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 8 transcript(s)...
Querying Taster for transcript #1: ENST00000354566
Querying Taster for transcript #2: ENST00000316356
Querying Taster for transcript #3: ENST00000525423
Querying Taster for transcript #4: ENST00000528231
Querying Taster for transcript #5: ENST00000527523
Querying Taster for transcript #6: ENST00000524452
Querying Taster for transcript #7: ENST00000389960
Querying Taster for transcript #8: ENST00000359152
MT speed 0 s - this script 6.716659 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SYTL2	polymorphism_automatic	0.00354099960267196	simple_aae		affected		T383M	single base exchange	rs641393		show file
SYTL2	polymorphism_automatic	0.00354099960267196	simple_aae		affected		T383M	single base exchange	rs641393		show file
SYTL2	polymorphism_automatic	0.00354099960267196	simple_aae		affected		T907M	single base exchange	rs641393		show file
SYTL2	polymorphism_automatic	0.999999999085422	without_aae		affected			single base exchange	rs641393		show file
SYTL2	polymorphism_automatic	0.999999999085422	without_aae		affected			single base exchange	rs641393		show file
SYTL2	polymorphism_automatic	0.999999999085422	without_aae		affected			single base exchange	rs641393		show file
SYTL2	polymorphism_automatic	0.999999999085422	without_aae		affected			single base exchange	rs641393		show file
SYTL2	polymorphism_automatic	0.999999999085422	without_aae		affected			single base exchange	rs641393		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.996459000397328 (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)

chr11:85436352G>AN/A show variant in all transcripts IGV

HGNC symbol

SYTL2

Ensembl transcript ID

ENST00000354566

Genbank transcript ID

NM_206927

UniProt peptide

Q9HCH5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1148C>T
cDNA.1160C>T
g.85833C>T

AA changes

T383M Score: 81 explain score(s)

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

383

frameshift

known variant

Reference ID: rs641393

database	homozygous (A/A)	heterozygous	allele carriers
1000G	710	1191	1901
ExAC	21670	-10573	11097

regulatory features

H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.623	0.938
	-0.235	0.875
(flanking)	3.219	0.9

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 increased	85831	wt: 0.31 / mu: 0.53	wt: GCTAGGGTACACCCTTCTCAAACGGAAATTTCGGAGACTGT mu: GCTAGGGTACACCCTTCTCAAATGGAAATTTCGGAGACTGT	tcaa\|ACGG
Donor marginally increased	85834	wt: 0.5422 / mu: 0.5451 (marginal change - not scored)	wt: CAAACGGAAATTTCG mu: CAAATGGAAATTTCG	AACG\|gaaa
Donor gained	85826	0.36	mu: ACCCTTCTCAAATGG	CCTT\|ctca

distance from splice site

1160

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

383

mutated

not conserved

383

Ptroglodytes

all identical

ENSPTRG00000004137

383

Mmulatta

all identical

ENSMMUG00000012449

904

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000030616

405

Ggallus

no alignment

ENSGALG00000014079

n/a

Trubripes

no alignment

ENSTRUG00000001148

n/a

Drerio

no alignment

ENSDARG00000061956

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000012793

n/a

protein features

start (aa)	end (aa)	feature	details
488	488	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
562	562	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
579	619	COMPBIAS	Ser-rich.	might get lost (downstream of altered splice site)
603	603	CONFLICT	S -> P (in Ref. 1; ABV82746).	might get lost (downstream of altered splice site)
629	733	DOMAIN	C2 1.	might get lost (downstream of altered splice site)
658	658	CONFLICT	A -> V (in Ref. 4; BAD18516).	might get lost (downstream of altered splice site)
682	682	CONFLICT	K -> M (in Ref. 7; AAI44116).	might get lost (downstream of altered splice site)
718	718	CONFLICT	I -> V (in Ref. 4; BAB15030).	might get lost (downstream of altered splice site)
778	880	DOMAIN	C2 2.	might get lost (downstream of altered splice site)
860	860	CONFLICT	A -> V (in Ref. 3; BAB13423).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3819 / 3819

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

1273 / 1273

position of stopcodon in wt / mu cDNA

3831 / 3831

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

13 / 13

chromosome

strand

-1

last intron/exon boundary

3686

theoretical NMD boundary in CDS

3623

length of CDS

3819

coding sequence (CDS) position

1148

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

1160

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

85833

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

85436352

original gDNA sequence snippet

TAGGGTACACCCTTCTCAAACGGAAATTTCGGAGACTGTAG

altered gDNA sequence snippet

TAGGGTACACCCTTCTCAAATGGAAATTTCGGAGACTGTAG

original cDNA sequence snippet

TAGGGTACACCCTTCTCAAACGGAAATTTCGGAGACTGTAG

altered cDNA sequence snippet

TAGGGTACACCCTTCTCAAATGGAAATTTCGGAGACTGTAG

wildtype AA sequence

MDEPNAEQVY NPSQFENLRK FWDLEANSNS KDNDKNITTT SQKNSAPFNR QKHKEFSDIK
LSGKNTHEAE VLLSPKKVMA REEMEKLNSK GILQVLPDEI TFPLSPLRKY TYQLPGNESS
KENVEKNTEG IVTPVFKEEK DYSEQEIQES IIKTNVLSKD CKDTFNDSLQ KLLSETSTPA
IQPSGGKVHG KQVLEPSVSE NRTWPQKTDF ADTEEEVKGP EKIINEHVDK TVVHPKVKRN
SLTASLDKLL KEATGTSPSP LQAKLAPVIT GTNSKLEEGR FFGKGIEQSH NTSADKREIL
APFPVRDETF GNTALLKKAE SGECQLSTQN LIQMAAEDSH PLDPTSQLSR KGSFGDVASP
PQDMLFPQDA HLVPQARVHP SQTEISETVE KVILPPRPVL NDVSAALQKL CGEVWLSYPA
GREVGPGEVN PEFPEAVQPV CSPLNPPGVI SPWATMDTIV PDRKDFYSSN VVPDKTHEVG
SYLAAQMSPS DQTLSSFASI VAQYGKGLPQ EVEEIVRETI VQPKSEFLEF SAGLEKLLKE
ETETFPSKYE SDTGNLSPSK LIGSTEEPRR ATSECHPEEL KETVEKAEAP LITESAFDAG
FEKLLKEITE APPYQPQVSV REETHEKESS QSEQTRFLGT VPHFYRAASQ TSEMKDKSNG
LESQVNQCDK MLGGDALVTD LLVDFCGSRS GVEIPRTPQL YVAHEIGTIK TVTPPEDRDS
ESGVAGGQGT LQEPGFGEAS EAISVSRNRQ PIPLLMNKEN STKTSKVELT LASPYMKQEK
EEEKEGFSES DFSDGNTSSN AESWRNPSSS EEEPSPVLKT LERSAARKMP SKSLEDISSD
SSNQAKVDNQ PEELVRSAED DEKPDQKPVT NECVPRISTV PTQPDNPFSH PDKLKRMSKS
VPAFLQDESD DRETDTASES SYQLSRHKKS PSSLTNLSSS SGMTSLSSVS GSVMSVYSGD
FGNLEVKGNI QFAIEYVESL KELHVFVAQC KDLAAADVKK QRSDPYVKAY LLPDKGKMGK
KKTLVVKKTL NPVYNEILRY KIEKQILKTQ KLNLSIWHRD TFKRNSFLGE VELDLETWDW
DNKQNKQLRW YPLKRKTAPV ALEAENRGEM KLALQYVPEP VPGKKLPTTG EVHIWVKECL
DLPLLRGSHL NSFVKCTILP DTSRKSRQKT RAVGKTTNPI FNHTMVYDGF RPEDLMEACV
ELTVWDHYKL TNQFLGGLRI GFGTGKSYGT EVDWMDSTSE EVALWEKMVN SPNTWIEATL
PLRMLLIAKI SK*

mutated AA sequence

MDEPNAEQVY NPSQFENLRK FWDLEANSNS KDNDKNITTT SQKNSAPFNR QKHKEFSDIK
LSGKNTHEAE VLLSPKKVMA REEMEKLNSK GILQVLPDEI TFPLSPLRKY TYQLPGNESS
KENVEKNTEG IVTPVFKEEK DYSEQEIQES IIKTNVLSKD CKDTFNDSLQ KLLSETSTPA
IQPSGGKVHG KQVLEPSVSE NRTWPQKTDF ADTEEEVKGP EKIINEHVDK TVVHPKVKRN
SLTASLDKLL KEATGTSPSP LQAKLAPVIT GTNSKLEEGR FFGKGIEQSH NTSADKREIL
APFPVRDETF GNTALLKKAE SGECQLSTQN LIQMAAEDSH PLDPTSQLSR KGSFGDVASP
PQDMLFPQDA HLVPQARVHP SQMEISETVE KVILPPRPVL NDVSAALQKL CGEVWLSYPA
GREVGPGEVN PEFPEAVQPV CSPLNPPGVI SPWATMDTIV PDRKDFYSSN VVPDKTHEVG
SYLAAQMSPS DQTLSSFASI VAQYGKGLPQ EVEEIVRETI VQPKSEFLEF SAGLEKLLKE
ETETFPSKYE SDTGNLSPSK LIGSTEEPRR ATSECHPEEL KETVEKAEAP LITESAFDAG
FEKLLKEITE APPYQPQVSV REETHEKESS QSEQTRFLGT VPHFYRAASQ TSEMKDKSNG
LESQVNQCDK MLGGDALVTD LLVDFCGSRS GVEIPRTPQL YVAHEIGTIK TVTPPEDRDS
ESGVAGGQGT LQEPGFGEAS EAISVSRNRQ PIPLLMNKEN STKTSKVELT LASPYMKQEK
EEEKEGFSES DFSDGNTSSN AESWRNPSSS EEEPSPVLKT LERSAARKMP SKSLEDISSD
SSNQAKVDNQ PEELVRSAED DEKPDQKPVT NECVPRISTV PTQPDNPFSH PDKLKRMSKS
VPAFLQDESD DRETDTASES SYQLSRHKKS PSSLTNLSSS SGMTSLSSVS GSVMSVYSGD
FGNLEVKGNI QFAIEYVESL KELHVFVAQC KDLAAADVKK QRSDPYVKAY LLPDKGKMGK
KKTLVVKKTL NPVYNEILRY KIEKQILKTQ KLNLSIWHRD TFKRNSFLGE VELDLETWDW
DNKQNKQLRW YPLKRKTAPV ALEAENRGEM KLALQYVPEP VPGKKLPTTG EVHIWVKECL
DLPLLRGSHL NSFVKCTILP DTSRKSRQKT RAVGKTTNPI FNHTMVYDGF RPEDLMEACV
ELTVWDHYKL TNQFLGGLRI GFGTGKSYGT EVDWMDSTSE EVALWEKMVN SPNTWIEATL
PLRMLLIAKI SK*

speed

1.02 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: 0.996459000397328 (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)

chr11:85436352G>AN/A show variant in all transcripts IGV

HGNC symbol

SYTL2

Ensembl transcript ID

ENST00000525423

Genbank transcript ID

NM_206928

UniProt peptide

Q9HCH5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1148C>T
cDNA.2720C>T
g.85833C>T

AA changes

T383M Score: 81 explain score(s)

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

383

frameshift

known variant

Reference ID: rs641393

database	homozygous (A/A)	heterozygous	allele carriers
1000G	710	1191	1901
ExAC	21670	-10573	11097

regulatory features

H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.623	0.938
	-0.235	0.875
(flanking)	3.219	0.9

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 increased	85831	wt: 0.31 / mu: 0.53	wt: GCTAGGGTACACCCTTCTCAAACGGAAATTTCGGAGACTGT mu: GCTAGGGTACACCCTTCTCAAATGGAAATTTCGGAGACTGT	tcaa\|ACGG
Donor marginally increased	85834	wt: 0.5422 / mu: 0.5451 (marginal change - not scored)	wt: CAAACGGAAATTTCG mu: CAAATGGAAATTTCG	AACG\|gaaa
Donor gained	85826	0.36	mu: ACCCTTCTCAAATGG	CCTT\|ctca

distance from splice site

1278

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

383

mutated

not conserved

383

Ptroglodytes

all identical

ENSPTRG00000004137

383

Mmulatta

all identical

ENSMMUG00000012449

904

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000030616

405

Ggallus

no alignment

ENSGALG00000014079

n/a

Trubripes

no alignment

ENSTRUG00000001148

n/a

Drerio

no alignment

ENSDARG00000061956

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000012793

n/a

protein features

start (aa)	end (aa)	feature	details
488	488	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
562	562	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
579	619	COMPBIAS	Ser-rich.	might get lost (downstream of altered splice site)
603	603	CONFLICT	S -> P (in Ref. 1; ABV82746).	might get lost (downstream of altered splice site)
629	733	DOMAIN	C2 1.	might get lost (downstream of altered splice site)
658	658	CONFLICT	A -> V (in Ref. 4; BAD18516).	might get lost (downstream of altered splice site)
682	682	CONFLICT	K -> M (in Ref. 7; AAI44116).	might get lost (downstream of altered splice site)
718	718	CONFLICT	I -> V (in Ref. 4; BAB15030).	might get lost (downstream of altered splice site)
778	880	DOMAIN	C2 2.	might get lost (downstream of altered splice site)
860	860	CONFLICT	A -> V (in Ref. 3; BAB13423).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3771 / 3771

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

1257 / 1257

position of stopcodon in wt / mu cDNA

5343 / 5343

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

1573 / 1573

chromosome

strand

-1

last intron/exon boundary

5198

theoretical NMD boundary in CDS

3575

length of CDS

3771

coding sequence (CDS) position

1148

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

2720

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

85833

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

85436352

original gDNA sequence snippet

TAGGGTACACCCTTCTCAAACGGAAATTTCGGAGACTGTAG

altered gDNA sequence snippet

TAGGGTACACCCTTCTCAAATGGAAATTTCGGAGACTGTAG

original cDNA sequence snippet

TAGGGTACACCCTTCTCAAACGGAAATTTCGGAGACTGTAG

altered cDNA sequence snippet

TAGGGTACACCCTTCTCAAATGGAAATTTCGGAGACTGTAG

wildtype AA sequence

MDEPNAEQVY NPSQFENLRK FWDLEANSNS KDNDKNITTT SQKNSAPFNR QKHKEFSDIK
LSGKNTHEAE VLLSPKKVMA REEMEKLNSK GILQVLPDEI TFPLSPLRKY TYQLPGNESS
KENVEKNTEG IVTPVFKEEK DYSEQEIQES IIKTNVLSKD CKDTFNDSLQ KLLSETSTPA
IQPSGGKVHG KQVLEPSVSE NRTWPQKTDF ADTEEEVKGP EKIINEHVDK TVVHPKVKRN
SLTASLDKLL KEATGTSPSP LQAKLAPVIT GTNSKLEEGR FFGKGIEQSH NTSADKREIL
APFPVRDETF GNTALLKKAE SGECQLSTQN LIQMAAEDSH PLDPTSQLSR KGSFGDVASP
PQDMLFPQDA HLVPQARVHP SQTEISETVE KVILPPRPVL NDVSAALQKL CGEVWLSYPA
GREVGPGEVN PEFPEAVQPV CSPLNPPGVI SPWATMDTIV PDRKDFYSSN VVPDKTHEVG
SYLAAQMSPS DQTLSSFASI VAQYGKGLPQ EVEEIVRETI VQPKSEFLEF SAGLEKLLKE
ETETFPSKYE SDTGNLSPSK LIGSTEEPRR ATSECHPEEL KETVEKAEAP LITESAFDAG
FEKLLKEITE APPYQPQVSV REETHEKESS QSEQTRFLGT VPHFYRAASQ TSEMKDKSNG
LESQVNQCDK MLGGDALVTD LLVDFCGSRS GVEIPRTPQL YVAHEIGTIK TVTPPEDRDS
ESGVAGGQGT LQEPGFGEAS EAISVSRNRQ PIPLLMNKEN STKTSKVELT LASPYMKQEK
EEEKEGFSES DFSDGNTSSN AESWRNPSSS EEEPSPVLKT LERSAARKMP SKSLEDISSD
SSNQAKVDNQ PEELVRSAED VSTVPTQPDN PFSHPDKLKR MSKSVPAFLQ DESDDRETDT
ASESSYQLSR HKKSPSSLTN LSSSSGMTSL SSVSGSVMSV YSGDFGNLEV KGNIQFAIEY
VESLKELHVF VAQCKDLAAA DVKKQRSDPY VKAYLLPDKG KMGKKKTLVV KKTLNPVYNE
ILRYKIEKQI LKTQKLNLSI WHRDTFKRNS FLGEVELDLE TWDWDNKQNK QLRWYPLKRK
TAPVALEAEN RGEMKLALQY VPEPVPGKKL PTTGEVHIWV KECLDLPLLR GSHLNSFVKC
TILPDTSRKS RQKTRAVGKT TNPIFNHTMV YDGFRPEDLM EACVELTVWD HYKLTNQFLG
GLRIGFGTGK SYGTEVDWMD STSEEVALWE KMVNSPNTWI EATLPLRMLL IAKISK*

mutated AA sequence

MDEPNAEQVY NPSQFENLRK FWDLEANSNS KDNDKNITTT SQKNSAPFNR QKHKEFSDIK
LSGKNTHEAE VLLSPKKVMA REEMEKLNSK GILQVLPDEI TFPLSPLRKY TYQLPGNESS
KENVEKNTEG IVTPVFKEEK DYSEQEIQES IIKTNVLSKD CKDTFNDSLQ KLLSETSTPA
IQPSGGKVHG KQVLEPSVSE NRTWPQKTDF ADTEEEVKGP EKIINEHVDK TVVHPKVKRN
SLTASLDKLL KEATGTSPSP LQAKLAPVIT GTNSKLEEGR FFGKGIEQSH NTSADKREIL
APFPVRDETF GNTALLKKAE SGECQLSTQN LIQMAAEDSH PLDPTSQLSR KGSFGDVASP
PQDMLFPQDA HLVPQARVHP SQMEISETVE KVILPPRPVL NDVSAALQKL CGEVWLSYPA
GREVGPGEVN PEFPEAVQPV CSPLNPPGVI SPWATMDTIV PDRKDFYSSN VVPDKTHEVG
SYLAAQMSPS DQTLSSFASI VAQYGKGLPQ EVEEIVRETI VQPKSEFLEF SAGLEKLLKE
ETETFPSKYE SDTGNLSPSK LIGSTEEPRR ATSECHPEEL KETVEKAEAP LITESAFDAG
FEKLLKEITE APPYQPQVSV REETHEKESS QSEQTRFLGT VPHFYRAASQ TSEMKDKSNG
LESQVNQCDK MLGGDALVTD LLVDFCGSRS GVEIPRTPQL YVAHEIGTIK TVTPPEDRDS
ESGVAGGQGT LQEPGFGEAS EAISVSRNRQ PIPLLMNKEN STKTSKVELT LASPYMKQEK
EEEKEGFSES DFSDGNTSSN AESWRNPSSS EEEPSPVLKT LERSAARKMP SKSLEDISSD
SSNQAKVDNQ PEELVRSAED VSTVPTQPDN PFSHPDKLKR MSKSVPAFLQ DESDDRETDT
ASESSYQLSR HKKSPSSLTN LSSSSGMTSL SSVSGSVMSV YSGDFGNLEV KGNIQFAIEY
VESLKELHVF VAQCKDLAAA DVKKQRSDPY VKAYLLPDKG KMGKKKTLVV KKTLNPVYNE
ILRYKIEKQI LKTQKLNLSI WHRDTFKRNS FLGEVELDLE TWDWDNKQNK QLRWYPLKRK
TAPVALEAEN RGEMKLALQY VPEPVPGKKL PTTGEVHIWV KECLDLPLLR GSHLNSFVKC
TILPDTSRKS RQKTRAVGKT TNPIFNHTMV YDGFRPEDLM EACVELTVWD HYKLTNQFLG
GLRIGFGTGK SYGTEVDWMD STSEEVALWE KMVNSPNTWI EATLPLRMLL IAKISK*

speed

0.98 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.996459000397328 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:85436352G>AN/A show variant in all transcripts IGV

HGNC symbol

SYTL2

Ensembl transcript ID

ENST00000359152

Genbank transcript ID

N/A

UniProt peptide

Q9HCH5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2720C>T
cDNA.2720C>T
g.85833C>T

AA changes

T907M Score: 81 explain score(s)

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

907

frameshift

known variant

Reference ID: rs641393

database	homozygous (A/A)	heterozygous	allele carriers
1000G	710	1191	1901
ExAC	21670	-10573	11097

regulatory features

H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.623	0.938
	-0.235	0.875
(flanking)	3.219	0.9

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 increased	85831	wt: 0.31 / mu: 0.53	wt: GCTAGGGTACACCCTTCTCAAACGGAAATTTCGGAGACTGT mu: GCTAGGGTACACCCTTCTCAAATGGAAATTTCGGAGACTGT	tcaa\|ACGG
Donor marginally increased	85834	wt: 0.5422 / mu: 0.5451 (marginal change - not scored)	wt: CAAACGGAAATTTCG mu: CAAATGGAAATTTCG	AACG\|gaaa
Donor gained	85826	0.36	mu: ACCCTTCTCAAATGG	CCTT\|ctca

distance from splice site

1278

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

907

mutated

not conserved

907

Ptroglodytes

all identical

ENSPTRG00000004137

383

Mmulatta

all identical

ENSMMUG00000012449

904

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000030616

410

Ggallus

no alignment

ENSGALG00000014079

n/a

Trubripes

no alignment

ENSTRUG00000001148

n/a

Drerio

no alignment

ENSDARG00000061956

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000012793

n/a

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5343 / 5343

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

1781 / 1781

position of stopcodon in wt / mu cDNA

5343 / 5343

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

1 / 1

chromosome

strand

-1

last intron/exon boundary

5198

theoretical NMD boundary in CDS

5147

length of CDS

5343

coding sequence (CDS) position

2720

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

2720

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

85833

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

85436352

original gDNA sequence snippet

TAGGGTACACCCTTCTCAAACGGAAATTTCGGAGACTGTAG

altered gDNA sequence snippet

TAGGGTACACCCTTCTCAAATGGAAATTTCGGAGACTGTAG

original cDNA sequence snippet

TAGGGTACACCCTTCTCAAACGGAAATTTCGGAGACTGTAG

altered cDNA sequence snippet

TAGGGTACACCCTTCTCAAATGGAAATTTCGGAGACTGTAG

wildtype AA sequence

MINSSLSMLF SYLEKYFYVA DELSHCVEPE PSQVPGGSSR DRQQGKPPPL PALKAKTSSR
SGPYATEIKK STDDSIFKVL DWFNRSSYSD DNKSFLQHPR GIESKEKTDS KSQVAVDLVT
DDTTLRENGS KTLSPSKIEL KPVRSDSPFQ AEGDMLVSES CQDNNVNIKS KFMNLSQKGT
PKEGPGILQP FESYGTPSQG SKNMDYSQDS KSPGKGNGAS PSNSNYSYSV LKESDAENQV
PCNTNNIGNL GEEEPKFHAH EENRGHSEVN FDSSTVVKEP GLKDNMNAER KSKVGNTYIL
KASLEPENIK STPGVANNGS PWKKPEVQFQ QEAGEVPKNQ VQREKYKRVS DRISFWEGEK
AGAKITHEKP TSSCSQEQPS AKAYQPVKKS QGVSSMDSLS TDQSEYNQAI PKRVVLDEDD
QASQLSNSYS SNKSKETKPQ IAGPSRYYLS AEQSDKVSLF QNKKNEPIKR SQVADSLPSR
RNITLPALQP PSNVGSERHA PLEKDRPLVR ESNANFKVMS LKERMDEPNA EQVYNPSQFE
NLRKFWDLEA NSNSKDNDKN ITTTSQKNSA PFNRQKHKEF SDIKLSGKNT HEAEVLLSPK
KVMAREEMEK LNSKGILQVL PDEITFPLSP LRKYTYQLPG NESSKENVEK NTEGIVTPVF
KEEKDYSEQE IQESIIKTNV LSKDCKDTFN DSLQKLLSET STPAIQPSGG KVHGKQVLEP
SVSENRTWPQ KTDFADTEEE VKGPEKIINE HVDKTVVHPK VKRNSLTASL DKLLKEATGT
SPSPLQAKLA PVITGTNSKL EEGRFFGKGI EQSHNTSADK REILAPFPVR DETFGNTALL
KKAESGECQL STQNLIQMAA EDSHPLDPTS QLSRKGSFGD VASPPQDMLF PQDAHLVPQA
RVHPSQTEIS ETVEKVILPP RPVLNDVSAA LQKLCGEVWL SYPAGREVGP GEVNPEFPEA
VQPVCSPLNP PGVISPWATM DTIVPDRKDF YSSNVVPDKT HEVGSYLAAQ MSPSDQTLSS
FASIVAQYGK GLPQEVEEIV RETIVQPKSE FLEFSAGLEK LLKEETETFP SKYESDTGNL
SPSKLIGSTE EPRRATSECH PEELKETVEK AEAPLITESA FDAGFEKLLK EITEAPPYQP
QVSVREETHE KESSQSEQTR FLGTVPHFYR AASQTSEMKD KSNGLESQVN QCDKMLGGDA
LVTDLLVDFC GSRSGVEIPR TPQLYVAHEI GTIKTVTPPE DRDSESGVAG GQGTLQEPGF
GEASEAISVS RNRQPIPLLM NKENSTKTSK VELTLASPYM KQEKEEEKEG FSESDFSDGN
TSSNAESWRN PSSSEEEPSP VLKTLERSAA RKMPSKSLED ISSDSSNQAK VDNQPEELVR
SAEDVSTVPT QPDNPFSHPD KLKRMSKSVP AFLQDESDDR ETDTASESSY QLSRHKKSPS
SLTNLSSSSG MTSLSSVSGS VMSVYSGDFG NLEVKGNIQF AIEYVESLKE LHVFVAQCKD
LAAADVKKQR SDPYVKAYLL PDKGKMGKKK TLVVKKTLNP VYNEILRYKI EKQILKTQKL
NLSIWHRDTF KRNSFLGEVE LDLETWDWDN KQNKQLRWYP LKRKTAPVAL EAENRGEMKL
ALQYVPEPVP GKKLPTTGEV HIWVKECLDL PLLRGSHLNS FVKCTILPDT SRKSRQKTRA
VGKTTNPIFN HTMVYDGFRP EDLMEACVEL TVWDHYKLTN QFLGGLRIGF GTGKSYGTEV
DWMDSTSEEV ALWEKMVNSP NTWIEATLPL RMLLIAKISK *

mutated AA sequence

MINSSLSMLF SYLEKYFYVA DELSHCVEPE PSQVPGGSSR DRQQGKPPPL PALKAKTSSR
SGPYATEIKK STDDSIFKVL DWFNRSSYSD DNKSFLQHPR GIESKEKTDS KSQVAVDLVT
DDTTLRENGS KTLSPSKIEL KPVRSDSPFQ AEGDMLVSES CQDNNVNIKS KFMNLSQKGT
PKEGPGILQP FESYGTPSQG SKNMDYSQDS KSPGKGNGAS PSNSNYSYSV LKESDAENQV
PCNTNNIGNL GEEEPKFHAH EENRGHSEVN FDSSTVVKEP GLKDNMNAER KSKVGNTYIL
KASLEPENIK STPGVANNGS PWKKPEVQFQ QEAGEVPKNQ VQREKYKRVS DRISFWEGEK
AGAKITHEKP TSSCSQEQPS AKAYQPVKKS QGVSSMDSLS TDQSEYNQAI PKRVVLDEDD
QASQLSNSYS SNKSKETKPQ IAGPSRYYLS AEQSDKVSLF QNKKNEPIKR SQVADSLPSR
RNITLPALQP PSNVGSERHA PLEKDRPLVR ESNANFKVMS LKERMDEPNA EQVYNPSQFE
NLRKFWDLEA NSNSKDNDKN ITTTSQKNSA PFNRQKHKEF SDIKLSGKNT HEAEVLLSPK
KVMAREEMEK LNSKGILQVL PDEITFPLSP LRKYTYQLPG NESSKENVEK NTEGIVTPVF
KEEKDYSEQE IQESIIKTNV LSKDCKDTFN DSLQKLLSET STPAIQPSGG KVHGKQVLEP
SVSENRTWPQ KTDFADTEEE VKGPEKIINE HVDKTVVHPK VKRNSLTASL DKLLKEATGT
SPSPLQAKLA PVITGTNSKL EEGRFFGKGI EQSHNTSADK REILAPFPVR DETFGNTALL
KKAESGECQL STQNLIQMAA EDSHPLDPTS QLSRKGSFGD VASPPQDMLF PQDAHLVPQA
RVHPSQMEIS ETVEKVILPP RPVLNDVSAA LQKLCGEVWL SYPAGREVGP GEVNPEFPEA
VQPVCSPLNP PGVISPWATM DTIVPDRKDF YSSNVVPDKT HEVGSYLAAQ MSPSDQTLSS
FASIVAQYGK GLPQEVEEIV RETIVQPKSE FLEFSAGLEK LLKEETETFP SKYESDTGNL
SPSKLIGSTE EPRRATSECH PEELKETVEK AEAPLITESA FDAGFEKLLK EITEAPPYQP
QVSVREETHE KESSQSEQTR FLGTVPHFYR AASQTSEMKD KSNGLESQVN QCDKMLGGDA
LVTDLLVDFC GSRSGVEIPR TPQLYVAHEI GTIKTVTPPE DRDSESGVAG GQGTLQEPGF
GEASEAISVS RNRQPIPLLM NKENSTKTSK VELTLASPYM KQEKEEEKEG FSESDFSDGN
TSSNAESWRN PSSSEEEPSP VLKTLERSAA RKMPSKSLED ISSDSSNQAK VDNQPEELVR
SAEDVSTVPT QPDNPFSHPD KLKRMSKSVP AFLQDESDDR ETDTASESSY QLSRHKKSPS
SLTNLSSSSG MTSLSSVSGS VMSVYSGDFG NLEVKGNIQF AIEYVESLKE LHVFVAQCKD
LAAADVKKQR SDPYVKAYLL PDKGKMGKKK TLVVKKTLNP VYNEILRYKI EKQILKTQKL
NLSIWHRDTF KRNSFLGEVE LDLETWDWDN KQNKQLRWYP LKRKTAPVAL EAENRGEMKL
ALQYVPEPVP GKKLPTTGEV HIWVKECLDL PLLRGSHLNS FVKCTILPDT SRKSRQKTRA
VGKTTNPIFN HTMVYDGFRP EDLMEACVEL TVWDHYKLTN QFLGGLRIGF GTGKSYGTEV
DWMDSTSEEV ALWEKMVNSP NTWIEATLPL RMLLIAKISK *

speed

0.96 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 9.14577656320414e-10 (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)

chr11:85436352G>AN/A show variant in all transcripts IGV

HGNC symbol

SYTL2

Ensembl transcript ID

ENST00000316356

Genbank transcript ID

NM_001162953

UniProt peptide

Q9HCH5

alteration type

single base exchange

alteration region

intron

DNA changes

g.85833C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs641393

database	homozygous (A/A)	heterozygous	allele carriers
1000G	710	1191	1901
ExAC	21670	-10573	11097

regulatory features

H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.623	0.938
	-0.235	0.875
(flanking)	3.219	0.9

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 increased	85831	wt: 0.31 / mu: 0.53	wt: GCTAGGGTACACCCTTCTCAAACGGAAATTTCGGAGACTGT mu: GCTAGGGTACACCCTTCTCAAATGGAAATTTCGGAGACTGT	tcaa\|ACGG
Donor marginally increased	85834	wt: 0.5422 / mu: 0.5451 (marginal change - not scored)	wt: CAAACGGAAATTTCG mu: CAAATGGAAATTTCG	AACG\|gaaa
Donor gained	85826	0.36	mu: ACCCTTCTCAAATGG	CCTT\|ctca

distance from splice site

2587

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
488	488	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
562	562	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
579	619	COMPBIAS	Ser-rich.	might get lost (downstream of altered splice site)
603	603	CONFLICT	S -> P (in Ref. 1; ABV82746).	might get lost (downstream of altered splice site)
629	733	DOMAIN	C2 1.	might get lost (downstream of altered splice site)
658	658	CONFLICT	A -> V (in Ref. 4; BAD18516).	might get lost (downstream of altered splice site)
682	682	CONFLICT	K -> M (in Ref. 7; AAI44116).	might get lost (downstream of altered splice site)
718	718	CONFLICT	I -> V (in Ref. 4; BAB15030).	might get lost (downstream of altered splice site)
778	880	DOMAIN	C2 2.	might get lost (downstream of altered splice site)
860	860	CONFLICT	A -> V (in Ref. 3; BAB13423).	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

566 / 566

chromosome

strand

-1

last intron/exon boundary

3228

theoretical NMD boundary in CDS

2612

length of CDS

2808

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)

85833

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

85436352

original gDNA sequence snippet

TAGGGTACACCCTTCTCAAACGGAAATTTCGGAGACTGTAG

altered gDNA sequence snippet

TAGGGTACACCCTTCTCAAATGGAAATTTCGGAGACTGTAG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MIDLSFLTEE EQEAIMKVLQ RDAALKRAEE ERVRHLPEKI KDDQQLKNMS GQWFYEAKAK
RHRDKIHGAD IIRASMRKKR PQIAAEQSKD RENGAKESWV NNVNKDAFLP PELAGVVEEP
EEDAAPASPS SSVVNPASSV IDMSQENTRK PNVSPEKQRK NPFNSSKLPE GHSSQQTKNE
QSKNGRTGLF QTSKEDELSE SKEKSTVADT SIQKLEKSKQ TLPGLSNGSQ IKAPIPKARK
MIYKSTDLNK DDNQSFPRQR TDSLKARGAP RGILKRNSSS SSTDSETLRY NHNFEPKSKI
VSPGLTIHER ISEKEHSLED NSSPNSLEPL KHVRFSAVKD ELPQSPGLIH GREVGEFSVL
ESDRLKNGME DAGDTEEFQS DPKPSQYRKP SLFHQSTSSP YVSKSETHQP MTSGSFPING
LHSHSEVLTA RPQSMENSPT INEPKDKSSE LTRLESVLPR SPADELSHCV EPEPSQVPGG
SSRDRQQGSE EEPSPVLKTL ERSAARKMPS KSLEDISSDS SNQAKVDNQP EELVRSAEDV
STVPTQPDNP FSHPDKLKRM SKSVPAFLQD ESDDRETDTA SESSYQLSRH KKSPSSLTNL
SSSSGMTSLS SVSGSVMSVY SGDFGNLEVK GNIQFAIEYV ESLKELHVFV AQCKDLAAAD
VKKQRSDPYV KAYLLPDKGK MGKKKTLVVK KTLNPVYNEI LRYKIEKQIL KTQKLNLSIW
HRDTFKRNSF LGEVELDLET WDWDNKQNKQ LRWYPLKRKT APVALEAENR GEMKLALQYV
PEPVPGKKLP TTGEVHIWVK ECLDLPLLRG SHLNSFVKCT ILPDTSRKSR QKTRAVGKTT
NPIFNHTMVY DGFRPEDLME ACVELTVWDH YKLTNQFLGG LRIGFGTGKS YGTEVDWMDS
TSEEVALWEK MVNSPNTWIE ATLPLRMLLI AKISK*

mutated AA sequence

N/A

speed

0.82 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 9.14577656320414e-10 (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)

chr11:85436352G>AN/A show variant in all transcripts IGV

HGNC symbol

SYTL2

Ensembl transcript ID

ENST00000528231

Genbank transcript ID

NM_001162951

UniProt peptide

Q9HCH5

alteration type

single base exchange

alteration region

intron

DNA changes

g.85833C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs641393

database	homozygous (A/A)	heterozygous	allele carriers
1000G	710	1191	1901
ExAC	21670	-10573	11097

regulatory features

H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.623	0.938
	-0.235	0.875
(flanking)	3.219	0.9

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 increased	85831	wt: 0.31 / mu: 0.53	wt: GCTAGGGTACACCCTTCTCAAACGGAAATTTCGGAGACTGT mu: GCTAGGGTACACCCTTCTCAAATGGAAATTTCGGAGACTGT	tcaa\|ACGG
Donor marginally increased	85834	wt: 0.5422 / mu: 0.5451 (marginal change - not scored)	wt: CAAACGGAAATTTCG mu: CAAATGGAAATTTCG	AACG\|gaaa
Donor gained	85826	0.36	mu: ACCCTTCTCAAATGG	CCTT\|ctca

distance from splice site

2587

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
488	488	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
562	562	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
579	619	COMPBIAS	Ser-rich.	might get lost (downstream of altered splice site)
603	603	CONFLICT	S -> P (in Ref. 1; ABV82746).	might get lost (downstream of altered splice site)
629	733	DOMAIN	C2 1.	might get lost (downstream of altered splice site)
658	658	CONFLICT	A -> V (in Ref. 4; BAD18516).	might get lost (downstream of altered splice site)
682	682	CONFLICT	K -> M (in Ref. 7; AAI44116).	might get lost (downstream of altered splice site)
718	718	CONFLICT	I -> V (in Ref. 4; BAB15030).	might get lost (downstream of altered splice site)
778	880	DOMAIN	C2 2.	might get lost (downstream of altered splice site)
860	860	CONFLICT	A -> V (in Ref. 3; BAB13423).	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

279 / 279

chromosome

strand

-1

last intron/exon boundary

2938

theoretical NMD boundary in CDS

2609

length of CDS

2805

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)

85833

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

85436352

original gDNA sequence snippet

TAGGGTACACCCTTCTCAAACGGAAATTTCGGAGACTGTAG

altered gDNA sequence snippet

TAGGGTACACCCTTCTCAAATGGAAATTTCGGAGACTGTAG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MIDLSFLTEE EQEAIMKVLQ RDAALKRAEE ERVRHLPEKI KDDQQLKNMS GQWFYEAKAK
RHRDKIHGAD IIRASMRKKR PQIAAEQSKD RENGAKESWV NNVNKDAFLP PELAGVVEEP
EEDAAPASPS SSVVNPASSV IDMSQENTRK PNVSPEKRKN PFNSSKLPEG HSSQQTKNEQ
SKNGRTGLFQ TSKEDELSES KEKSTVADTS IQKLEKSKQT LPGLSNGSQI KAPIPKARKM
IYKSTDLNKD DNQSFPRQRT DSLKARGAPR GILKRNSSSS STDSETLRYN HNFEPKSKIV
SPGLTIHERI SEKEHSLEDN SSPNSLEPLK HVRFSAVKDE LPQSPGLIHG REVGEFSVLE
SDRLKNGMED AGDTEEFQSD PKPSQYRKPS LFHQSTSSPY VSKSETHQPM TSGSFPINGL
HSHSEVLTAR PQSMENSPTI NEPKDKSSEL TRLESVLPRS PADELSHCVE PEPSQVPGGS
SRDRQQGSEE EPSPVLKTLE RSAARKMPSK SLEDISSDSS NQAKVDNQPE ELVRSAEDVS
TVPTQPDNPF SHPDKLKRMS KSVPAFLQDE SDDRETDTAS ESSYQLSRHK KSPSSLTNLS
SSSGMTSLSS VSGSVMSVYS GDFGNLEVKG NIQFAIEYVE SLKELHVFVA QCKDLAAADV
KKQRSDPYVK AYLLPDKGKM GKKKTLVVKK TLNPVYNEIL RYKIEKQILK TQKLNLSIWH
RDTFKRNSFL GEVELDLETW DWDNKQNKQL RWYPLKRKTA PVALEAENRG EMKLALQYVP
EPVPGKKLPT TGEVHIWVKE CLDLPLLRGS HLNSFVKCTI LPDTSRKSRQ KTRAVGKTTN
PIFNHTMVYD GFRPEDLMEA CVELTVWDHY KLTNQFLGGL RIGFGTGKSY GTEVDWMDST
SEEVALWEKM VNSPNTWIEA TLPLRMLLIA KISK*

mutated AA sequence

N/A

speed

0.63 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 9.14577656320414e-10 (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)

chr11:85436352G>AN/A show variant in all transcripts IGV

HGNC symbol

SYTL2

Ensembl transcript ID

ENST00000524452

Genbank transcript ID

N/A

UniProt peptide

Q9HCH5

alteration type

single base exchange

alteration region

intron

DNA changes

g.85833C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs641393

database	homozygous (A/A)	heterozygous	allele carriers
1000G	710	1191	1901
ExAC	21670	-10573	11097

regulatory features

H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.623	0.938
	-0.235	0.875
(flanking)	3.219	0.9

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 increased	85831	wt: 0.31 / mu: 0.53	wt: GCTAGGGTACACCCTTCTCAAACGGAAATTTCGGAGACTGT mu: GCTAGGGTACACCCTTCTCAAATGGAAATTTCGGAGACTGT	tcaa\|ACGG
Donor marginally increased	85834	wt: 0.5422 / mu: 0.5451 (marginal change - not scored)	wt: CAAACGGAAATTTCG mu: CAAATGGAAATTTCG	AACG\|gaaa
Donor gained	85826	0.36	mu: ACCCTTCTCAAATGG	CCTT\|ctca

distance from splice site

2587

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
488	488	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
562	562	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
579	619	COMPBIAS	Ser-rich.	might get lost (downstream of altered splice site)
603	603	CONFLICT	S -> P (in Ref. 1; ABV82746).	might get lost (downstream of altered splice site)
629	733	DOMAIN	C2 1.	might get lost (downstream of altered splice site)
658	658	CONFLICT	A -> V (in Ref. 4; BAD18516).	might get lost (downstream of altered splice site)
682	682	CONFLICT	K -> M (in Ref. 7; AAI44116).	might get lost (downstream of altered splice site)
718	718	CONFLICT	I -> V (in Ref. 4; BAB15030).	might get lost (downstream of altered splice site)
778	880	DOMAIN	C2 2.	might get lost (downstream of altered splice site)
860	860	CONFLICT	A -> V (in Ref. 3; BAB13423).	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

1 / 1

chromosome

strand

-1

last intron/exon boundary

2588

theoretical NMD boundary in CDS

2537

length of CDS

2733

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)

85833

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

85436352

original gDNA sequence snippet

TAGGGTACACCCTTCTCAAACGGAAATTTCGGAGACTGTAG

altered gDNA sequence snippet

TAGGGTACACCCTTCTCAAATGGAAATTTCGGAGACTGTAG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MIDLSFLTEE EQEAIMKVLQ RDAALKRAEE ERVRHLPEKI KDDQQLKNMS GQWFYEAKAK
RHRDKIHGAD IIRASMRKKR PQIAAEQSKD RENGAKESWV NNVNKDAFLP PELAGVVEEP
EEDAAPASPS SSVVNPASSV IDMSQENTRK PNVSPEKRKN PFNSSKLPEG HSSQQTKNEQ
SKNGRTGLFQ TSKEDELSES KEKSTVADTS IQKLEKSKQT LPGLSNGSQI KAPIPKARKM
IYKSTDLNKD DNQSFPRQRT DSLKARGAPR GILKRNSSSS STDSETLRYN HNFEPKSKIV
SPGLTIHERI SEKEHSLEDN SSPNSLEPLK HVRFSAVKDE LPQSPGLIHG REVGEFSVLE
SDRLKNGMED AGDTEEFQSD PKPSQYRKPS LFHQSTSSPY VSKSETHQPM TSGSFPINGL
HSHSEVLTAR PQSMENSPTI NEPKDKSSEL TRLESVLPRS PADELSHCVE PEPSQVPGGS
SRDRQQGSEE EPSPVLKTLE RSAARKMPSK SLEDISSDSS NQAKVDNQPE ELVRSAEDDE
KPDQKPVTNE CVPRISTVPT QPDNPFSHPD KLKRMSKSVP AFLQDEVSGS VMSVYSGDFG
NLEVKGNIQF AIEYVESLKE LHVFVAQCKD LAAADVKKQR SDPYVKAYLL PDKGKMGKKK
TLVVKKTLNP VYNEILRYKI EKQILKTQKL NLSIWHRDTF KRNSFLGEVE LDLETWDWDN
KQNKQLRWYP LKRKTAPVAL EAENRGEMKL ALQYVPEPVP GKKLPTTGEV HIWVKECLDL
PLLRGSHLNS FVKCTILPDT SRKSRQKTRA VGKTTNPIFN HTMVYDGFRP EDLMEACVEL
TVWDHYKLTN QFLGGLRIGF GTGKSYGTEV DWMDSTSEEV ALWEKMVNSP NTWIEATLPL
RMLLIAKISK *

mutated AA sequence

N/A

speed

0.63 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 9.14577656320414e-10 (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)

chr11:85436352G>AN/A show variant in all transcripts IGV

HGNC symbol

SYTL2

Ensembl transcript ID

ENST00000527523

Genbank transcript ID

N/A

UniProt peptide

Q9HCH5

alteration type

single base exchange

alteration region

intron

DNA changes

g.85833C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs641393

database	homozygous (A/A)	heterozygous	allele carriers
1000G	710	1191	1901
ExAC	21670	-10573	11097

regulatory features

H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.623	0.938
	-0.235	0.875
(flanking)	3.219	0.9

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 increased	85831	wt: 0.31 / mu: 0.53	wt: GCTAGGGTACACCCTTCTCAAACGGAAATTTCGGAGACTGT mu: GCTAGGGTACACCCTTCTCAAATGGAAATTTCGGAGACTGT	tcaa\|ACGG
Donor marginally increased	85834	wt: 0.5422 / mu: 0.5451 (marginal change - not scored)	wt: CAAACGGAAATTTCG mu: CAAATGGAAATTTCG	AACG\|gaaa
Donor gained	85826	0.36	mu: ACCCTTCTCAAATGG	CCTT\|ctca

distance from splice site

2587

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
488	488	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
562	562	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
579	619	COMPBIAS	Ser-rich.	might get lost (downstream of altered splice site)
603	603	CONFLICT	S -> P (in Ref. 1; ABV82746).	might get lost (downstream of altered splice site)
629	733	DOMAIN	C2 1.	might get lost (downstream of altered splice site)
658	658	CONFLICT	A -> V (in Ref. 4; BAD18516).	might get lost (downstream of altered splice site)
682	682	CONFLICT	K -> M (in Ref. 7; AAI44116).	might get lost (downstream of altered splice site)
718	718	CONFLICT	I -> V (in Ref. 4; BAB15030).	might get lost (downstream of altered splice site)
778	880	DOMAIN	C2 2.	might get lost (downstream of altered splice site)
860	860	CONFLICT	A -> V (in Ref. 3; BAB13423).	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

232 / 232

chromosome

strand

-1

last intron/exon boundary

2795

theoretical NMD boundary in CDS

2513

length of CDS

2709

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)

85833

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

85436352

original gDNA sequence snippet

TAGGGTACACCCTTCTCAAACGGAAATTTCGGAGACTGTAG

altered gDNA sequence snippet

TAGGGTACACCCTTCTCAAATGGAAATTTCGGAGACTGTAG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MSGQWFYEAK AKRHRDKIHG ADIIRASMRK KRPQIAAEQS KDRENGAKES WVNNVNKDAF
LPPELAGVVE EPEEDAAPAS PSSSVVNPAS SVIDMSQENT RKPNVSPEKR KNPFNSSKLP
EGHSSQQTKN EQSKNGRTGL FQTSKEDELS ESKEKSTVAD TSIQKLEKSK QTLPGLSNGS
QIKAPIPKAR KMIYKSTDLN KDDNQSFPRQ RTDSLKARGA PRGILKRNSS SSSTDSETLR
YNHNFEPKSK IVSPGLTIHE RISEKEHSLE DNSSPNSLEP LKHVRFSAVK DELPQSPGLI
HGREVGEFSV LESDRLKNGM EDAGDTEEFQ SDPKPSQYRK PSLFHQSTSS PYVSKSETHQ
PMTSGSFPIN GLHSHSEVLT ARPQSMENSP TINEPKDKSS ELTRLESVLP RSPADELSHC
VEPEPSQVPG GSSRDRQQGS EEEPSPVLKT LERSAARKMP SKSLEDISSD SSNQAKVDNQ
PEELVRSAED DEKPDQKPVT NECVPRISTV PTQPDNPFSH PDKLKRMSKS VPAFLQDESD
DRETDTASES SYQLSRHKKS PSSLTNLSSS SGMTSLSSVS GSVMSVYSGD FGNLEVKGNI
QFAIEYVESL KELHVFVAQC KDLAAADVKK QRSDPYVKAY LLPDKGKMGK KKTLVVKKTL
NPVYNEILRY KIEKQILKTQ KLNLSIWHRD TFKRNSFLGE VELDLETWDW DNKQNKQLRW
YPLKRKTAPV ALEAENRGEM KLALQYVPEP VPGKKLPTTG EVHIWVKECL DLPLLRGSHL
NSFVKCTILP DTSRKSRQKT RAVGKTTNPI FNHTMVYDGF RPEDLMEACV ELTVWDHYKL
TNQFLGGLRI GFGTGKSYGT EVDWMDSTSE EVALWEKMVN SPNTWIEATL PLRMLLIAKI
SK*

mutated AA sequence

N/A

speed

0.78 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 9.14577656320414e-10 (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)

chr11:85436352G>AN/A show variant in all transcripts IGV

HGNC symbol

SYTL2

Ensembl transcript ID

ENST00000389960

Genbank transcript ID

NM_032943

UniProt peptide

Q9HCH5

alteration type

single base exchange

alteration region

intron

DNA changes

g.85833C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs641393

database	homozygous (A/A)	heterozygous	allele carriers
1000G	710	1191	1901
ExAC	21670	-10573	11097

regulatory features

H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.623	0.938
	-0.235	0.875
(flanking)	3.219	0.9

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 increased	85831	wt: 0.31 / mu: 0.53	wt: GCTAGGGTACACCCTTCTCAAACGGAAATTTCGGAGACTGT mu: GCTAGGGTACACCCTTCTCAAATGGAAATTTCGGAGACTGT	tcaa\|ACGG
Donor marginally increased	85834	wt: 0.5422 / mu: 0.5451 (marginal change - not scored)	wt: CAAACGGAAATTTCG mu: CAAATGGAAATTTCG	AACG\|gaaa
Donor gained	85826	0.36	mu: ACCCTTCTCAAATGG	CCTT\|ctca

distance from splice site

2587

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
488	488	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
562	562	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
579	619	COMPBIAS	Ser-rich.	might get lost (downstream of altered splice site)
603	603	CONFLICT	S -> P (in Ref. 1; ABV82746).	might get lost (downstream of altered splice site)
629	733	DOMAIN	C2 1.	might get lost (downstream of altered splice site)
658	658	CONFLICT	A -> V (in Ref. 4; BAD18516).	might get lost (downstream of altered splice site)
682	682	CONFLICT	K -> M (in Ref. 7; AAI44116).	might get lost (downstream of altered splice site)
718	718	CONFLICT	I -> V (in Ref. 4; BAB15030).	might get lost (downstream of altered splice site)
778	880	DOMAIN	C2 2.	might get lost (downstream of altered splice site)
860	860	CONFLICT	A -> V (in Ref. 3; BAB13423).	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

572 / 572

chromosome

strand

-1

last intron/exon boundary

3159

theoretical NMD boundary in CDS

2537

length of CDS

2733

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)

85833

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

85436352

original gDNA sequence snippet

TAGGGTACACCCTTCTCAAACGGAAATTTCGGAGACTGTAG

altered gDNA sequence snippet

TAGGGTACACCCTTCTCAAATGGAAATTTCGGAGACTGTAG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MIDLSFLTEE EQEAIMKVLQ RDAALKRAEE ERVRHLPEKI KDDQQLKNMS GQWFYEAKAK
RHRDKIHGAD IIRASMRKKR PQIAAEQSKD RENGAKESWV NNVNKDAFLP PELAGVVEEP
EEDAAPASPS SSVVNPASSV IDMSQENTRK PNVSPEKRKN PFNSSKLPEG HSSQQTKNEQ
SKNGRTGLFQ TSKEDELSES KEKSTVADTS IQKLEKSKQT LPGLSNGSQI KAPIPKARKM
IYKSTDLNKD DNQSFPRQRT DSLKARGAPR GILKRNSSSS STDSETLRYN HNFEPKSKIV
SPGLTIHERI SEKEHSLEDN SSPNSLEPLK HVRFSAVKDE LPQSPGLIHG REVGEFSVLE
SDRLKNGMED AGDTEEFQSD PKPSQYRKPS LFHQSTSSPY VSKSETHQPM TSGSFPINGL
HSHSEVLTAR PQSMENSPTI NEPKDKSSEL TRLESVLPRS PADELSHCVE PEPSQVPGGS
SRDRQQGSEE EPSPVLKTLE RSAARKMPSK SLEDISSDSS NQAKVDNQPE ELVRSAEDDE
KPDQKPVTNE CVPRISTVPT QPDNPFSHPD KLKRMSKSVP AFLQDEVSGS VMSVYSGDFG
NLEVKGNIQF AIEYVESLKE LHVFVAQCKD LAAADVKKQR SDPYVKAYLL PDKGKMGKKK
TLVVKKTLNP VYNEILRYKI EKQILKTQKL NLSIWHRDTF KRNSFLGEVE LDLETWDWDN
KQNKQLRWYP LKRKTAPVAL EAENRGEMKL ALQYVPEPVP GKKLPTTGEV HIWVKECLDL
PLLRGSHLNS FVKCTILPDT SRKSRQKTRA VGKTTNPIFN HTMVYDGFRP EDLMEACVEL
TVWDHYKLTN QFLGGLRIGF GTGKSYGTEV DWMDSTSEEV ALWEKMVNSP NTWIEATLPL
RMLLIAKISK *

mutated AA sequence

N/A

speed

0.77 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems