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: ENST00000371026
Querying Taster for transcript #2: ENST00000431318
MT speed 1.6 s - this script 3.634662 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
WDR78	polymorphism_automatic	0.079597418228264	simple_aae		affected		R832Q	single base exchange	rs482082		show file
WDR78	polymorphism_automatic	0.104594969932363	simple_aae		affected		R545Q	single base exchange	rs482082		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.920402581771736 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:67288045C>TN/A show variant in all transcripts IGV

HGNC symbol

WDR78

Ensembl transcript ID

ENST00000371026

Genbank transcript ID

NM_024763

UniProt peptide

Q5VTH9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2495G>A
cDNA.2551G>A
g.102526G>A

AA changes

R832Q Score: 43 explain score(s)

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

832

frameshift

known variant

Reference ID: rs482082

database	homozygous (T/T)	heterozygous	allele carriers
1000G	679	1220	1899
ExAC	15457	1853	17310

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.209	1
	1.164	0.975
(flanking)	1.345	0.858

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	102527	sequence motif lost	-	wt: CCGG\|gtaa mu: CCAG.gtaa
Donor marginally increased	102526	wt: 0.9888 / mu: 0.9968 (marginal change - not scored)	wt: TGGCCGGGTAAGACT mu: TGGCCAGGTAAGACT	GCCG\|ggta
Donor marginally increased	102522	wt: 0.9517 / mu: 0.9895 (marginal change - not scored)	wt: AAACTGGCCGGGTAA mu: AAACTGGCCAGGTAA	ACTG\|gccg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

832

mutated

all conserved

832

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000000641

826

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000035126

791

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000006622

770

Drerio

all conserved

ENSDARG00000044400

763

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000020368

783

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2547 / 2547

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

849 / 849

position of stopcodon in wt / mu cDNA

2603 / 2603

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

57 / 57

chromosome

strand

-1

last intron/exon boundary

2553

theoretical NMD boundary in CDS

2446

length of CDS

2547

coding sequence (CDS) position

2495

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

2551

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

102526

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

67288045

original gDNA sequence snippet

TACTGTTTTGGAAACTGGCCGGGTAAGACTCAAGAGTAAAA

altered gDNA sequence snippet

TACTGTTTTGGAAACTGGCCAGGTAAGACTCAAGAGTAAAA

original cDNA sequence snippet

TACTGTTTTGGAAACTGGCCGGGGAGATATAATGGATACTT

altered cDNA sequence snippet

TACTGTTTTGGAAACTGGCCAGGGAGATATAATGGATACTT

wildtype AA sequence

MTPGKHSGAS ARAANGGAWG YRDFRGGQKK GWCTTPQLVA TMPVSPAGSH KQQNFGLNNA
TQPKKSISFF ATMKATSVKG YTGANQSRMA VSKTVLIPPE LKTVEKPNPN IKTTQVFDIN
GTDVTPRPLY HPDPLTGTAK PSKLLTSQEG SLGSEFISSY SLYQNTINPS TLGQFTRSVL
GSSTVSKSSV SASESIAEDL EEPSYKRERL TSFTDLQVIR AAPEKIVTKE DLEKNIEIIL
TETETLRFFD LPTVMVSVES EEAEKVTQRN KNYEVLCRNR LGNDLYVERM MQTFNGAPKN
KDVQCDKIIM EDKGIMSTAW DLYDSYNAME LVSLSVKQSV VESSSKANVL PKDQDQRLPG
STTEKNSETS SLMDIENVIL AKIHEDEEDH SDAILKSDKF HQDLFFMERV LMENIFQPKL
AAYRQLPVLK EPEPEEPEDV LESAKHEEVE EESKKEEEEE IHAEESTIPA NLERLWSFSC
DLTKGLNVSS LAWNKTNPDL LAVGYGHFGF KEQKRGLACC WSIKNPMWPE RIYQSPYGVT
AVDFSIGAPN LLAVGYHNGT IAIYNVRSNS NVPVLDSSES PQKHLGPVWQ LQWIEQDRGT
TGDGKREILV SISADGRISK WVIRKGLDCY DLMRLKRTTA ASNKKGGEKE KKDEALISRQ
APGMCFAFHP KDTNIYLAGT EEGHIHKCSC SYNEQYLDTY RGHKGPVYKV TWNPFCHDVF
LSCSADWGVI IWQQENVKPS LSFYPATSVV YDVAWSPKSS YIFAAANENR VEIWDLHIST
LDPLIVNTAN PGIKFTTILF AKQTDCLLVG DSDGQVSVYE LRNMPTVLET GRGDIMDTLL
GSKSNQSA*

mutated AA sequence

speed

0.80 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: 0.895405030067637 (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)

chr1:67288045C>TN/A show variant in all transcripts IGV

HGNC symbol

WDR78

Ensembl transcript ID

ENST00000431318

Genbank transcript ID

N/A

UniProt peptide

Q5VTH9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1634G>A
cDNA.2452G>A
g.102526G>A

AA changes

R545Q Score: 43 explain score(s)

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

545

frameshift

known variant

Reference ID: rs482082

database	homozygous (T/T)	heterozygous	allele carriers
1000G	679	1220	1899
ExAC	15457	1853	17310

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.209	1
	1.164	0.975
(flanking)	1.345	0.858

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	102527	sequence motif lost	-	wt: CCGG\|gtaa mu: CCAG.gtaa
Donor marginally increased	102526	wt: 0.9888 / mu: 0.9968 (marginal change - not scored)	wt: TGGCCGGGTAAGACT mu: TGGCCAGGTAAGACT	GCCG\|ggta
Donor marginally increased	102522	wt: 0.9517 / mu: 0.9895 (marginal change - not scored)	wt: AAACTGGCCGGGTAA mu: AAACTGGCCAGGTAA	ACTG\|gccg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

545

mutated

all conserved

545

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000000641

826

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000035126

791

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000006622

770

Drerio

all conserved

ENSDARG00000044400

763

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000020368

783

protein features

start (aa)	end (aa)	feature	details
534	574	REPEAT	WD 1.	lost
583	631	REPEAT	WD 2.	might get lost (downstream of altered splice site)
658	698	REPEAT	WD 3.	might get lost (downstream of altered splice site)
702	742	REPEAT	WD 4.	might get lost (downstream of altered splice site)
745	784	REPEAT	WD 5.	might get lost (downstream of altered splice site)
790	829	REPEAT	WD 6.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1686 / 1686

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

562 / 562

position of stopcodon in wt / mu cDNA

2504 / 2504

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

819 / 819

chromosome

strand

-1

last intron/exon boundary

2454

theoretical NMD boundary in CDS

1585

length of CDS

1686

coding sequence (CDS) position

1634

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

2452

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

102526

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

67288045

original gDNA sequence snippet

TACTGTTTTGGAAACTGGCCGGGTAAGACTCAAGAGTAAAA

altered gDNA sequence snippet

TACTGTTTTGGAAACTGGCCAGGTAAGACTCAAGAGTAAAA

original cDNA sequence snippet

TACTGTTTTGGAAACTGGCCGGGGAGATATAATGGATACTT

altered cDNA sequence snippet

TACTGTTTTGGAAACTGGCCAGGGAGATATAATGGATACTT

wildtype AA sequence

MVSVESEEAE KVTQRNKNYE VLCRNRLGND LYVERMMQTF NGAPKNKDVQ CDKIIMEDKG
IMSTAWDLYD SYNAMELVSL SVKQSVVESS SKANVLPKDQ DQRLPGSTTE KNSETSSLMD
IENVILAKIH EDEEDHSDAI LKSDKFHQDL FFMERVLMEN IFQPKLAAYR QLPVLKEPEP
EEPEDVLESA KHEEVEEESK KEEEEEIHAE ESTIPANLER LWSFSCDLTK GLNVSSLAWN
KTNPDLLAVG YGHFGFKEQK RGLACCWSIK NPMWPERIYQ SPYGVTAVDF SIGAPNLLAV
GYHNGTIAIY NVRSNSNVPV LDSSESPQKH LGPVWQLQWI EQDRGTTGDG KREILVSISA
DGRISKWVIR KGLDCYDLMR LKRTTAASNK KGGEKEKKDE ALISRQAPGM CFAFHPKGPV
YKVTWNPFCH DVFLSCSADW GVIIWQQENV KPSLSFYPAT SVVYDVAWSP KSSYIFAAAN
ENRVEIWDLH ISTLDPLIVN TANPGIKFTT ILFAKQTDCL LVGDSDGQVS VYELRNMPTV
LETGRGDIMD TLLGSKSNQS A*

mutated AA sequence

speed

0.80 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems