIHHQRIHT GEKPYICSEC
GSSFRKHSNL TQHQRIHTGE KPHKCDECGK TFQTKANLSQ HQRIHSGEKP YKCKECGKAF
CQSPSLIKHQ RIHTGEKPYK CKECGKAFTQ STPLTKHQRI HTGERPYKCS ECGKAFIQSI
CLIRHQRSHT GEKPYKCNEC GKGFNQNTCL TQHMRIHTGE KPYKCKECGK AFAHSSSLTE
HHRTHTGEKL YKCSECEKTF RKYAHLSEHY RIHTGEKPYE CIECGKFFRH SSVLFRHQKL
HSGD*

speed

0.54 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: 0.999994894429821 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:44763037A>CN/A show variant in all transcripts IGV

HGNC symbol

ZNF502

Ensembl transcript ID

ENST00000436624

Genbank transcript ID

N/A

UniProt peptide

Q8TBZ5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.728A>C
cDNA.882A>C
g.8903A>C

AA changes

E243A Score: 107 explain score(s)

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

243

frameshift

known variant

Reference ID: rs7640654

database	homozygous (C/C)	heterozygous	allele carriers
1000G	861	975	1836
ExAC	18120	-3473	14647

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.357	0.102
	0.987	0.395
(flanking)	0.207	0.481

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	8896	wt: 0.9945 / mu: 0.9959 (marginal change - not scored)	wt: ATAAATGCAATGAAT mu: ATAAATGCAATGCAT	AAAT\|gcaa

distance from splice site

673

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

243

mutated

not conserved

243

Ptroglodytes

all identical

ENSPTRG00000022973

243

Mmulatta

all identical

ENSMMUG00000009542

243

Fcatus

all identical

ENSFCAG00000004663

241

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
239	261	ZN_FING	C2H2-type 4.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1635 / 1635

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

545 / 545

position of stopcodon in wt / mu cDNA

1789 / 1789

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

155 / 155

chromosome

strand

last intron/exon boundary

210

theoretical NMD boundary in CDS

length of CDS

1635

coding sequence (CDS) position

728

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

882

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

8903

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

44763037

original gDNA sequence snippet

GAAACCTTATAAATGCAATGAATGTGGGAATTCCTTCCGCA

altered gDNA sequence snippet

GAAACCTTATAAATGCAATGCATGTGGGAATTCCTTCCGCA

original cDNA sequence snippet

GAAACCTTATAAATGCAATGAATGTGGGAATTCCTTCCGCA

altered cDNA sequence snippet

GAAACCTTATAAATGCAATGCATGTGGGAATTCCTTCCGCA

wildtype AA sequence

mutated AA sequence

MLNMQGAEER DIRRETCPGW VNKNKPALEQ DVCKIDSSGI VVKRFQEDEY QDSTFEEKYA
CEGMKENSPR EIAESCLFQE GGFGRITFIH KEAPPEIISQ GYNFEKSLLL TSSLVTRLRV
STEESLHQWE TSNIQTNDIS DQSKCPTLCT QKKSWKCNEC GKTFTQSSSL TQHQRTHTGE
RPYTCEECGK AFSRSSFLVQ HQRIHTGVKP YGCEQCGKTF RCRSFLTQHQ RIHTGEKPYK
CNACGNSFRN HSHLTEHQRI HTGEKPYKCN RCGKAFNQNT HLIHHQRIHT GEKPYICSEC
GSSFRKHSNL TQHQRIHTGE KPHKCDECGK TFQTKANLSQ HQRIHSGEKP YKCKECGKAF
CQSPSLIKHQ RIHTGEKPYK CKECGKAFTQ STPLTKHQRI HTGERPYKCS ECGKAFIQSI
CLIRHQRSHT GEKPYKCNEC GKGFNQNTCL TQHMRIHTGE KPYKCKECGK AFAHSSSLTE
HHRTHTGEKL YKCSECEKTF RKYAHLSEHY RIHTGEKPYE CIECGKFFRH SSVLFRHQKL
HSGD*

speed

0.53 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999994894429821 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:44763037A>CN/A show variant in all transcripts IGV

HGNC symbol

ZNF502

Ensembl transcript ID

ENST00000449836

Genbank transcript ID

NM_001134441

UniProt peptide

Q8TBZ5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.728A>C
cDNA.889A>C
g.8903A>C

AA changes

E243A Score: 107 explain score(s)

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

243

frameshift

known variant

Reference ID: rs7640654

database	homozygous (C/C)	heterozygous	allele carriers
1000G	861	975	1836
ExAC	18120	-3473	14647

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.357	0.102
	0.987	0.395
(flanking)	0.207	0.481

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	8896	wt: 0.9945 / mu: 0.9959 (marginal change - not scored)	wt: ATAAATGCAATGAAT mu: ATAAATGCAATGCAT	AAAT\|gcaa

distance from splice site

673

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

243

mutated

not conserved

243

Ptroglodytes

all identical

ENSPTRG00000022973

243

Mmulatta

all identical

ENSMMUG00000009542

243

Fcatus

all identical

ENSFCAG00000004663

241

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
239	261	ZN_FING	C2H2-type 4.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1635 / 1635

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

545 / 545

position of stopcodon in wt / mu cDNA

1796 / 1796

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

162 / 162

chromosome

strand

last intron/exon boundary

217

theoretical NMD boundary in CDS

length of CDS

1635

coding sequence (CDS) position

728

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

889

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

8903

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

44763037

original gDNA sequence snippet

GAAACCTTATAAATGCAATGAATGTGGGAATTCCTTCCGCA

altered gDNA sequence snippet

GAAACCTTATAAATGCAATGCATGTGGGAATTCCTTCCGCA

original cDNA sequence snippet

GAAACCTTATAAATGCAATGAATGTGGGAATTCCTTCCGCA

altered cDNA sequence snippet

GAAACCTTATAAATGCAATGCATGTGGGAATTCCTTCCGCA

wildtype AA sequence

mutated AA sequence

MLNMQGAEER DIRRETCPGW VNKNKPALEQ DVCKIDSSGI VVKRFQEDEY QDSTFEEKYA
CEGMKENSPR EIAESCLFQE GGFGRITFIH KEAPPEIISQ GYNFEKSLLL TSSLVTRLRV
STEESLHQWE TSNIQTNDIS DQSKCPTLCT QKKSWKCNEC GKTFTQSSSL TQHQRTHTGE
RPYTCEECGK AFSRSSFLVQ HQRIHTGVKP YGCEQCGKTF RCRSFLTQHQ RIHTGEKPYK
CNACGNSFRN HSHLTEHQRI HTGEKPYKCN RCGKAFNQNT HLIHHQRIHT GEKPYICSEC
GSSFRKHSNL TQHQRIHTGE KPHKCDECGK TFQTKANLSQ HQRIHSGEKP YKCKECGKAF
CQSPSLIKHQ RIHTGEKPYK CKECGKAFTQ STPLTKHQRI HTGERPYKCS ECGKAFIQSI
CLIRHQRSHT GEKPYKCNEC GKGFNQNTCL TQHMRIHTGE KPYKCKECGK AFAHSSSLTE
HHRTHTGEKL YKCSECEKTF RKYAHLSEHY RIHTGEKPYE CIECGKFFRH SSVLFRHQKL
HSGD*

speed

1.38 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems