MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000276594
MT speed 0 s - this script 3.068682 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PRDM14	polymorphism_automatic	0.058108146373023	simple_aae		affected		K244E	single base exchange	rs3750228		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.941891853626977 (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)

chr8:70980738T>CN/A show variant in all transcripts IGV

HGNC symbol

PRDM14

Ensembl transcript ID

ENST00000276594

Genbank transcript ID

NM_024504

UniProt peptide

Q9GZV8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.730A>G
cDNA.932A>G
g.3191A>G

AA changes

K244E Score: 56 explain score(s)

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

244

frameshift

known variant

Reference ID: rs3750228

database	homozygous (C/C)	heterozygous	allele carriers
1000G	121	757	878
ExAC	1802	16298	18100

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.571	0.984
	0.86	0.994
(flanking)	1.15	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
Acc marginally increased	3186	wt: 0.3724 / mu: 0.4007 (marginal change - not scored)	wt: TGATTCTCTTCCTCAAACTCTGGATAAAGACTCCCTTCAAC mu: TGATTCTCTTCCTCAAACTCTGGATGAAGACTCCCTTCAAC	ctct\|GGAT
Acc increased	3182	wt: 0.35 / mu: 0.41	wt: GATCTGATTCTCTTCCTCAAACTCTGGATAAAGACTCCCTT mu: GATCTGATTCTCTTCCTCAAACTCTGGATGAAGACTCCCTT	caaa\|CTCT
Acc increased	3184	wt: 0.33 / mu: 0.45	wt: TCTGATTCTCTTCCTCAAACTCTGGATAAAGACTCCCTTCA mu: TCTGATTCTCTTCCTCAAACTCTGGATGAAGACTCCCTTCA	aact\|CTGG
Acc marginally increased	3181	wt: 0.8891 / mu: 0.9026 (marginal change - not scored)	wt: GGATCTGATTCTCTTCCTCAAACTCTGGATAAAGACTCCCT mu: GGATCTGATTCTCTTCCTCAAACTCTGGATGAAGACTCCCT	tcaa\|ACTC
Acc increased	3183	wt: 0.33 / mu: 0.52	wt: ATCTGATTCTCTTCCTCAAACTCTGGATAAAGACTCCCTTC mu: ATCTGATTCTCTTCCTCAAACTCTGGATGAAGACTCCCTTC	aaac\|TCTG
Acc gained	3187	0.34	mu: GATTCTCTTCCTCAAACTCTGGATGAAGACTCCCTTCAACT	tctg\|GATG
Donor gained	3190	0.45	mu: CTGGATGAAGACTCC	GGAT\|gaag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

244

mutated

all conserved

244

Ptroglodytes

all identical

ENSPTRG00000020331

244

Mmulatta

all identical

ENSMMUG00000014191

244

Fcatus

all identical

ENSFCAG00000001436

243

Mmusculus

all identical

ENSMUSG00000042414

234

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000011758

225

Drerio

not conserved

ENSDARG00000045371

196

Dmelanogaster

no homologue

Celegans

no alignment

F47E1.3

n/a

Xtropicalis

all conserved

ENSXETG00000015915

protein features

start (aa)	end (aa)	feature	details
253	371	DOMAIN	SET.	might get lost (downstream of altered splice site)
400	424	ZN_FING	C2H2-type 1; atypical.	might get lost (downstream of altered splice site)
432	455	ZN_FING	C2H2-type 2.	might get lost (downstream of altered splice site)
461	483	ZN_FING	C2H2-type 3.	might get lost (downstream of altered splice site)
489	511	ZN_FING	C2H2-type 4.	might get lost (downstream of altered splice site)
517	540	ZN_FING	C2H2-type 5.	might get lost (downstream of altered splice site)
546	568	ZN_FING	C2H2-type 6.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1716 / 1716

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

572 / 572

position of stopcodon in wt / mu cDNA

1918 / 1918

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

203 / 203

chromosome

strand

-1

last intron/exon boundary

1691

theoretical NMD boundary in CDS

1438

length of CDS

1716

coding sequence (CDS) position

730

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

932

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

3191

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

70980738

original gDNA sequence snippet

CTCTTCCTCAAACTCTGGATAAAGACTCCCTTCAACTTCCA

altered gDNA sequence snippet

CTCTTCCTCAAACTCTGGATGAAGACTCCCTTCAACTTCCA

original cDNA sequence snippet

CTCTTCCTCAAACTCTGGATAAAGACTCCCTTCAACTTCCA

altered cDNA sequence snippet

CTCTTCCTCAAACTCTGGATGAAGACTCCCTTCAACTTCCA

wildtype AA sequence

MALPRPSEAV PQDKVCYPPE SSPQNLAAYY TPFPSYGHYR NSLATVEEDF QPFRQLEAAA
SAAPAMPPFP FRMAPPLLSP GLGLQREPLY DLPWYSKLPP WYPIPHVPRE VPPFLSSSHE
YAGASSEDLG HQIIGGDNES GPCCGPDTLI PPPPADASLL PEGLRTSQLL PCSPSKQSED
GPKPSNQEGK SPARFQFTEE DLHFVLYGVT PSLEHPASLH HAISGLLVPP DSSGSDSLPQ
TLDKDSLQLP EGLCLMQTVF GEVPHFGVFC SSFIAKGVRF GPFQGKVVNA SEVKTYGDNS
VMWEIFEDGH LSHFIDGKGG TGNWMSYVNC ARFPKEQNLV AVQCQGHIFY ESCKEIHQNQ
ELLVWYGDCY EKFLDIPVSL QVTEPGKQPS GPSEESAEGY RCERCGKVFT YKYYRDKHLK
YTPCVDKGDR KFPCSLCKRS FEKRDRLRIH ILHVHEKHRP HKCSTCGKCF SQSSSLNKHM
RVHSGDRPYQ CVYCTKRFTA SSILRTHIRQ HSGEKPFKCK YCGKSFASHA AHDSHVRRSH
KEDDGCSCSI CGKIFSDQET FYSHMKFHED Y*

mutated AA sequence

MALPRPSEAV PQDKVCYPPE SSPQNLAAYY TPFPSYGHYR NSLATVEEDF QPFRQLEAAA
SAAPAMPPFP FRMAPPLLSP GLGLQREPLY DLPWYSKLPP WYPIPHVPRE VPPFLSSSHE
YAGASSEDLG HQIIGGDNES GPCCGPDTLI PPPPADASLL PEGLRTSQLL PCSPSKQSED
GPKPSNQEGK SPARFQFTEE DLHFVLYGVT PSLEHPASLH HAISGLLVPP DSSGSDSLPQ
TLDEDSLQLP EGLCLMQTVF GEVPHFGVFC SSFIAKGVRF GPFQGKVVNA SEVKTYGDNS
VMWEIFEDGH LSHFIDGKGG TGNWMSYVNC ARFPKEQNLV AVQCQGHIFY ESCKEIHQNQ
ELLVWYGDCY EKFLDIPVSL QVTEPGKQPS GPSEESAEGY RCERCGKVFT YKYYRDKHLK
YTPCVDKGDR KFPCSLCKRS FEKRDRLRIH ILHVHEKHRP HKCSTCGKCF SQSSSLNKHM
RVHSGDRPYQ CVYCTKRFTA SSILRTHIRQ HSGEKPFKCK YCGKSFASHA AHDSHVRRSH
KEDDGCSCSI CGKIFSDQET FYSHMKFHED Y*

speed

1.01 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

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

Problems