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: ENST00000433976
Querying Taster for transcript #2: ENST00000306502
Querying Taster for transcript #3: ENST00000378337
MT speed 1.88 s - this script 3.115014 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ZNF778	polymorphism_automatic	0.00296119784831606	simple_aae				K122T	single base exchange	rs28417933		show file
ZNF778	polymorphism_automatic	0.00544750885808998	simple_aae				K164T	single base exchange	rs28417933		show file

some transcripts had annotation problems and are not shown

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.997038802151684 (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)

chr16:89293271A>CN/A show variant in all transcripts IGV

HGNC symbol

ZNF778

Ensembl transcript ID

ENST00000306502

Genbank transcript ID

N/A

UniProt peptide

Q96MU6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.365A>C
cDNA.535A>C
g.9154A>C

AA changes

K122T Score: 78 explain score(s)

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

122

frameshift

known variant

Reference ID: rs28417933

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1018	939	1957
ExAC	-	-	-

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.414	0.967
	2.523	0.997
(flanking)	1.112	0.999

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	9156	wt: 0.9076 / mu: 0.9447 (marginal change - not scored)	wt: TCAAAATTGGAGAGC mu: TCACAATTGGAGAGC	AAAA\|ttgg

distance from splice site

170

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

122

mutated

not conserved

122

Ptroglodytes

all identical

ENSPTRG00000008475

122

Mmulatta

no homologue

Fcatus

no homologue

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
115	140	ZN_FING	C2H2-type 1; degenerate.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2064 / 2064

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

688 / 688

position of stopcodon in wt / mu cDNA

2234 / 2234

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

171 / 171

chromosome

strand

last intron/exon boundary

366

theoretical NMD boundary in CDS

145

length of CDS

2064

coding sequence (CDS) position

365

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

535

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

9154

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

89293271

original gDNA sequence snippet

ATGCCAGAAAACCTTGTTCAAAATTGGAGAGCAGTTTTCCG

altered gDNA sequence snippet

ATGCCAGAAAACCTTGTTCACAATTGGAGAGCAGTTTTCCG

original cDNA sequence snippet

ATGCCAGAAAACCTTGTTCAAAATTGGAGAGCAGTTTTCCG

altered cDNA sequence snippet

ATGCCAGAAAACCTTGTTCACAATTGGAGAGCAGTTTTCCG

wildtype AA sequence

MLENYENLAS VGHHLFQPSV IYWLEQEEEL RAGRRAVLQE WRLKTKGPAL RQDRSWFRAS
NETQTARSHN GGQLCDRTQC GEAFSEHSGL STHVRTQNTG DSCVSNHYER DFFIPCQKTL
FKIGEQFSVL GQCGKAFSST PNVVSQQACT RDRSLDYSSC GEVFLNQSYL QARAGSHNGE
ETWKWKPCGK ALTHSMGCAT PVEMHAVRNP HVCRECGKAF RYTAYLTGRV QVHPGEKPCE
LEECGKASPV SSSLTQHVRI HAAEKPCECK ECGKAFTGLS GLSKHVQTDP GQKPYECKDC
GKACGGFYLL NEHGKTHTRE KPFACVVCGK YFRNSSCLNN HVRIHTGIKP YTCSYCGKAF
TVRCGLTRHV RTHTGEKPYT CKDCGKAFCT SSGLTEHVRT HTGEKPYECK DCGKSFTVSS
SLTEHARIHT GEKPYECKQC GKAFTGRSGL TKHMRTHTGE KPYECKDCGK AYNRVYLLNE
HVKTHTEEKP FICTVCRKSF RNSSCLNKHI QIHTGIKPYE CKDCGKTFTV SSSLTEHIRT
HTGEKPYECK VCGKAFTTSS HLIVHIRTHT GEKPYICKEC GKAFASSSHL IEHRRTHTGE
KPYICNECGK AFRASSHLHK HGRIHTGQKP YKCKECGKAY NRFYLLKEHL KTYTEEQVFV
CKDCGKSFKN SSCLNHHTQI HTDEKPF*

mutated AA sequence

MLENYENLAS VGHHLFQPSV IYWLEQEEEL RAGRRAVLQE WRLKTKGPAL RQDRSWFRAS
NETQTARSHN GGQLCDRTQC GEAFSEHSGL STHVRTQNTG DSCVSNHYER DFFIPCQKTL
FTIGEQFSVL GQCGKAFSST PNVVSQQACT RDRSLDYSSC GEVFLNQSYL QARAGSHNGE
ETWKWKPCGK ALTHSMGCAT PVEMHAVRNP HVCRECGKAF RYTAYLTGRV QVHPGEKPCE
LEECGKASPV SSSLTQHVRI HAAEKPCECK ECGKAFTGLS GLSKHVQTDP GQKPYECKDC
GKACGGFYLL NEHGKTHTRE KPFACVVCGK YFRNSSCLNN HVRIHTGIKP YTCSYCGKAF
TVRCGLTRHV RTHTGEKPYT CKDCGKAFCT SSGLTEHVRT HTGEKPYECK DCGKSFTVSS
SLTEHARIHT GEKPYECKQC GKAFTGRSGL TKHMRTHTGE KPYECKDCGK AYNRVYLLNE
HVKTHTEEKP FICTVCRKSF RNSSCLNKHI QIHTGIKPYE CKDCGKTFTV SSSLTEHIRT
HTGEKPYECK VCGKAFTTSS HLIVHIRTHT GEKPYICKEC GKAFASSSHL IEHRRTHTGE
KPYICNECGK AFRASSHLHK HGRIHTGQKP YKCKECGKAY NRFYLLKEHL KTYTEEQVFV
CKDCGKSFKN SSCLNHHTQI HTDEKPF*

speed

1.10 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: 0.99455249114191 (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)

chr16:89293271A>CN/A show variant in all transcripts IGV

HGNC symbol

ZNF778

Ensembl transcript ID

ENST00000433976

Genbank transcript ID

NM_182531

UniProt peptide

Q96MU6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.491A>C
cDNA.823A>C
g.9154A>C

AA changes

K164T Score: 78 explain score(s)

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

164

frameshift

known variant

Reference ID: rs28417933

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1018	939	1957
ExAC	-	-	-

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.414	0.967
	2.523	0.997
(flanking)	1.112	0.999

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	9156	wt: 0.9076 / mu: 0.9447 (marginal change - not scored)	wt: TCAAAATTGGAGAGC mu: TCACAATTGGAGAGC	AAAA\|ttgg

distance from splice site

170

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

164

mutated

not conserved

164

Ptroglodytes

all identical

ENSPTRG00000008475

122

Mmulatta

no homologue

Fcatus

no homologue

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
164	164	CONFLICT	K -> T (in Ref. 1; BAB71183).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2190 / 2190

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

730 / 730

position of stopcodon in wt / mu cDNA

2522 / 2522

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

333 / 333

chromosome

strand

last intron/exon boundary

654

theoretical NMD boundary in CDS

271

length of CDS

2190

coding sequence (CDS) position

491

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

823

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

9154

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

89293271

original gDNA sequence snippet

ATGCCAGAAAACCTTGTTCAAAATTGGAGAGCAGTTTTCCG

altered gDNA sequence snippet

ATGCCAGAAAACCTTGTTCACAATTGGAGAGCAGTTTTCCG

original cDNA sequence snippet

ATGCCAGAAAACCTTGTTCAAAATTGGAGAGCAGTTTTCCG

altered cDNA sequence snippet

ATGCCAGAAAACCTTGTTCACAATTGGAGAGCAGTTTTCCG

wildtype AA sequence

MAAPDLAHGG HVSRDSVCLH EEQTQAAGMV AGWLINCYQD AVTFDDVAVD FTQEEWTLLD
PSQRDLYRDV MLENYENLAS VEWRLKTKGP ALRQDRSWFR ASNETQTARS HNGGQLCDRT
QCGEAFSEHS GLSTHVRTQN TGDSCVSNHY ERDFFIPCQK TLFKIGEQFS VLGQCGKAFS
STPNVVSQQA CTRDRSLDYS SCGEVFLNQS YLQARAGSHN GEETWKWKPC GKALTHSMGC
ATPVEMHAVR NPHVCRECGK AFRYTAYLTG RVQVHPGEKP CELEECGKAS PVSSSLTQHV
RIHAAEKPCE CKECGKAFTG LSGLSKHVQT DPGQKPYECK DCGKACGGFY LLNEHGKTHT
REKPFACVVC GKYFRNSSCL NNHVRIHTGI KPYTCSYCGK AFTVRCGLTR HVRTHTGEKP
YTCKDCGKAF CTSSGLTEHV RTHTGEKPYE CKDCGKSFTV SSSLTEHARI HTGEKPYECK
QCGKAFTGRS GLTKHMRTHT GEKPYECKDC GKAYNRVYLL NEHVKTHTEE KPFICTVCRK
SFRNSSCLNK HIQIHTGIKP YECKDCGKTF TVSSSLTEHI RTHTGEKPYE CKVCGKAFTT
SSHLIVHIRT HTGEKPYICK ECGKAFASSS HLIEHRRTHT GEKPYICNEC GKAFRASSHL
HKHGRIHTGQ KPYKCKECGK AYNRFYLLKE HLKTYTEEQV FVCKDCGKSF KNSSCLNHHT
QIHTDEKPF*

mutated AA sequence

MAAPDLAHGG HVSRDSVCLH EEQTQAAGMV AGWLINCYQD AVTFDDVAVD FTQEEWTLLD
PSQRDLYRDV MLENYENLAS VEWRLKTKGP ALRQDRSWFR ASNETQTARS HNGGQLCDRT
QCGEAFSEHS GLSTHVRTQN TGDSCVSNHY ERDFFIPCQK TLFTIGEQFS VLGQCGKAFS
STPNVVSQQA CTRDRSLDYS SCGEVFLNQS YLQARAGSHN GEETWKWKPC GKALTHSMGC
ATPVEMHAVR NPHVCRECGK AFRYTAYLTG RVQVHPGEKP CELEECGKAS PVSSSLTQHV
RIHAAEKPCE CKECGKAFTG LSGLSKHVQT DPGQKPYECK DCGKACGGFY LLNEHGKTHT
REKPFACVVC GKYFRNSSCL NNHVRIHTGI KPYTCSYCGK AFTVRCGLTR HVRTHTGEKP
YTCKDCGKAF CTSSGLTEHV RTHTGEKPYE CKDCGKSFTV SSSLTEHARI HTGEKPYECK
QCGKAFTGRS GLTKHMRTHT GEKPYECKDC GKAYNRVYLL NEHVKTHTEE KPFICTVCRK
SFRNSSCLNK HIQIHTGIKP YECKDCGKTF TVSSSLTEHI RTHTGEKPYE CKVCGKAFTT
SSHLIVHIRT HTGEKPYICK ECGKAFASSS HLIEHRRTHT GEKPYICNEC GKAFRASSHL
HKHGRIHTGQ KPYKCKECGK AYNRFYLLKE HLKTYTEEQV FVCKDCGKSF KNSSCLNHHT
QIHTDEKPF*

speed

0.78 s

Problems

data problem

No NCBI gene ID found for this transcript

back to results table