MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000307296
Querying Taster for transcript #2: ENST00000457054
MT speed 0 s - this script 3.142101 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PDCD6IP	polymorphism_automatic	0.999999991722931	simple_aae				V378I	single base exchange	rs3203777		show file
PDCD6IP	polymorphism_automatic	0.999999991722931	simple_aae				V383I	single base exchange	rs3203777		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 8.27706896406314e-09 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:33879770G>AN/A show variant in all transcripts IGV

HGNC symbol

PDCD6IP

Ensembl transcript ID

ENST00000307296

Genbank transcript ID

NM_013374

UniProt peptide

Q8WUM4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1132G>A
cDNA.1509G>A
g.39927G>A

AA changes

V378I Score: 29 explain score(s)

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

378

frameshift

known variant

Reference ID: rs3203777

database	homozygous (A/A)	heterozygous	allele carriers
1000G	332	806	1138
ExAC	10035	12697	22732

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.332	0.073
	4.149	0.998
(flanking)	4.792	1

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

378

mutated

all conserved

378

Ptroglodytes

all identical

ENSPTRG00000014735

378

Mmulatta

all identical

ENSMMUG00000014069

378

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000032504

383

Ggallus

all identical

ENSGALG00000012043

381

Trubripes

all identical

ENSTRUG00000013431

382

Drerio

all identical

ENSDARG00000025269

382

Dmelanogaster

all identical

FBgn0086346

380

Celegans

all identical

R10E12.1

384

Xtropicalis

all conserved

ENSXETG00000017906

377

protein features

start (aa)	end (aa)	feature	details
3	392	DOMAIN	BRO1.	lost
176	503	REGION	Interaction with CHMP4A, CHMP4B and CHMP4C.	lost
176	868	REGION	Interaction with EIAV p9.	lost
361	398	HELIX		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2607 / 2607

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

869 / 869

position of stopcodon in wt / mu cDNA

2984 / 2984

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

378 / 378

chromosome

strand

last intron/exon boundary

2810

theoretical NMD boundary in CDS

2382

length of CDS

2607

coding sequence (CDS) position

1132

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

1509

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

39927

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

33879770

original gDNA sequence snippet

ATCAGAGGAAAGCCGATTTGGTTAACAGATCAATTGCTCAG

altered gDNA sequence snippet

ATCAGAGGAAAGCCGATTTGATTAACAGATCAATTGCTCAG

original cDNA sequence snippet

ATCAGAGGAAAGCCGATTTGGTTAACAGATCAATTGCTCAG

altered cDNA sequence snippet

ATCAGAGGAAAGCCGATTTGATTAACAGATCAATTGCTCAG

wildtype AA sequence

MATFISVQLK KTSEVDLAKP LVKFIQQTYP SGGEEQAQYC RAAEELSKLR RAAVGRPLDK
HEGALETLLR YYDQICSIEP KFPFSENQIC LTFTWKDAFD KGSLFGGSVK LALASLGYEK
SCVLFNCAAL ASQIAAEQNL DNDEGLKIAA KHYQFASGAF LHIKETVLSA LSREPTVDIS
PDTVGTLSLI MLAQAQEVFF LKATRDKMKD AIIAKLANQA ADYFGDAFKQ CQYKDTLPKE
VFPVLAAKHC IMQANAEYHQ SILAKQQKKF GEEIARLQHA AELIKTVASR YDEYVNVKDF
SDKINRALAA AKKDNDFIYH DRVPDLKDLD PIGKATLVKS TPVNVPISQK FTDLFEKMVP
VSVQQSLAAY NQRKADLVNR SIAQMREATT LANGVLASLN LPAAIEDVSG DTVPQSILTK
SRSVIEQGGI QTVDQLIKEL PELLQRNREI LDESLRLLDE EEATDNDLRA KFKERWQRTP
SNELYKPLRA EGTNFRTVLD KAVQADGQVK ECYQSHRDTI VLLCKPEPEL NAAIPSANPA
KTMQGSEVVN VLKSLLSNLD EVKKEREGLE NDLKSVNFDM TSKFLTALAQ DGVINEEALS
VTELDRVYGG LTTKVQESLK KQEGLLKNIQ VSHQEFSKMK QSNNEANLRE EVLKNLATAY
DNFVELVANL KEGTKFYNEL TEILVRFQNK CSDIVFARKT ERDELLKDLQ QSIAREPSAP
SIPTPAYQSS PAGGHAPTPP TPAPRTMPPT KPQPPARPPP PVLPANRAPS ATAPSPVGAG
TAAPAPSQTP GSAPPPQAQG PPYPTYPGYP GYCQMPMPMG YNPYAYGQYN MPYPPVYHQS
PGQAPYPGPQ QPSYPFPQPP QQSYYPQQ*

mutated AA sequence

MATFISVQLK KTSEVDLAKP LVKFIQQTYP SGGEEQAQYC RAAEELSKLR RAAVGRPLDK
HEGALETLLR YYDQICSIEP KFPFSENQIC LTFTWKDAFD KGSLFGGSVK LALASLGYEK
SCVLFNCAAL ASQIAAEQNL DNDEGLKIAA KHYQFASGAF LHIKETVLSA LSREPTVDIS
PDTVGTLSLI MLAQAQEVFF LKATRDKMKD AIIAKLANQA ADYFGDAFKQ CQYKDTLPKE
VFPVLAAKHC IMQANAEYHQ SILAKQQKKF GEEIARLQHA AELIKTVASR YDEYVNVKDF
SDKINRALAA AKKDNDFIYH DRVPDLKDLD PIGKATLVKS TPVNVPISQK FTDLFEKMVP
VSVQQSLAAY NQRKADLINR SIAQMREATT LANGVLASLN LPAAIEDVSG DTVPQSILTK
SRSVIEQGGI QTVDQLIKEL PELLQRNREI LDESLRLLDE EEATDNDLRA KFKERWQRTP
SNELYKPLRA EGTNFRTVLD KAVQADGQVK ECYQSHRDTI VLLCKPEPEL NAAIPSANPA
KTMQGSEVVN VLKSLLSNLD EVKKEREGLE NDLKSVNFDM TSKFLTALAQ DGVINEEALS
VTELDRVYGG LTTKVQESLK KQEGLLKNIQ VSHQEFSKMK QSNNEANLRE EVLKNLATAY
DNFVELVANL KEGTKFYNEL TEILVRFQNK CSDIVFARKT ERDELLKDLQ QSIAREPSAP
SIPTPAYQSS PAGGHAPTPP TPAPRTMPPT KPQPPARPPP PVLPANRAPS ATAPSPVGAG
TAAPAPSQTP GSAPPPQAQG PPYPTYPGYP GYCQMPMPMG YNPYAYGQYN MPYPPVYHQS
PGQAPYPGPQ QPSYPFPQPP QQSYYPQQ*

speed

0.74 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: 8.27706896406314e-09 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:33879770G>AN/A show variant in all transcripts IGV

HGNC symbol

PDCD6IP

Ensembl transcript ID

ENST00000457054

Genbank transcript ID

NM_001162429

UniProt peptide

Q8WUM4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1147G>A
cDNA.1302G>A
g.39927G>A

AA changes

V383I Score: 29 explain score(s)

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

383

frameshift

known variant

Reference ID: rs3203777

database	homozygous (A/A)	heterozygous	allele carriers
1000G	332	806	1138
ExAC	10035	12697	22732

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.332	0.073
	4.149	0.998
(flanking)	4.792	1

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

383

mutated

all conserved

383

Ptroglodytes

all identical

ENSPTRG00000014735

378

Mmulatta

all identical

ENSMMUG00000014069

378

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000032504

383

Ggallus

all identical

ENSGALG00000012043

381

Trubripes

all identical

ENSTRUG00000013431

382

Drerio

all identical

ENSDARG00000025269

382

Dmelanogaster

all identical

FBgn0086346

380

Celegans

all identical

R10E12.1

384

Xtropicalis

all conserved

ENSXETG00000017906

377

protein features

start (aa)	end (aa)	feature	details
3	392	DOMAIN	BRO1.	lost
176	503	REGION	Interaction with CHMP4A, CHMP4B and CHMP4C.	lost
176	868	REGION	Interaction with EIAV p9.	lost
361	398	HELIX		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2622 / 2622

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

874 / 874

position of stopcodon in wt / mu cDNA

2777 / 2777

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

156 / 156

chromosome

strand

last intron/exon boundary

2603

theoretical NMD boundary in CDS

2397

length of CDS

2622

coding sequence (CDS) position

1147

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

1302

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

39927

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

33879770

original gDNA sequence snippet

ATCAGAGGAAAGCCGATTTGGTTAACAGATCAATTGCTCAG

altered gDNA sequence snippet

ATCAGAGGAAAGCCGATTTGATTAACAGATCAATTGCTCAG

original cDNA sequence snippet

ATCAGAGGAAAGCCGATTTGGTTAACAGATCAATTGCTCAG

altered cDNA sequence snippet

ATCAGAGGAAAGCCGATTTGATTAACAGATCAATTGCTCAG

wildtype AA sequence

MATFISVQLK KTSEVDLAKP LVKFIQQTYP SGGEEQAQYC RAAEELSKLR RAAVGRPLDK
HEGALETLLR YYDQICSIEP KFPFSENQIC LTFTWKDAFD KGSLFGGSVK LALASLGYEK
SCVLFNCAAL ASQIAAEQNL DNDEGLKIAA KHYQFASGAF LHIKETVLSA LSREPTVDIS
PDTVGTLSLI MLAQAQEVFF LKATRDKMKD AIIAKLANQA ADYFGDAFKQ CQYKDTLPKY
FYFQEVFPVL AAKHCIMQAN AEYHQSILAK QQKKFGEEIA RLQHAAELIK TVASRYDEYV
NVKDFSDKIN RALAAAKKDN DFIYHDRVPD LKDLDPIGKA TLVKSTPVNV PISQKFTDLF
EKMVPVSVQQ SLAAYNQRKA DLVNRSIAQM REATTLANGV LASLNLPAAI EDVSGDTVPQ
SILTKSRSVI EQGGIQTVDQ LIKELPELLQ RNREILDESL RLLDEEEATD NDLRAKFKER
WQRTPSNELY KPLRAEGTNF RTVLDKAVQA DGQVKECYQS HRDTIVLLCK PEPELNAAIP
SANPAKTMQG SEVVNVLKSL LSNLDEVKKE REGLENDLKS VNFDMTSKFL TALAQDGVIN
EEALSVTELD RVYGGLTTKV QESLKKQEGL LKNIQVSHQE FSKMKQSNNE ANLREEVLKN
LATAYDNFVE LVANLKEGTK FYNELTEILV RFQNKCSDIV FARKTERDEL LKDLQQSIAR
EPSAPSIPTP AYQSSPAGGH APTPPTPAPR TMPPTKPQPP ARPPPPVLPA NRAPSATAPS
PVGAGTAAPA PSQTPGSAPP PQAQGPPYPT YPGYPGYCQM PMPMGYNPYA YGQYNMPYPP
VYHQSPGQAP YPGPQQPSYP FPQPPQQSYY PQQ*

mutated AA sequence

MATFISVQLK KTSEVDLAKP LVKFIQQTYP SGGEEQAQYC RAAEELSKLR RAAVGRPLDK
HEGALETLLR YYDQICSIEP KFPFSENQIC LTFTWKDAFD KGSLFGGSVK LALASLGYEK
SCVLFNCAAL ASQIAAEQNL DNDEGLKIAA KHYQFASGAF LHIKETVLSA LSREPTVDIS
PDTVGTLSLI MLAQAQEVFF LKATRDKMKD AIIAKLANQA ADYFGDAFKQ CQYKDTLPKY
FYFQEVFPVL AAKHCIMQAN AEYHQSILAK QQKKFGEEIA RLQHAAELIK TVASRYDEYV
NVKDFSDKIN RALAAAKKDN DFIYHDRVPD LKDLDPIGKA TLVKSTPVNV PISQKFTDLF
EKMVPVSVQQ SLAAYNQRKA DLINRSIAQM REATTLANGV LASLNLPAAI EDVSGDTVPQ
SILTKSRSVI EQGGIQTVDQ LIKELPELLQ RNREILDESL RLLDEEEATD NDLRAKFKER
WQRTPSNELY KPLRAEGTNF RTVLDKAVQA DGQVKECYQS HRDTIVLLCK PEPELNAAIP
SANPAKTMQG SEVVNVLKSL LSNLDEVKKE REGLENDLKS VNFDMTSKFL TALAQDGVIN
EEALSVTELD RVYGGLTTKV QESLKKQEGL LKNIQVSHQE FSKMKQSNNE ANLREEVLKN
LATAYDNFVE LVANLKEGTK FYNELTEILV RFQNKCSDIV FARKTERDEL LKDLQQSIAR
EPSAPSIPTP AYQSSPAGGH APTPPTPAPR TMPPTKPQPP ARPPPPVLPA NRAPSATAPS
PVGAGTAAPA PSQTPGSAPP PQAQGPPYPT YPGYPGYCQM PMPMGYNPYA YGQYNMPYPP
VYHQSPGQAP YPGPQQPSYP FPQPPQQSYY PQQ*

speed

0.41 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems