MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000269973
Querying Taster for transcript #2: ENST00000589703
MT speed 1.68 s - this script 3.704745 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ZNF45	polymorphism_automatic	0.031371043047531	simple_aae		affected		R255K	single base exchange	rs399098		show file
ZNF45	polymorphism_automatic	0.031371043047531	simple_aae		affected		R255K	single base exchange	rs399098		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.968628956952469 (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)

chr19:44418824C>TN/A show variant in all transcripts IGV

HGNC symbol

ZNF45

Ensembl transcript ID

ENST00000269973

Genbank transcript ID

NM_003425

UniProt peptide

Q02386

alteration type

single base exchange

alteration region

CDS

DNA changes

c.764G>A
cDNA.1855G>A
g.20607G>A

AA changes

R255K Score: 26 explain score(s)

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

255

frameshift

known variant

Reference ID: rs399098

database	homozygous (T/T)	heterozygous	allele carriers
1000G	487	1101	1588
ExAC	14609	3549	18158

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.378	0.858
	0.979	0.961
(flanking)	2.649	0.995

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	20602	wt: 0.21 / mu: 0.97	wt: GAGTGTGGGAGGAAT mu: GAGTGTGGGAAGAAT	GTGT\|ggga
Donor marginally increased	20604	wt: 0.2063 / mu: 0.2482 (marginal change - not scored)	wt: GTGTGGGAGGAATGT mu: GTGTGGGAAGAATGT	GTGG\|gagg

distance from splice site

529

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

255

mutated

all conserved

255

Ptroglodytes

all identical

ENSPTRG00000011098

255

Mmulatta

all identical

ENSMMUG00000021474

256

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000074282

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
248	275	ZN_FING	C2H2-type 4.	lost
276	298	ZN_FING	C2H2-type 5.	might get lost (downstream of altered splice site)
304	326	ZN_FING	C2H2-type 6.	might get lost (downstream of altered splice site)
332	354	ZN_FING	C2H2-type 7.	might get lost (downstream of altered splice site)
360	382	ZN_FING	C2H2-type 8.	might get lost (downstream of altered splice site)
388	410	ZN_FING	C2H2-type 9.	might get lost (downstream of altered splice site)
416	438	ZN_FING	C2H2-type 10.	might get lost (downstream of altered splice site)
444	466	ZN_FING	C2H2-type 11.	might get lost (downstream of altered splice site)
455	455	CONFLICT	Q -> R (in Ref. 5; CAA36562).	might get lost (downstream of altered splice site)
472	494	ZN_FING	C2H2-type 12.	might get lost (downstream of altered splice site)
500	522	ZN_FING	C2H2-type 13.	might get lost (downstream of altered splice site)
528	550	ZN_FING	C2H2-type 14.	might get lost (downstream of altered splice site)
556	578	ZN_FING	C2H2-type 15.	might get lost (downstream of altered splice site)
584	606	ZN_FING	C2H2-type 16.	might get lost (downstream of altered splice site)
612	634	ZN_FING	C2H2-type 17.	might get lost (downstream of altered splice site)
640	662	ZN_FING	C2H2-type 18.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2049 / 2049

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

683 / 683

position of stopcodon in wt / mu cDNA

3140 / 3140

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

1092 / 1092

chromosome

strand

-1

last intron/exon boundary

1327

theoretical NMD boundary in CDS

185

length of CDS

2049

coding sequence (CDS) position

764

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

1855

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

20607

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

44418824

original gDNA sequence snippet

CAAATATGAAGAGTGTGGGAGGAATGTTGGGAAAAGCTCAC

altered gDNA sequence snippet

CAAATATGAAGAGTGTGGGAAGAATGTTGGGAAAAGCTCAC

original cDNA sequence snippet

CAAATATGAAGAGTGTGGGAGGAATGTTGGGAAAAGCTCAC

altered cDNA sequence snippet

CAAATATGAAGAGTGTGGGAAGAATGTTGGGAAAAGCTCAC

wildtype AA sequence

MTKSKEAVTF KDVAVVFSEE ELQLLDLAQR KLYRDVMLEN FRNVVSVGHQ STPDGLPQLE
REEKLWMMKM ATQRDNSSGA KNLKEMETLQ EVGLRYLPHE ELFCSQIWQQ ITRELIKYQD
SVVNIQRTGC QLEKRDDLHY KDEGFSNQSS HLQVHRVHTG EKPYKGEHCV KSFSWSSHLQ
INQRAHAGEK PYKCEKCDNA FRRFSSLQAH QRVHSRAKSY TNDASYRSFS QRSHLPHHQR
VPTGENPYKY EECGRNVGKS SHCQAPLIVH TGEKPYKCEE CGVGFSQRSY LQVHLKVHTG
KKPYKCEECG KSFSWRSRLQ AHERIHTGEK PYKCNACGKS FSYSSHLNIH CRIHTGEKPY
KCEECGKGFS VGSHLQAHQI SHTGEKPYKC EECGKGFCRA SNLLDHQRGH TGEKPYQCDA
CGKGFSRSSD FNIHFRVHTG EKPYKCEECG KGFSQASNLL AHQRGHTGEK PYKCGTCGKG
FSRSSDLNVH CRIHTGEKPY KCERCGKAFS QFSSLQVHQR VHTGEKPYQC AECGKGFSVG
SQLQAHQRCH TGEKPYQCEE CGKGFCRASN FLAHRGVHTG EKPYRCDVCG KRFRQRSYLQ
AHQRVHTGER PYKCEECGKV FSWSSYLQAH QRVHTGEKPY KCEECGKGFS WSSSLIIHQR
VHADDEGDKD FPSSEDSHRK TR*

mutated AA sequence

MTKSKEAVTF KDVAVVFSEE ELQLLDLAQR KLYRDVMLEN FRNVVSVGHQ STPDGLPQLE
REEKLWMMKM ATQRDNSSGA KNLKEMETLQ EVGLRYLPHE ELFCSQIWQQ ITRELIKYQD
SVVNIQRTGC QLEKRDDLHY KDEGFSNQSS HLQVHRVHTG EKPYKGEHCV KSFSWSSHLQ
INQRAHAGEK PYKCEKCDNA FRRFSSLQAH QRVHSRAKSY TNDASYRSFS QRSHLPHHQR
VPTGENPYKY EECGKNVGKS SHCQAPLIVH TGEKPYKCEE CGVGFSQRSY LQVHLKVHTG
KKPYKCEECG KSFSWRSRLQ AHERIHTGEK PYKCNACGKS FSYSSHLNIH CRIHTGEKPY
KCEECGKGFS VGSHLQAHQI SHTGEKPYKC EECGKGFCRA SNLLDHQRGH TGEKPYQCDA
CGKGFSRSSD FNIHFRVHTG EKPYKCEECG KGFSQASNLL AHQRGHTGEK PYKCGTCGKG
FSRSSDLNVH CRIHTGEKPY KCERCGKAFS QFSSLQVHQR VHTGEKPYQC AECGKGFSVG
SQLQAHQRCH TGEKPYQCEE CGKGFCRASN FLAHRGVHTG EKPYRCDVCG KRFRQRSYLQ
AHQRVHTGER PYKCEECGKV FSWSSYLQAH QRVHTGEKPY KCEECGKGFS WSSSLIIHQR
VHADDEGDKD FPSSEDSHRK TR*

speed

0.90 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: 0.968628956952469 (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)

chr19:44418824C>TN/A show variant in all transcripts IGV

HGNC symbol

ZNF45

Ensembl transcript ID

ENST00000589703

Genbank transcript ID

N/A

UniProt peptide

Q02386

alteration type

single base exchange

alteration region

CDS

DNA changes

c.764G>A
cDNA.866G>A
g.20607G>A

AA changes

R255K Score: 26 explain score(s)

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

255

frameshift

known variant

Reference ID: rs399098

database	homozygous (T/T)	heterozygous	allele carriers
1000G	487	1101	1588
ExAC	14609	3549	18158

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.378	0.858
	0.979	0.961
(flanking)	2.649	0.995

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	20602	wt: 0.21 / mu: 0.97	wt: GAGTGTGGGAGGAAT mu: GAGTGTGGGAAGAAT	GTGT\|ggga
Donor marginally increased	20604	wt: 0.2063 / mu: 0.2482 (marginal change - not scored)	wt: GTGTGGGAGGAATGT mu: GTGTGGGAAGAATGT	GTGG\|gagg

distance from splice site

529

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

255

mutated

all conserved

255

Ptroglodytes

all identical

ENSPTRG00000011098

255

Mmulatta

all identical

ENSMMUG00000021474

256

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000074282

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
248	275	ZN_FING	C2H2-type 4.	lost
276	298	ZN_FING	C2H2-type 5.	might get lost (downstream of altered splice site)
304	326	ZN_FING	C2H2-type 6.	might get lost (downstream of altered splice site)
332	354	ZN_FING	C2H2-type 7.	might get lost (downstream of altered splice site)
360	382	ZN_FING	C2H2-type 8.	might get lost (downstream of altered splice site)
388	410	ZN_FING	C2H2-type 9.	might get lost (downstream of altered splice site)
416	438	ZN_FING	C2H2-type 10.	might get lost (downstream of altered splice site)
444	466	ZN_FING	C2H2-type 11.	might get lost (downstream of altered splice site)
455	455	CONFLICT	Q -> R (in Ref. 5; CAA36562).	might get lost (downstream of altered splice site)
472	494	ZN_FING	C2H2-type 12.	might get lost (downstream of altered splice site)
500	522	ZN_FING	C2H2-type 13.	might get lost (downstream of altered splice site)
528	550	ZN_FING	C2H2-type 14.	might get lost (downstream of altered splice site)
556	578	ZN_FING	C2H2-type 15.	might get lost (downstream of altered splice site)
584	606	ZN_FING	C2H2-type 16.	might get lost (downstream of altered splice site)
612	634	ZN_FING	C2H2-type 17.	might get lost (downstream of altered splice site)
640	662	ZN_FING	C2H2-type 18.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2049 / 2049

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

683 / 683

position of stopcodon in wt / mu cDNA

2151 / 2151

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

103 / 103

chromosome

strand

-1

last intron/exon boundary

338

theoretical NMD boundary in CDS

185

length of CDS

2049

coding sequence (CDS) position

764

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

866

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

20607

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

44418824

original gDNA sequence snippet

CAAATATGAAGAGTGTGGGAGGAATGTTGGGAAAAGCTCAC

altered gDNA sequence snippet

CAAATATGAAGAGTGTGGGAAGAATGTTGGGAAAAGCTCAC

original cDNA sequence snippet

CAAATATGAAGAGTGTGGGAGGAATGTTGGGAAAAGCTCAC

altered cDNA sequence snippet

CAAATATGAAGAGTGTGGGAAGAATGTTGGGAAAAGCTCAC

wildtype AA sequence

mutated AA sequence

MTKSKEAVTF KDVAVVFSEE ELQLLDLAQR KLYRDVMLEN FRNVVSVGHQ STPDGLPQLE
REEKLWMMKM ATQRDNSSGA KNLKEMETLQ EVGLRYLPHE ELFCSQIWQQ ITRELIKYQD
SVVNIQRTGC QLEKRDDLHY KDEGFSNQSS HLQVHRVHTG EKPYKGEHCV KSFSWSSHLQ
INQRAHAGEK PYKCEKCDNA FRRFSSLQAH QRVHSRAKSY TNDASYRSFS QRSHLPHHQR
VPTGENPYKY EECGKNVGKS SHCQAPLIVH TGEKPYKCEE CGVGFSQRSY LQVHLKVHTG
KKPYKCEECG KSFSWRSRLQ AHERIHTGEK PYKCNACGKS FSYSSHLNIH CRIHTGEKPY
KCEECGKGFS VGSHLQAHQI SHTGEKPYKC EECGKGFCRA SNLLDHQRGH TGEKPYQCDA
CGKGFSRSSD FNIHFRVHTG EKPYKCEECG KGFSQASNLL AHQRGHTGEK PYKCGTCGKG
FSRSSDLNVH CRIHTGEKPY KCERCGKAFS QFSSLQVHQR VHTGEKPYQC AECGKGFSVG
SQLQAHQRCH TGEKPYQCEE CGKGFCRASN FLAHRGVHTG EKPYRCDVCG KRFRQRSYLQ
AHQRVHTGER PYKCEECGKV FSWSSYLQAH QRVHTGEKPY KCEECGKGFS WSSSLIIHQR
VHADDEGDKD FPSSEDSHRK TR*

speed

0.78 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems