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: ENST00000265944
Querying Taster for transcript #2: ENST00000543632
MT speed 0 s - this script 4.111674 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
MYO3A	polymorphism_automatic	3.55330209700355e-11	simple_aae		affected		T1284S	single base exchange	rs3740231		show file
MYO3A	polymorphism_automatic	7.98557470149674e-08	without_aae		affected			single base exchange	rs3740231		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999964467 (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)

chr10:26463043A>TN/A show variant in all transcripts IGV

HGNC symbol

MYO3A

Ensembl transcript ID

ENST00000265944

Genbank transcript ID

NM_017433

UniProt peptide

Q8NEV4

alteration type

single base exchange

alteration region

CDS

DNA changes

c.3850A>T
cDNA.4016A>T
g.239848A>T

AA changes

T1284S Score: 58 explain score(s)

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

1284

frameshift

known variant

Reference ID: rs3740231

database	homozygous (T/T)	heterozygous	allele carriers
1000G	380	1146	1526
ExAC	10607	11553	22160

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.887	0
	-0.738	0
(flanking)	0.157	0.001

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 gained	239841	0.52	mu: TCCTTTAAAAAATCT	CTTT\|aaaa

distance from splice site

444

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1284

mutated

all conserved

1284

Ptroglodytes

all identical

ENSPTRG00000002371

1284

Mmulatta

not conserved

ENSMMUG00000012229

1291

Fcatus

no alignment

ENSFCAG00000002336

n/a

Mmusculus

all identical

ENSMUSG00000025716

1293

Ggallus

all identical

ENSGALG00000007647

1287

ESSSKASVKI

Trubripes

no alignment

ENSTRUG00000001734

n/a

Drerio

not conserved

ENSDARG00000010186

1392

Dmelanogaster

no alignment

FBgn0002938

n/a

Celegans

not conserved

Y11D7A.14

1001

TIAK

DEKA

Xtropicalis

all identical

ENSXETG00000018713

1287

IQEG

protein features

start (aa)	end (aa)	feature	details
1346	1375	DOMAIN	IQ 3.	might get lost (downstream of altered splice site)
1355	1355	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1378	1378	CONFLICT	R -> K (in Ref. 1 and 2).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4851 / 4851

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

1617 / 1617

position of stopcodon in wt / mu cDNA

5017 / 5017

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

167 / 167

chromosome

strand

last intron/exon boundary

4897

theoretical NMD boundary in CDS

4680

length of CDS

4851

coding sequence (CDS) position

3850

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

4016

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

239848

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

26463043

original gDNA sequence snippet

ATGAGACTTCCTTTAAAAAAACTTTGGAACCTACACTTAGC

altered gDNA sequence snippet

ATGAGACTTCCTTTAAAAAATCTTTGGAACCTACACTTAGC

original cDNA sequence snippet

ATGAGACTTCCTTTAAAAAAACTTTGGAACCTACACTTAGC

altered cDNA sequence snippet

ATGAGACTTCCTTTAAAAAATCTTTGGAACCTACACTTAGC

wildtype AA sequence

MFPLIGKTII FDNFPDPSDT WEITETIGKG TYGKVFKVLN KKNGQKAAVK ILDPIHDIDE
EIEAEYNILK ALSDHPNVVR FYGIYFKKDK VNGDKLWLVL ELCSGGSVTD LVKGFLKRGE
RMSEPLIAYI LHEALMGLQH LHNNKTIHRD VKGNNILLTT EGGVKLVDFG VSAQLTSTRH
RRNTSVGTPF WMAPEVIACE QQLDTTYDAR CDTWSLGITA IELGDGDPPL ADLHPMRALF
KIPRNPPPKL RQPELWSAEF NDFISKCLTK DYEKRPTVSE LLQHKFITQI EGKDVMLQKQ
LTEFIGIHQC MGGTEKARRE RIHTKKGNFN RPLISNLKDV DDLATLEILD ENTVSEQLEK
CYSRDQIYVY VGDILIALNP FQSLGLYSTK HSKLYIGSKR TASPPHIFAM ADLGYQSMIT
YNSDQCIVIS GESGAGKTEN AHLLVQQLTV LGKANNRTLQ EKILQVNNLV EAFGNACTII
NDNSSRFGKY LEMKFTSSGA VVGAQISEYL LEKSRVIHQA IGEKNFHIFY YIYAGLAEKK
KLAHYKLPEN KPPRYLQNDH LRTVQDIMNN SFYKSQYELI EQCFKVIGFT MEQLGSIYSI
LAAILNVGNI EFSSVATEHQ IDKSHISNHT ALENCASLLC IRADELQEAL TSHCVVTRGE
TIIRPNTVEK ATDVRDAMAK TLYGRLFSWI VNCINSLLKH DSSPSGNGDE LSIGILDIFG
FENFKKNSFE QLCINIANEQ IQYYYNQHVF AWEQNEYLNE DVDARVIEYE DNWPLLDMFL
QKPMGLLSLL DEESRFPKAT DQTLVEKFEG NLKSQYFWRP KRMELSFGIH HYAGKVLYNA
SGFLAKNRDT LPTDIVLLLR SSDNSVIRQL VNHPLTKTGN LPHSKTKNVI NYQMRTSEKL
INLAKGDTGE ATRHARETTN MKTQTVASYF RYSLMDLLSK MVVGQPHFVR CIKPNSERQA
RKYDKEKVLL QLRYTGILET ARIRRLGFSH RILFANFIKR YYLLCYKSSE EPRMSPDTCA
TILEKAGLDN WALGKTKVFL KYYHVEQLNL MRKEAIDKLI LIQACVRAFL CSRRYQKIQE
KRKESAIIIQ SAARGHLVRK QRKEIVDMKN TAVTTIQTSD QEFDYKKNFE NTRESFVKKQ
AENAISANER FISAPNNKGS VSVVKTSTFK PEEETTNAVE SNNRVYQTPK KMNNVYEEEV
KQEFYLVGPE VSPKQKSVKD LEENSNLRKV EKEEAMIQSY YQRYTEERNC EESKAAYLER
KAISERPSYP VPWLAENETS FKKTLEPTLS QRSIYQNANS MEKEKKTSVV TQRAPICSQE
EGRGRLRHET VKERQVEPVT QAQEEEDKAA VFIQSKYRGY KRRQQLRKDK MSSFKHQRIV
TTPTEVARNT HNLYSYPTKH EEINNIKKKD NKDSKATSER EACGLAIFSK QISKLSEEYF
ILQKKLNEMI LSQQLKSLYL GVSHHKPINR RVSSQQCLSG VCKGEEPKIL RPPRRPRKPK
TLNNPEDSTY YYLLHKSIQE EKRRPRKDSQ GKLLDLEDFY YKEFLPSRSG PKEHSPSLRE
RRPQQELQNQ CIKANERCWA AESPEKEEER EPAANPYDFR RLLRKTSQRR RLVQQS*

mutated AA sequence

MFPLIGKTII FDNFPDPSDT WEITETIGKG TYGKVFKVLN KKNGQKAAVK ILDPIHDIDE
EIEAEYNILK ALSDHPNVVR FYGIYFKKDK VNGDKLWLVL ELCSGGSVTD LVKGFLKRGE
RMSEPLIAYI LHEALMGLQH LHNNKTIHRD VKGNNILLTT EGGVKLVDFG VSAQLTSTRH
RRNTSVGTPF WMAPEVIACE QQLDTTYDAR CDTWSLGITA IELGDGDPPL ADLHPMRALF
KIPRNPPPKL RQPELWSAEF NDFISKCLTK DYEKRPTVSE LLQHKFITQI EGKDVMLQKQ
LTEFIGIHQC MGGTEKARRE RIHTKKGNFN RPLISNLKDV DDLATLEILD ENTVSEQLEK
CYSRDQIYVY VGDILIALNP FQSLGLYSTK HSKLYIGSKR TASPPHIFAM ADLGYQSMIT
YNSDQCIVIS GESGAGKTEN AHLLVQQLTV LGKANNRTLQ EKILQVNNLV EAFGNACTII
NDNSSRFGKY LEMKFTSSGA VVGAQISEYL LEKSRVIHQA IGEKNFHIFY YIYAGLAEKK
KLAHYKLPEN KPPRYLQNDH LRTVQDIMNN SFYKSQYELI EQCFKVIGFT MEQLGSIYSI
LAAILNVGNI EFSSVATEHQ IDKSHISNHT ALENCASLLC IRADELQEAL TSHCVVTRGE
TIIRPNTVEK ATDVRDAMAK TLYGRLFSWI VNCINSLLKH DSSPSGNGDE LSIGILDIFG
FENFKKNSFE QLCINIANEQ IQYYYNQHVF AWEQNEYLNE DVDARVIEYE DNWPLLDMFL
QKPMGLLSLL DEESRFPKAT DQTLVEKFEG NLKSQYFWRP KRMELSFGIH HYAGKVLYNA
SGFLAKNRDT LPTDIVLLLR SSDNSVIRQL VNHPLTKTGN LPHSKTKNVI NYQMRTSEKL
INLAKGDTGE ATRHARETTN MKTQTVASYF RYSLMDLLSK MVVGQPHFVR CIKPNSERQA
RKYDKEKVLL QLRYTGILET ARIRRLGFSH RILFANFIKR YYLLCYKSSE EPRMSPDTCA
TILEKAGLDN WALGKTKVFL KYYHVEQLNL MRKEAIDKLI LIQACVRAFL CSRRYQKIQE
KRKESAIIIQ SAARGHLVRK QRKEIVDMKN TAVTTIQTSD QEFDYKKNFE NTRESFVKKQ
AENAISANER FISAPNNKGS VSVVKTSTFK PEEETTNAVE SNNRVYQTPK KMNNVYEEEV
KQEFYLVGPE VSPKQKSVKD LEENSNLRKV EKEEAMIQSY YQRYTEERNC EESKAAYLER
KAISERPSYP VPWLAENETS FKKSLEPTLS QRSIYQNANS MEKEKKTSVV TQRAPICSQE
EGRGRLRHET VKERQVEPVT QAQEEEDKAA VFIQSKYRGY KRRQQLRKDK MSSFKHQRIV
TTPTEVARNT HNLYSYPTKH EEINNIKKKD NKDSKATSER EACGLAIFSK QISKLSEEYF
ILQKKLNEMI LSQQLKSLYL GVSHHKPINR RVSSQQCLSG VCKGEEPKIL RPPRRPRKPK
TLNNPEDSTY YYLLHKSIQE EKRRPRKDSQ GKLLDLEDFY YKEFLPSRSG PKEHSPSLRE
RRPQQELQNQ CIKANERCWA AESPEKEEER EPAANPYDFR RLLRKTSQRR RLVQQS*

speed

1.19 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: 0.999999920144253 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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)

chr10:26463043A>TN/A show variant in all transcripts IGV

HGNC symbol

MYO3A

Ensembl transcript ID

ENST00000543632

Genbank transcript ID

N/A

UniProt peptide

Q8NEV4

alteration type

single base exchange

alteration region

intron

DNA changes

g.239848A>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs3740231

database	homozygous (T/T)	heterozygous	allele carriers
1000G	380	1146	1526
ExAC	10607	11553	22160

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.887	0
	-0.738	0
(flanking)	0.157	0.001

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 gained	239841	0.52	mu: TCCTTTAAAAAATCT	CTTT\|aaaa

distance from splice site

37729

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
340	1041	DOMAIN	Myosin head-like.	might get lost (downstream of altered splice site)
636	636	CONFLICT	A -> V (in Ref. 1 and 2).	might get lost (downstream of altered splice site)
848	851	CONFLICT	RDTL -> KTLV (in Ref. 2; AAF70861).	might get lost (downstream of altered splice site)
886	890	CONFLICT	TKNVI -> LKML (in Ref. 2; AAF70861).	might get lost (downstream of altered splice site)
1055	1084	DOMAIN	IQ 1.	might get lost (downstream of altered splice site)
1082	1111	DOMAIN	IQ 2.	might get lost (downstream of altered splice site)
1099	1099	CONFLICT	R -> G (in Ref. 1 and 2).	might get lost (downstream of altered splice site)
1217	1217	CONFLICT	S -> F (in Ref. 1 and 2).	might get lost (downstream of altered splice site)
1346	1375	DOMAIN	IQ 3.	might get lost (downstream of altered splice site)
1355	1355	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1378	1378	CONFLICT	R -> K (in Ref. 1 and 2).	might get lost (downstream of altered splice site)

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

61 / 61

chromosome

strand

last intron/exon boundary

1837

theoretical NMD boundary in CDS

1726

length of CDS

1995

coding sequence (CDS) position

N/A

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

N/A

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

239848

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

26463043

original gDNA sequence snippet

ATGAGACTTCCTTTAAAAAAACTTTGGAACCTACACTTAGC

altered gDNA sequence snippet

ATGAGACTTCCTTTAAAAAATCTTTGGAACCTACACTTAGC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

mutated AA sequence

N/A

speed

0.93 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems