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: ENST00000449207
Querying Taster for transcript #2: ENST00000407825
MT speed 0 s - this script 3.192686 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PRDM7	polymorphism_automatic	1.31680222281716e-11	simple_aae				D90E	single base exchange	rs12925933		show file
PRDM7	polymorphism_automatic	5.05167572395493e-06	without_aae					single base exchange	rs12925933		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999986832 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:90141355A>CN/A show variant in all transcripts IGV

HGNC symbol

PRDM7

Ensembl transcript ID

ENST00000449207

Genbank transcript ID

NM_001098173

UniProt peptide

Q9NQW5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.270T>G
cDNA.290T>G
g.17126T>G

AA changes

D90E Score: 45 explain score(s)

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

frameshift

known variant

Reference ID: rs12925933

database	homozygous (C/C)	heterozygous	allele carriers
1000G	516	924	1440
ExAC	20430	-8093	12337

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.955	0.028
	0.042	0.026
(flanking)	0.041	0.025

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	17120	wt: 0.9703 / mu: 0.9975 (marginal change - not scored)	wt: GACACAGAAGATTCC mu: GACACAGAAGAGTCC	CACA\|gaag
Donor marginally increased	17118	wt: 0.9891 / mu: 0.9928 (marginal change - not scored)	wt: ATGACACAGAAGATT mu: ATGACACAGAAGAGT	GACA\|caga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000008502

Mmulatta

no alignment

ENSMMUG00000000407

n/a

Fcatus

no alignment

ENSFCAG00000003804

n/a

Mmusculus

all identical

ENSMUSG00000051977

Ggallus

no homologue

Trubripes

no alignment

ENSTRUG00000009314

n/a

Drerio

no alignment

ENSDARG00000005382

n/a

Dmelanogaster

no homologue

Celegans

no alignment

T21B10.5

n/a

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1479 / 1479

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

493 / 493

position of stopcodon in wt / mu cDNA

1499 / 1499

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

21 / 21

chromosome

strand

-1

last intron/exon boundary

1254

theoretical NMD boundary in CDS

1183

length of CDS

1479

coding sequence (CDS) position

270

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

290

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

17126

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

90141355

original gDNA sequence snippet

CAGGTGGATGACACAGAAGATTCCGATGAAGAATGGACACC

altered gDNA sequence snippet

CAGGTGGATGACACAGAAGAGTCCGATGAAGAATGGACACC

original cDNA sequence snippet

CAGGTGGATGACACAGAAGATTCCGATGAAGAATGGACACC

altered cDNA sequence snippet

CAGGTGGATGACACAGAAGAGTCCGATGAAGAATGGACACC

wildtype AA sequence

MSPERSQEES PEGDTERTER KPMVKDAFKD ISIYFTKEEW AEMGDWEKTR YRNVKMNYNA
LITVGLRATR PAFMCHRRQA IKLQVDDTED SDEEWTPRQQ VKPPWMAFRG EQSKHQKGMP
KASFNNESSL RELSGTPNLL NTSDSEQAQK PVSPPGEAST SGQHSRLKLE LRRKETEGKM
YSLRERKGHA YKEISEPQDD DYLYCEMCQN FFIDSCAAHG PPTFVKDSAV DKGHPNRSAL
SLPPGLRIGP SGIPQAGLGV WNEASDLPLG LHFGPYEGRI TEDEEAANSG YSWLITKGRN
CYEYVDGKDK SSANWMRYVN CARDDEEQNL VAFQYHRQIF YRTCRVIRPG CELLVWSGDE
YGQELGIRSS IEPAESLGQA VNCWSGMGMS MARNWASSGA ASGRKSSWQG ENQSQRSIHV
PHAVWPFQVK NFSVNMWNAI TPLRTSQDHL QENFSNQRIP AQGIRIRSGN ILIHAAVMTK
PKVKRSKKGP NS*

mutated AA sequence

MSPERSQEES PEGDTERTER KPMVKDAFKD ISIYFTKEEW AEMGDWEKTR YRNVKMNYNA
LITVGLRATR PAFMCHRRQA IKLQVDDTEE SDEEWTPRQQ VKPPWMAFRG EQSKHQKGMP
KASFNNESSL RELSGTPNLL NTSDSEQAQK PVSPPGEAST SGQHSRLKLE LRRKETEGKM
YSLRERKGHA YKEISEPQDD DYLYCEMCQN FFIDSCAAHG PPTFVKDSAV DKGHPNRSAL
SLPPGLRIGP SGIPQAGLGV WNEASDLPLG LHFGPYEGRI TEDEEAANSG YSWLITKGRN
CYEYVDGKDK SSANWMRYVN CARDDEEQNL VAFQYHRQIF YRTCRVIRPG CELLVWSGDE
YGQELGIRSS IEPAESLGQA VNCWSGMGMS MARNWASSGA ASGRKSSWQG ENQSQRSIHV
PHAVWPFQVK NFSVNMWNAI TPLRTSQDHL QENFSNQRIP AQGIRIRSGN ILIHAAVMTK
PKVKRSKKGP NS*

speed

0.84 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: without_aae, prob: 0.999994948324276 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:90141355A>CN/A show variant in all transcripts IGV

HGNC symbol

PRDM7

Ensembl transcript ID

ENST00000407825

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.290T>G
g.17126T>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs12925933

database	homozygous (C/C)	heterozygous	allele carriers
1000G	516	924	1440
ExAC	20430	-8093	12337

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.955	0.028
	0.042	0.026
(flanking)	0.041	0.025

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	17120	wt: 0.9703 / mu: 0.9975 (marginal change - not scored)	wt: GACACAGAAGATTCC mu: GACACAGAAGAGTCC	CACA\|gaag
Donor marginally increased	17118	wt: 0.9891 / mu: 0.9928 (marginal change - not scored)	wt: ATGACACAGAAGATT mu: ATGACACAGAAGAGT	GACA\|caga

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

639 / 639

chromosome

strand

-1

last intron/exon boundary

971

theoretical NMD boundary in CDS

282

length of CDS

516

coding sequence (CDS) position

N/A

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

290

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

17126

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

90141355

original gDNA sequence snippet

CAGGTGGATGACACAGAAGATTCCGATGAAGAATGGACACC

altered gDNA sequence snippet

CAGGTGGATGACACAGAAGAGTCCGATGAAGAATGGACACC

original cDNA sequence snippet

CAGGTGGATGACACAGAAGATTCCGATGAAGAATGGACACC

altered cDNA sequence snippet

CAGGTGGATGACACAGAAGAGTCCGATGAAGAATGGACACC

wildtype AA sequence

MCQNFFIDSC AAHGPPTFVK DSAVDKGHPN RSALSLPPGL RIGPSGIPQA GLGVWNEASD
LPLGLHFGPY EGRITEDEEA ANSGYSWLIT KGRNCYEYVD GKDKSSANWM RTKARDPSMS
LMLSGLFKSK ISQSTCGTQS LLSELPRTIC KKTSPTRESL PRGSESGAAI F*

mutated AA sequence

N/A

speed

0.41 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems