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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000280333
Querying Taster for transcript #2: ENST00000522781
Querying Taster for transcript #3: ENST00000424811
MT speed 0 s - this script 4.11024 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
INSYN2A	polymorphism_automatic	1.15699005931447e-10	simple_aae				A147V	single base exchange	rs11594560		show file
INSYN2A	polymorphism_automatic	1.15699005931447e-10	simple_aae				A147V	single base exchange	rs11594560		show file
DOCK1	polymorphism_automatic	0.000755586598345959	without_aae		affected			single base exchange	rs11594560		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999884301 (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)

chr10:128974220G>AN/A show variant in all transcripts IGV

HGNC symbol

INSYN2A

Ensembl transcript ID

ENST00000522781

Genbank transcript ID

NM_001039762

UniProt peptide

Q6ZSG2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.440C>T
cDNA.996C>T
g.20203C>T

AA changes

A147V Score: 64 explain score(s)

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

147

frameshift

known variant

Reference ID: rs11594560

database	homozygous (A/A)	heterozygous	allele carriers
1000G	121	588	709
ExAC	3956	21065	25021

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-3.5	0
	1.672	0.003
(flanking)	-0.299	0

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	20196	wt: 0.9027 / mu: 0.9515 (marginal change - not scored)	wt: TTCTAACAGATGCGA mu: TTCTAACAGATGTGA	CTAA\|caga

distance from splice site

445

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

147

mutated

not conserved

147

Ptroglodytes

all identical

ENSPTRG00000003050

147

Mmulatta

all identical

ENSMMUG00000018550

147

Fcatus

no alignment

ENSFCAG00000007355

n/a

Mmusculus

all conserved

ENSMUSG00000073805

147

Ggallus

not conserved

ENSGALG00000013934

147

Trubripes

not conserved

ENSTRUG00000008477

147

SLDE

Drerio

not conserved

ENSDARG00000079559

138

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000005213

146

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1440 / 1440

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

480 / 480

position of stopcodon in wt / mu cDNA

1996 / 1996

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

557 / 557

chromosome

strand

-1

last intron/exon boundary

1813

theoretical NMD boundary in CDS

1206

length of CDS

1440

coding sequence (CDS) position

440

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

996

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

20203

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

128974220

original gDNA sequence snippet

CAATGGGTTTCTAACAGATGCGAAAGAGAAGAACGAGGCTG

altered gDNA sequence snippet

CAATGGGTTTCTAACAGATGTGAAAGAGAAGAACGAGGCTG

original cDNA sequence snippet

CAATGGGTTTCTAACAGATGCGAAAGAGAAGAACGAGGCTG

altered cDNA sequence snippet

CAATGGGTTTCTAACAGATGTGAAAGAGAAGAACGAGGCTG

wildtype AA sequence

MVSKDTGKCI LTTSESEVEP AACLALEMKY ALDPNRQIKK RNKALQVRFK DICEAQNEQR
DTQLSSGQLG EKREAKPVSC RAAYRKYMTV PARRSIPNVT KSTGVQTSPD LKKCYQTFPL
DRKKGNLKSL PAADPFKSQN NGFLTDAKEK NEAGPMEEAR PCGAGRVHKT TALVFHSNQH
MNTVDQPLGV NCTEPCKSPE PLSYGEAALQ NSTRPPSEEP DYQLLGRAKQ DRGRPNSEEP
APPALRRVFK TEVATVYAPA LSARAPEPGL SDSAAASQWS LCPADDERRR ATHLNGLQAP
SETALACSPP MQCLSPECSE QPSQTHTPPG LGNQPSPTAV AAGEECQRIV PHTEVVDLKA
QLQMMENLIS SSQETIKVLL GVIQELEKGE AHREGLSYRT GQDTANCDTC RNSACIIYSV
ELDFKQQEDK LQPVLRKLHP IEETQVIPSP YSQETYSSTP KQKSKTESKK HGRWKLWFL*

mutated AA sequence

MVSKDTGKCI LTTSESEVEP AACLALEMKY ALDPNRQIKK RNKALQVRFK DICEAQNEQR
DTQLSSGQLG EKREAKPVSC RAAYRKYMTV PARRSIPNVT KSTGVQTSPD LKKCYQTFPL
DRKKGNLKSL PAADPFKSQN NGFLTDVKEK NEAGPMEEAR PCGAGRVHKT TALVFHSNQH
MNTVDQPLGV NCTEPCKSPE PLSYGEAALQ NSTRPPSEEP DYQLLGRAKQ DRGRPNSEEP
APPALRRVFK TEVATVYAPA LSARAPEPGL SDSAAASQWS LCPADDERRR ATHLNGLQAP
SETALACSPP MQCLSPECSE QPSQTHTPPG LGNQPSPTAV AAGEECQRIV PHTEVVDLKA
QLQMMENLIS SSQETIKVLL GVIQELEKGE AHREGLSYRT GQDTANCDTC RNSACIIYSV
ELDFKQQEDK LQPVLRKLHP IEETQVIPSP YSQETYSSTP KQKSKTESKK HGRWKLWFL*

speed

0.57 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: 0.999999999884301 (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)

chr10:128974220G>AN/A show variant in all transcripts IGV

HGNC symbol

INSYN2A

Ensembl transcript ID

ENST00000424811

Genbank transcript ID

N/A

UniProt peptide

Q6ZSG2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.440C>T
cDNA.578C>T
g.20203C>T

AA changes

A147V Score: 64 explain score(s)

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

147

frameshift

known variant

Reference ID: rs11594560

database	homozygous (A/A)	heterozygous	allele carriers
1000G	121	588	709
ExAC	3956	21065	25021

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-3.5	0
	1.672	0.003
(flanking)	-0.299	0

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	20196	wt: 0.9027 / mu: 0.9515 (marginal change - not scored)	wt: TTCTAACAGATGCGA mu: TTCTAACAGATGTGA	CTAA\|caga

distance from splice site

445

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

147

mutated

not conserved

147

Ptroglodytes

all identical

ENSPTRG00000003050

147

Mmulatta

all identical

ENSMMUG00000018550

147

Fcatus

no alignment

ENSFCAG00000007355

n/a

Mmusculus

all conserved

ENSMUSG00000073805

147

Ggallus

not conserved

ENSGALG00000013934

147

Trubripes

not conserved

ENSTRUG00000008477

147

SLDE

Drerio

not conserved

ENSDARG00000079559

138

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000005213

146

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1368 / 1368

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

456 / 456

position of stopcodon in wt / mu cDNA

1506 / 1506

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

139 / 139

chromosome

strand

-1

last intron/exon boundary

1323

theoretical NMD boundary in CDS

1134

length of CDS

1368

coding sequence (CDS) position

440

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

578

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

20203

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

128974220

original gDNA sequence snippet

CAATGGGTTTCTAACAGATGCGAAAGAGAAGAACGAGGCTG

altered gDNA sequence snippet

CAATGGGTTTCTAACAGATGTGAAAGAGAAGAACGAGGCTG

original cDNA sequence snippet

CAATGGGTTTCTAACAGATGCGAAAGAGAAGAACGAGGCTG

altered cDNA sequence snippet

CAATGGGTTTCTAACAGATGTGAAAGAGAAGAACGAGGCTG

wildtype AA sequence

MVSKDTGKCI LTTSESEVEP AACLALEMKY ALDPNRQIKK RNKALQVRFK DICEAQNEQR
DTQLSSGQLG EKREAKPVSC RAAYRKYMTV PARRSIPNVT KSTGVQTSPD LKKCYQTFPL
DRKKGNLKSL PAADPFKSQN NGFLTDAKEK NEAGPMEEAR PCGAGRVHKT TALVFHSNQH
MNTVDQPLGV NCTEPCKSPE PLSYGEAALQ NSTRPPSEEP DYQLLGRAKQ DRGRPNSEEP
APPALRRVFK TEVATVYAPA LSARAPEPGL SDSAAASQWS LCPADDERRR ATHLNGLQAP
SETALACSPP MQCLSPECSE QPSQTHTPPG LGNQPSPTAV AAGEECQRIV PHTEVVDLKA
QLQMMENLIS SSQETIKVLL GVIQELEKGE AHREGVELDF KQQEDKLQPV LRKLHPIEET
QVIPSPYSQE TYSSTPKQKS KTESKKHGRW KLWFL*

mutated AA sequence

MVSKDTGKCI LTTSESEVEP AACLALEMKY ALDPNRQIKK RNKALQVRFK DICEAQNEQR
DTQLSSGQLG EKREAKPVSC RAAYRKYMTV PARRSIPNVT KSTGVQTSPD LKKCYQTFPL
DRKKGNLKSL PAADPFKSQN NGFLTDVKEK NEAGPMEEAR PCGAGRVHKT TALVFHSNQH
MNTVDQPLGV NCTEPCKSPE PLSYGEAALQ NSTRPPSEEP DYQLLGRAKQ DRGRPNSEEP
APPALRRVFK TEVATVYAPA LSARAPEPGL SDSAAASQWS LCPADDERRR ATHLNGLQAP
SETALACSPP MQCLSPECSE QPSQTHTPPG LGNQPSPTAV AAGEECQRIV PHTEVVDLKA
QLQMMENLIS SSQETIKVLL GVIQELEKGE AHREGVELDF KQQEDKLQPV LRKLHPIEET
QVIPSPYSQE TYSSTPKQKS KTESKKHGRW KLWFL*

speed

1.32 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 0.999244413401654 (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)

chr10:128974220G>AN/A show variant in all transcripts IGV

HGNC symbol

DOCK1

Ensembl transcript ID

ENST00000280333

Genbank transcript ID

NM_001380

UniProt peptide

Q14185

alteration type

single base exchange

alteration region

intron

DNA changes

g.380243G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs11594560

database	homozygous (A/A)	heterozygous	allele carriers
1000G	121	588	709
ExAC	3956	21065	25021

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-3.5	0
	1.672	0.003
(flanking)	-0.299	0

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	380237	wt: 0.7019 / mu: 0.7387 (marginal change - not scored)	wt: TGGGTCCAGCCTCGTTCTTCTCTTTCGCATCTGTTAGAAAC mu: TGGGTCCAGCCTCGTTCTTCTCTTTCACATCTGTTAGAAAC	ttct\|CTTT
Acc marginally increased	380246	wt: 0.9917 / mu: 0.9933 (marginal change - not scored)	wt: CCTCGTTCTTCTCTTTCGCATCTGTTAGAAACCCATTGTTT mu: CCTCGTTCTTCTCTTTCACATCTGTTAGAAACCCATTGTTT	gcat\|CTGT
Acc marginally increased	380243	wt: 0.9873 / mu: 0.9909 (marginal change - not scored)	wt: CAGCCTCGTTCTTCTCTTTCGCATCTGTTAGAAACCCATTG mu: CAGCCTCGTTCTTCTCTTTCACATCTGTTAGAAACCCATTG	ttcg\|CATC
Acc gained	380245	0.51	mu: GCCTCGTTCTTCTCTTTCACATCTGTTAGAAACCCATTGTT	caca\|TCTG

distance from splice site

48192

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1207	1617	DOMAIN	DHR-2.	might get lost (downstream of altered splice site)
1401	1402	MUTAGEN	YI->AA: Abolishes Rac GEF activity.	might get lost (downstream of altered splice site)
1487	1489	MUTAGEN	ISP->AAA: Abolishes Rac GEF activity.	might get lost (downstream of altered splice site)
1687	1695	REGION	Phosphoinositide-binding (Potential).	might get lost (downstream of altered splice site)
1751	1751	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1756	1756	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
1793	1819	REGION	Interaction with NCK2 second and third SH3 domain (minor).	might get lost (downstream of altered splice site)
1799	1805	MOTIF	SH3-binding; interaction with CRK (Potential).	might get lost (downstream of altered splice site)
1811	1811	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
1820	1836	REGION	Interaction with NCK2 third SH3 domain (major).	might get lost (downstream of altered splice site)
1837	1852	REGION	Interaction with NCK2 (minor).	might get lost (downstream of altered splice site)
1838	1843	MOTIF	SH3-binding; interaction with CRK (Potential).	might get lost (downstream of altered splice site)
1857	1857	CONFLICT	A -> T (in Ref. 1; BAA09454).	might get lost (downstream of altered splice site)
1858	1858	MOD_RES	Phosphoserine.	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

110 / 110

chromosome

strand

last intron/exon boundary

5612

theoretical NMD boundary in CDS

5452

length of CDS

5598

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)

380243

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

128974220

original gDNA sequence snippet

CAGCCTCGTTCTTCTCTTTCGCATCTGTTAGAAACCCATTG

altered gDNA sequence snippet

CAGCCTCGTTCTTCTCTTTCACATCTGTTAGAAACCCATTG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MTRWVPTKRE EKYGVAFYNY DARGADELSL QIGDTVHILE TYEGWYRGYT LRKKSKKGIF
PASYIHLKEA IVEGKGQHET VIPGDLPLIQ EVTTTLREWS TIWRQLYVQD NREMFRSVRH
MIYDLIEWRS QILSGTLPQD ELKELKKKVT AKIDYGNRIL DLDLVVRDED GNILDPELTS
TISLFRAHEI ASKQVEERLQ EEKSQKQNID INRQAKFAAT PSLALFVNLK NVVCKIGEDA
EVLMSLYDPV ESKFISENYL VRWSSSGLPK DIDRLHNLRA VFTDLGSKDL KREKISFVCQ
IVRVGRMELR DNNTRKLTSG LRRPFGVAVM DVTDIINGKV DDEDKQHFIP FQPVAGENDF
LQTVINKVIA AKEVNHKGQG LWVTLKLLPG DIHQIRKEFP HLVDRTTAVA RKTGFPEIIM
PGDVRNDIYV TLVQGDFDKG SKTTAKNVEV TVSVYDEDGK RLEHVIFPGA GDEAISEYKS
VIYYQVKQPR WFETVKVAIP IEDVNRSHLR FTFRHRSSQD SKDKSEKIFA LAFVKLMRYD
GTTLRDGEHD LIVYKAEAKK LEDAATYLSL PSTKAELEEK GHSATGKSMQ SLGSCTISKD
SFQISTLVCS TKLTQNVDLL GLLKWRSNTS LLQQNLRQLM KVDGGEVVKF LQDTLDALFN
IMMENSESET FDTLVFDALV FIIGLIADRK FQHFNPVLET YIKKHFSATL AYTKLTKVLK
NYVDGAEKPG VNEQLYKAMK ALESIFKFIV RSRILFNQLY ENKGEADFVE SLLQLFRSIN
DMMSSMSDQT VRVKGAALKY LPTIVNDVKL VFDPKELSKM FTEFILNVPM GLLTIQKLYC
LIEIVHSDLF TQHDCREILL PMMTDQLKYH LERQEDLEAC CQLLSHILEV LYRKDVGPTQ
RHVQIIMEKL LRTVNRTVIS MGRDSELIGN FVACMTAILR QMEDYHYAHL IKTFGKMRTD
VVDFLMETFI MFKNLIGKNV YPFDWVIMNM VQNKVFLRAI NQYADMLNKK FLDQANFELQ
LWNNYFHLAV AFLTQESLQL ENFSSAKRAK ILNKYGDMRR QIGFEIRDMW YNLGQHKIKF
IPEMVGPILE MTLIPETELR KATIPIFFDM MQCEFHSTRS FQMFENEIIT KLDHEVEGGR
GDEQYKVLFD KILLEHCRKH KYLAKTGETF VKLVVRLMER LLDYRTIMHD ENKENRMSCT
VNVLNFYKEI EREEMYIRYL YKLCDLHKEC DNYTEAAYTL LLHAKLLKWS EDVCVAHLTQ
RDGYQATTQG QLKEQLYQEI IHYFDKGKMW EEAIALGKEL AEQYENEMFD YEQLSELLKK
QAQFYENIVK VIRPKPDYFA VGYYGQGFPT FLRGKVFIYR GKEYERREDF EARLLTQFPN
AEKMKTTSPP GDDIKNSPGQ YIQCFTVKPK LDLPPKFHRP VSEQIVSFYR VNEVQRFEYS
RPIRKGEKNP DNEFANMWIE RTIYTTAYKL PGILRWFEVK SVFMVEISPL ENAIETMQLT
NDKINSMVQQ HLDDPSLPIN PLSMLLNGIV DPAVMGGFAN YEKAFFTDRY LQEHPEAHEK
IEKLKDLIAW QIPFLAEGIR IHGDKVTEAL RPFHERMEAC FKQLKEKVEK EYGVRIMPSS
LDDRRGSRPR SMVRSFTMPS SSRPLSVASV SSLSSDSTPS RPGSDGFALE PLLPKKMHSR
SQDKLDKDDL EKEKKDKKKE KRNSKHQEIF EKEFKPTDIS LQQSEAVILS ETISPLRPQR
PKSQVMNVIG SERRFSVSPS SPSSQQTPPP VTPRAKLSFS MQSSLELNGM TGADVADVPP
PLPLKGSVAD YGNLMENQDL LGSPTPPPPP PHQRHLPPPL PSKTPPPPPP KTTRKQASVD
SGIVQ*

mutated AA sequence

N/A

speed

0.79 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems