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: ENST00000341529
Querying Taster for transcript #2: ENST00000539168
MT speed 0.75 s - this script 2.952014 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CDH5	polymorphism_automatic	3.53338562697481e-06	simple_aae				I517T	single base exchange	rs1049970		show file
CDH5	polymorphism_automatic	0.999999999998613	without_aae					single base exchange	rs1049970		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999996466614373 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM1212658)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:66432423T>CN/A show variant in all transcripts IGV

HGNC symbol

CDH5

Ensembl transcript ID

ENST00000341529

Genbank transcript ID

NM_001795

UniProt peptide

P33151

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1550T>C
cDNA.1698T>C
g.31891T>C

AA changes

I517T Score: 89 explain score(s)

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

517

frameshift

known variant

Reference ID: rs1049970

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1404	920	2324
ExAC	31780	-30793	987

known disease mutation at this position, please check HGMD for details (HGMD ID CM1212658)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.163	0.99
	1.517	0.998
(flanking)	0.719	0.999

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

517

mutated

not conserved

517

Ptroglodytes

not conserved

ENSPTRG00000008190

517

Mmulatta

not conserved

ENSMMUG00000023525

518

Fcatus

not conserved

ENSFCAG00000015244

513

Mmusculus

not conserved

ENSMUSG00000031871

516

Ggallus

not conserved

ENSGALG00000005272

512

Trubripes

all conserved

ENSTRUG00000009855

507

Drerio

not conserved

ENSDARG00000075549

513

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000020009

511

protein features

start (aa)	end (aa)	feature	details
48	599	TOPO_DOM	Extracellular (Potential).	lost
478	593	DOMAIN	Cadherin 5.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2355 / 2355

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

785 / 785

position of stopcodon in wt / mu cDNA

2503 / 2503

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

149 / 149

chromosome

strand

last intron/exon boundary

1986

theoretical NMD boundary in CDS

1787

length of CDS

2355

coding sequence (CDS) position

1550

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

1698

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

31891

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

66432423

original gDNA sequence snippet

AAACGTGAAGTTCAAATTCATCTTGAATACTGAGAACAACT

altered gDNA sequence snippet

AAACGTGAAGTTCAAATTCACCTTGAATACTGAGAACAACT

original cDNA sequence snippet

AAACGTGAAGTTCAAATTCATCTTGAATACTGAGAACAACT

altered cDNA sequence snippet

AAACGTGAAGTTCAAATTCACCTTGAATACTGAGAACAACT

wildtype AA sequence

MQRLMMLLAT SGACLGLLAV AAVAAAGANP AQRDTHSLLP THRRQKRDWI WNQMHIDEEK
NTSLPHHVGK IKSSVSRKNA KYLLKGEYVG KVFRVDAETG DVFAIERLDR ENISEYHLTA
VIVDKDTGEN LETPSSFTIK VHDVNDNWPV FTHRLFNASV PESSAVGTSV ISVTAVDADD
PTVGDHASVM YQILKGKEYF AIDNSGRIIT ITKSLDREKQ ARYEIVVEAR DAQGLRGDSG
TATVLVTLQD INDNFPFFTQ TKYTFVVPED TRVGTSVGSL FVEDPDEPQN RMTKYSILRG
DYQDAFTIET NPAHNEGIIK PMKPLDYEYI QQYSFIVEAT DPTIDLRYMS PPAGNRAQVI
INITDVDEPP IFQQPFYHFQ LKENQKKPLI GTVLAMDPDA ARHSIGYSIR RTSDKGQFFR
VTKKGDIYNE KELDREVYPW YNLTVEAKEL DSTGTPTGKE SIVQVHIEVL DENDNAPEFA
KPYQPKVCEN AVHGQLVLQI SAIDKDITPR NVKFKFILNT ENNFTLTDNH DNTANITVKY
GQFDREHTKV HFLPVVISDN GMPSRTGTST LTVAVCKCNE QGEFTFCEDM AAQVGVSIQA
VVAILLCILT ITVITLLIFL RRRLRKQARA HGKSVPEIHE QLVTYDEEGG GEMDTTSYDV
SVLNSVRRGG AKPPRPALDA RPSLYAQVQK PPRHAPGAHG GPGEMAAMIE VKKDEADHDG
DGPPYDTLHI YGYEGSESIA ESLSSLGTDS SDSDVDYDFL NDWGPRFKML AELYGSDPRE
ELLY*

mutated AA sequence

MQRLMMLLAT SGACLGLLAV AAVAAAGANP AQRDTHSLLP THRRQKRDWI WNQMHIDEEK
NTSLPHHVGK IKSSVSRKNA KYLLKGEYVG KVFRVDAETG DVFAIERLDR ENISEYHLTA
VIVDKDTGEN LETPSSFTIK VHDVNDNWPV FTHRLFNASV PESSAVGTSV ISVTAVDADD
PTVGDHASVM YQILKGKEYF AIDNSGRIIT ITKSLDREKQ ARYEIVVEAR DAQGLRGDSG
TATVLVTLQD INDNFPFFTQ TKYTFVVPED TRVGTSVGSL FVEDPDEPQN RMTKYSILRG
DYQDAFTIET NPAHNEGIIK PMKPLDYEYI QQYSFIVEAT DPTIDLRYMS PPAGNRAQVI
INITDVDEPP IFQQPFYHFQ LKENQKKPLI GTVLAMDPDA ARHSIGYSIR RTSDKGQFFR
VTKKGDIYNE KELDREVYPW YNLTVEAKEL DSTGTPTGKE SIVQVHIEVL DENDNAPEFA
KPYQPKVCEN AVHGQLVLQI SAIDKDITPR NVKFKFTLNT ENNFTLTDNH DNTANITVKY
GQFDREHTKV HFLPVVISDN GMPSRTGTST LTVAVCKCNE QGEFTFCEDM AAQVGVSIQA
VVAILLCILT ITVITLLIFL RRRLRKQARA HGKSVPEIHE QLVTYDEEGG GEMDTTSYDV
SVLNSVRRGG AKPPRPALDA RPSLYAQVQK PPRHAPGAHG GPGEMAAMIE VKKDEADHDG
DGPPYDTLHI YGYEGSESIA ESLSSLGTDS SDSDVDYDFL NDWGPRFKML AELYGSDPRE
ELLY*

speed

0.45 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: 1.3868373172375e-12 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM1212658)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:66432423T>CN/A show variant in all transcripts IGV

HGNC symbol

CDH5

Ensembl transcript ID

ENST00000539168

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.701T>C
g.31891T>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs1049970

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1404	920	2324
ExAC	31780	-30793	987

known disease mutation at this position, please check HGMD for details (HGMD ID CM1212658)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.163	0.99
	1.517	0.998
(flanking)	0.719	0.999

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

splice sites

no abrogation of potential splice sites

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

835 / 835

chromosome

strand

last intron/exon boundary

989

theoretical NMD boundary in CDS

104

length of CDS

672

coding sequence (CDS) position

N/A

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

701

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

31891

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

66432423

original gDNA sequence snippet

AAACGTGAAGTTCAAATTCATCTTGAATACTGAGAACAACT

altered gDNA sequence snippet

AAACGTGAAGTTCAAATTCACCTTGAATACTGAGAACAACT

original cDNA sequence snippet

AAACGTGAAGTTCAAATTCATCTTGAATACTGAGAACAACT

altered cDNA sequence snippet

AAACGTGAAGTTCAAATTCACCTTGAATACTGAGAACAACT

wildtype AA sequence

MPSRTGTSTL TVAVCKCNEQ GEFTFCEDMA AQVGVSIQAV VAILLCILTI TVITLLIFLR
RRLRKQARAH GKSVPEIHEQ LVTYDEEGGG EMDTTSYDVS VLNSVRRGGA KPPRPALDAR
PSLYAQVQKP PRHAPGAHGG PGEMAAMIEV KKDEADHDGD GPPYDTLHIY GYEGSESIAE
SLSSLGTDSS DSDVDYDFLN DWGPRFKMLA ELYGSDPREE LLY*

mutated AA sequence

N/A

speed

0.30 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems