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: ENST00000312026
Querying Taster for transcript #2: ENST00000536263
MT speed 0 s - this script 3.393901 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ZNF417	polymorphism_automatic	0	simple_aae		affected		N495S	single base exchange	rs10416584		show file
ZNF417	polymorphism_automatic	0	simple_aae		affected		N296S	single base exchange	rs10416584		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 1 (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)

chr19:58420162T>CN/A show variant in all transcripts IGV

HGNC symbol

ZNF417

Ensembl transcript ID

ENST00000312026

Genbank transcript ID

NM_152475

UniProt peptide

Q8TAU3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1484A>G
cDNA.1683A>G
g.7817A>G

AA changes

N495S Score: 46 explain score(s)

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

495

frameshift

known variant

Reference ID: rs10416584

database	homozygous (C/C)	heterozygous	allele carriers
1000G	274	1028	1302
ExAC	6332	20103	26435

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me3, Histone, Histone 4 Lysine 20 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.077	0
	-3.194	0
(flanking)	-1.44	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
Donor increased	7816	wt: 0.20 / mu: 0.92	wt: AATGCAATGAATGTG mu: AATGCAGTGAATGTG	TGCA\|atga
Donor gained	7811	0.66	mu: GTATGAATGCAGTGA	ATGA\|atgc

distance from splice site

1321

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

495

mutated

all conserved

495

Ptroglodytes

all conserved

ENSPTRG00000028866

497

Mmulatta

all conserved

ENSMMUG00000017400

498

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
492	514	ZN_FING	C2H2-type 11.	lost
520	542	ZN_FING	C2H2-type 12.	might get lost (downstream of altered splice site)
548	570	ZN_FING	C2H2-type 13.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1728 / 1728

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

576 / 576

position of stopcodon in wt / mu cDNA

1927 / 1927

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

200 / 200

chromosome

strand

-1

last intron/exon boundary

363

theoretical NMD boundary in CDS

113

length of CDS

1728

coding sequence (CDS) position

1484

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

1683

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

7817

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

58420162

original gDNA sequence snippet

AGAAAGGCCGTATGAATGCAATGAATGTGGGAAATCATTTC

altered gDNA sequence snippet

AGAAAGGCCGTATGAATGCAGTGAATGTGGGAAATCATTTC

original cDNA sequence snippet

AGAAAGGCCGTATGAATGCAATGAATGTGGGAAATCATTTC

altered cDNA sequence snippet

AGAAAGGCCGTATGAATGCAGTGAATGTGGGAAATCATTTC

wildtype AA sequence

MAAAAPRRPT QQGTVTFEDV AVNFSQEEWC LLSEAQRCLY RDVMLENLAL ISSLGCWCGS
KDEEAPCKQR ISVQRESQSR TPRAGVSPKK AHPCEMCGLI LEDVFHFADH QETHHKQKLN
RSGACGKNLD DTAYLHQHQK QHIGEKFYRK SVREASFVKK RKLRVSQEPF VFREFGKDVL
PSSGLCQEAA AVEKTDSETM HGPPFQEGKT NYSCGKRTKA FSTKHSVIPH QKLFTRDGCY
VCSDCGKSFS RYVSFSNHQR DHTAKGPYDC GECGKSYSRK SSLIQHQRVH TGKTAYPCEE
CGKSFSQKGS LISHQRVHTG ERPYECREYG KSFGQKGNLI QHQQGHTGER AYHCGECGKS
FRQKFCFINH QRVHTGERPY KCGECGKSFG QKGNLVQHQR GHTGERPYEC KECGKSFRYR
SHLTEHQRLH TGERPYNCRE CGKLFNRKYH LLVHERVHTG ERPYACEVCG KLFGNKNCVT
IHQRIHTGER PYECNECGKS FLSSSALHVH KRVHSGQKPY KCSECGKSFA ECSSLIKHRR
IHTGERPYEC TKCGKTFQRS STLLHHQSSH RRKAL*

mutated AA sequence

MAAAAPRRPT QQGTVTFEDV AVNFSQEEWC LLSEAQRCLY RDVMLENLAL ISSLGCWCGS
KDEEAPCKQR ISVQRESQSR TPRAGVSPKK AHPCEMCGLI LEDVFHFADH QETHHKQKLN
RSGACGKNLD DTAYLHQHQK QHIGEKFYRK SVREASFVKK RKLRVSQEPF VFREFGKDVL
PSSGLCQEAA AVEKTDSETM HGPPFQEGKT NYSCGKRTKA FSTKHSVIPH QKLFTRDGCY
VCSDCGKSFS RYVSFSNHQR DHTAKGPYDC GECGKSYSRK SSLIQHQRVH TGKTAYPCEE
CGKSFSQKGS LISHQRVHTG ERPYECREYG KSFGQKGNLI QHQQGHTGER AYHCGECGKS
FRQKFCFINH QRVHTGERPY KCGECGKSFG QKGNLVQHQR GHTGERPYEC KECGKSFRYR
SHLTEHQRLH TGERPYNCRE CGKLFNRKYH LLVHERVHTG ERPYACEVCG KLFGNKNCVT
IHQRIHTGER PYECSECGKS FLSSSALHVH KRVHSGQKPY KCSECGKSFA ECSSLIKHRR
IHTGERPYEC TKCGKTFQRS STLLHHQSSH RRKAL*

speed

0.95 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: 1 (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)

chr19:58420162T>CN/A show variant in all transcripts IGV

HGNC symbol

ZNF417

Ensembl transcript ID

ENST00000536263

Genbank transcript ID

N/A

UniProt peptide

Q8TAU3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.887A>G
cDNA.1841A>G
g.7817A>G

AA changes

N296S Score: 46 explain score(s)

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

296

frameshift

known variant

Reference ID: rs10416584

database	homozygous (C/C)	heterozygous	allele carriers
1000G	274	1028	1302
ExAC	6332	20103	26435

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me3, Histone, Histone 4 Lysine 20 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-2.077	0
	-3.194	0
(flanking)	-1.44	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
Donor increased	7816	wt: 0.20 / mu: 0.92	wt: AATGCAATGAATGTG mu: AATGCAGTGAATGTG	TGCA\|atga
Donor gained	7811	0.66	mu: GTATGAATGCAGTGA	ATGA\|atgc

distance from splice site

606

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

296

mutated

all conserved

296

Ptroglodytes

all conserved

ENSPTRG00000028866

497

Mmulatta

all conserved

ENSMMUG00000017400

498

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
296	318	ZN_FING	C2H2-type 4.	lost
316	316	CONFLICT	R -> L (in Ref. 2; AAH25783).	might get lost (downstream of altered splice site)
324	346	ZN_FING	C2H2-type 5; degenerate.	might get lost (downstream of altered splice site)
352	374	ZN_FING	C2H2-type 6.	might get lost (downstream of altered splice site)
380	402	ZN_FING	C2H2-type 7.	might get lost (downstream of altered splice site)
408	430	ZN_FING	C2H2-type 8.	might get lost (downstream of altered splice site)
436	458	ZN_FING	C2H2-type 9.	might get lost (downstream of altered splice site)
464	486	ZN_FING	C2H2-type 10.	might get lost (downstream of altered splice site)
492	514	ZN_FING	C2H2-type 11.	might get lost (downstream of altered splice site)
520	542	ZN_FING	C2H2-type 12.	might get lost (downstream of altered splice site)
548	570	ZN_FING	C2H2-type 13.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1131 / 1131

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

377 / 377

position of stopcodon in wt / mu cDNA

2085 / 2085

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

955 / 955

chromosome

strand

-1

last intron/exon boundary

521

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

1131

coding sequence (CDS) position

887

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

1841

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

7817

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

58420162

original gDNA sequence snippet

AGAAAGGCCGTATGAATGCAATGAATGTGGGAAATCATTTC

altered gDNA sequence snippet

AGAAAGGCCGTATGAATGCAGTGAATGTGGGAAATCATTTC

original cDNA sequence snippet

AGAAAGGCCGTATGAATGCAATGAATGTGGGAAATCATTTC

altered cDNA sequence snippet

AGAAAGGCCGTATGAATGCAGTGAATGTGGGAAATCATTTC

wildtype AA sequence

MHGPPFQEGK TNYSCGKRTK AFSTKHSVIP HQKLFTRDGC YVCSDCGKSF SRYVSFSNHQ
RDHTAKGPYD CGECGKSYSR KSSLIQHQRV HTGKTAYPCE ECGKSFSQKG SLISHQRVHT
GERPYECREY GKSFGQKGNL IQHQQGHTGE RAYHCGECGK SFRQKFCFIN HQRVHTGERP
YKCGECGKSF GQKGNLVQHQ RGHTGERPYE CKECGKSFRY RSHLTEHQRL HTGERPYNCR
ECGKLFNRKY HLLVHERVHT GERPYACEVC GKLFGNKNCV TIHQRIHTGE RPYECNECGK
SFLSSSALHV HKRVHSGQKP YKCSECGKSF AECSSLIKHR RIHTGERPYE CTKCGKTFQR
SSTLLHHQSS HRRKAL*

mutated AA sequence

MHGPPFQEGK TNYSCGKRTK AFSTKHSVIP HQKLFTRDGC YVCSDCGKSF SRYVSFSNHQ
RDHTAKGPYD CGECGKSYSR KSSLIQHQRV HTGKTAYPCE ECGKSFSQKG SLISHQRVHT
GERPYECREY GKSFGQKGNL IQHQQGHTGE RAYHCGECGK SFRQKFCFIN HQRVHTGERP
YKCGECGKSF GQKGNLVQHQ RGHTGERPYE CKECGKSFRY RSHLTEHQRL HTGERPYNCR
ECGKLFNRKY HLLVHERVHT GERPYACEVC GKLFGNKNCV TIHQRIHTGE RPYECSECGK
SFLSSSALHV HKRVHSGQKP YKCSECGKSF AECSSLIKHR RIHTGERPYE CTKCGKTFQR
SSTLLHHQSS HRRKAL*

speed

0.45 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems