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 5 transcript(s)...
Querying Taster for transcript #1: ENST00000261866
Querying Taster for transcript #2: ENST00000535302
Querying Taster for transcript #3: ENST00000427534
Querying Taster for transcript #4: ENST00000558319
Querying Taster for transcript #5: ENST00000559193
MT speed 0 s - this script 4.901371 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SPG11	polymorphism_automatic	2.92247004374246e-10	simple_aae		affected		F463S	single base exchange	rs3759871		show file
SPG11	polymorphism_automatic	2.92247004374246e-10	simple_aae		affected		F463S	single base exchange	rs3759871		show file
SPG11	polymorphism_automatic	2.92247004374246e-10	simple_aae		affected		F463S	single base exchange	rs3759871		show file
SPG11	polymorphism_automatic	2.92247004374246e-10	simple_aae		affected		F463S	single base exchange	rs3759871		show file
SPG11	polymorphism_automatic	2.92247004374246e-10	simple_aae		affected		F463S	single base exchange	rs3759871		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999707753 (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)

chr15:44943757A>GN/A show variant in all transcripts IGV

HGNC symbol

SPG11

Ensembl transcript ID

ENST00000261866

Genbank transcript ID

NM_025137

UniProt peptide

Q96JI7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1388T>C
cDNA.1405T>C
g.12120T>C

AA changes

F463S Score: 155 explain score(s)

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

463

frameshift

known variant

Reference ID: rs3759871

database	homozygous (G/G)	heterozygous	allele carriers
1000G	562	1254	1816
ExAC	13393	5981	19374

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.303	0.004
	0.69	0.009
(flanking)	0.267	0.012

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	12127	wt: 0.8616 / mu: 0.8772 (marginal change - not scored)	wt: GGCATGCAGTGTTTTTCCCTTGGCACAAAGTGTATTCCTGT mu: GGCATGCAGTGTTCTTCCCTTGGCACAAAGTGTATTCCTGT	cctt\|GGCA
Donor increased	12111	wt: 0.65 / mu: 0.76	wt: GGGCATGCAGTGTTT mu: GGGCATGCAGTGTTC	GCAT\|gcag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

463

mutated

not conserved

463

Ptroglodytes

all identical

ENSPTRG00000007016

463

Mmulatta

all identical

ENSMMUG00000014291

460

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000033396

456

Ggallus

all conserved

ENSGALG00000008180

471

Trubripes

not conserved

ENSTRUG00000014452

394

Drerio

no alignment

ENSDARG00000045968

n/a

Dmelanogaster

no alignment

FBgn0034786

n/a

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000025297

341

protein features

start (aa)	end (aa)	feature	details
1	1237	TOPO_DOM	Extracellular (Potential).	lost
612	612	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1046	1046	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1205	1205	CONFLICT	N -> K (in Ref. 5; CAH10686).	might get lost (downstream of altered splice site)
1238	1258	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1259	1471	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1472	1492	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1493	2443	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
1674	1674	CONFLICT	R -> G (in Ref. 6; BAC03600).	might get lost (downstream of altered splice site)
1955	1955	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1958	1958	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1961	1961	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
2253	2253	CONFLICT	D -> G (in Ref. 4; AAH94704).	might get lost (downstream of altered splice site)
2378	2378	CONFLICT	F -> L (in Ref. 6; BAB15065).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

7332 / 7332

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

2444 / 2444

position of stopcodon in wt / mu cDNA

7349 / 7349

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

18 / 18

chromosome

strand

-1

last intron/exon boundary

7169

theoretical NMD boundary in CDS

7101

length of CDS

7332

coding sequence (CDS) position

1388

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

1405

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

12120

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

44943757

original gDNA sequence snippet

GACCCAGGGCATGCAGTGTTTTTCCCTTGGCACAAAGTGTA

altered gDNA sequence snippet

GACCCAGGGCATGCAGTGTTCTTCCCTTGGCACAAAGTGTA

original cDNA sequence snippet

GACCCAGGGCATGCAGTGTTTTTCCCTTGGCACAAAGTGTA

altered cDNA sequence snippet

GACCCAGGGCATGCAGTGTTCTTCCCTTGGCACAAAGTGTA

wildtype AA sequence

MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCFSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVEILKEKN
YFSEKEKRTI DFVHQVEKLY LGHFQENMQI QSFPRYWIKE QDFFKHKSVL DSFLKYDCKD
EFNKQDHRIV LNWALWWDQL TQESILLPRI SPEEYKSYSP EALWRYLTAR HDWLNIILWI
GEFQTQHSYA SLQQNKWPLL TVDVINQNTS CNNYMRNEIL DKLARNGVFL ASELEDFECF
LLRLSRIGGV IQDTLPVQNY KTKEGWDFHS QFILYCLEHS LQHLLYVYLD CYKLSPENCP
FLEKKELHEA HPWFEFLVQC RQVASNLTDP KLIFQASLAN AQILIPTNQA SVSSMLLEGH
TLLALATTMY SPGGVSQVVQ NEENENCLKK VDPQLLKMAL TPYPKLKTAL FPQCTPPSVL
PSDITIYHLI QSLSPFDPSR LFGWQSANTL AIGDAWSHLP HFSSPDLVNK YAIVERLNFA
YYLHNGRPSF AFGTFLVQEL IKSKTPKQLI QQVGNEAYVI GLSSFHIPSI GAACVCFLEL
LGLDSLKLRV DMKVANIILS YKCRNEDAQY SFIRESVAEK LSKLADGEKT TTEELLVLLE
EGTWNSIQQQ EIKRLSSESS SQWALVVQFC RLHNMKLSIS YLRECAKAND WLQFIIHSQL
HNYHPAEVKS LIQYFSPVIQ DHLRLAFENL PSVPTSKMDS DQVCNKCPQE LQGSKQEMTD
LFEILLQCSE EPDSWHWLLV EAVKQQAPIL SVLASCLQGA SAISCLCVWI ITSVEDNVAT
EAMGHIQDST EDHTWNLEDL SVIWRTLLTR QKSKTLIRGF QLFFKDSPLL LVMEMYELCM
FFRNYKEAEA KLLEFQKSLE TLNTAATKVH PVIPAMWLED QVCFLLKLML QQCKTQYELG
KLLQLFVERE HLFSDGPDVK KLCILCQILK DTSIAINHTI ITSYSIENLQ HECRSILERL
QTDGQFALAR RVAELAELPV DNLVIKEITQ EMQTLKHIEQ WSLKQARIDF WKKCHENFKK
NSISSKAASS FFSTQAHVAC EHPTGWSSME ERHLLLTLAG HWLAQEDVVP LDKLEELEKQ
IWLCRITQHT LGRNQEETEP RFSRQISTSG ELSFDSLASE FSFSKLAALN TSKYLELNSL
PSKETCENRL DWKEQESLNF LIGRLLDDGC VHEASRVCRY FHFYNPDVAL VLHCRALASG
EASMEDLHPE IHALLQSAEL LEEEAPDIPL RRVHSTSSLD SQKFVTVPSS NEVVTNLEVL
TSKCLHGKNY CRQVLCLYDL AKELGCSYTD VAAQDGEAML RKILASQQPD RCKRAQAFIS
TQGLKPDTVA ELVAEEVTRE LLTSSQGTGH KQMFNPTEES QTFLQLTTLC QDRTLVGMKL
LDKISSVPHG ELSCTTELLI LAHHCFTLTC HMEGIIRVLQ AAHMLTDNHL APSEEYGLVV
RLLTGIGRYN EMTYIFDLLH KKHYFEVLMR KKLDPSGTLK TALLDYIKRC RPGDSEKHNM
IALCFSMCRE IGENHEAAAR IQLKLIESQP WEDSLKDGHQ LKQLLLKALT LMLDAAESYA
KDSCVRQAQH CQRLTKLITL QIHFLNTGQN TMLINLGRHK LMDCILALPR FYQASIVAEA
YDFVPDWAEI LYQQVILKGD FNYLEEFKQQ RLLKSSIFEE ISKKYKQHQP TDMVMENLKK
LLTYCEDVYL YYKLAYEHKF YEIVNVLLKD PQTGCCLKDM LAG*

mutated AA sequence

MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCSSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVEILKEKN
YFSEKEKRTI DFVHQVEKLY LGHFQENMQI QSFPRYWIKE QDFFKHKSVL DSFLKYDCKD
EFNKQDHRIV LNWALWWDQL TQESILLPRI SPEEYKSYSP EALWRYLTAR HDWLNIILWI
GEFQTQHSYA SLQQNKWPLL TVDVINQNTS CNNYMRNEIL DKLARNGVFL ASELEDFECF
LLRLSRIGGV IQDTLPVQNY KTKEGWDFHS QFILYCLEHS LQHLLYVYLD CYKLSPENCP
FLEKKELHEA HPWFEFLVQC RQVASNLTDP KLIFQASLAN AQILIPTNQA SVSSMLLEGH
TLLALATTMY SPGGVSQVVQ NEENENCLKK VDPQLLKMAL TPYPKLKTAL FPQCTPPSVL
PSDITIYHLI QSLSPFDPSR LFGWQSANTL AIGDAWSHLP HFSSPDLVNK YAIVERLNFA
YYLHNGRPSF AFGTFLVQEL IKSKTPKQLI QQVGNEAYVI GLSSFHIPSI GAACVCFLEL
LGLDSLKLRV DMKVANIILS YKCRNEDAQY SFIRESVAEK LSKLADGEKT TTEELLVLLE
EGTWNSIQQQ EIKRLSSESS SQWALVVQFC RLHNMKLSIS YLRECAKAND WLQFIIHSQL
HNYHPAEVKS LIQYFSPVIQ DHLRLAFENL PSVPTSKMDS DQVCNKCPQE LQGSKQEMTD
LFEILLQCSE EPDSWHWLLV EAVKQQAPIL SVLASCLQGA SAISCLCVWI ITSVEDNVAT
EAMGHIQDST EDHTWNLEDL SVIWRTLLTR QKSKTLIRGF QLFFKDSPLL LVMEMYELCM
FFRNYKEAEA KLLEFQKSLE TLNTAATKVH PVIPAMWLED QVCFLLKLML QQCKTQYELG
KLLQLFVERE HLFSDGPDVK KLCILCQILK DTSIAINHTI ITSYSIENLQ HECRSILERL
QTDGQFALAR RVAELAELPV DNLVIKEITQ EMQTLKHIEQ WSLKQARIDF WKKCHENFKK
NSISSKAASS FFSTQAHVAC EHPTGWSSME ERHLLLTLAG HWLAQEDVVP LDKLEELEKQ
IWLCRITQHT LGRNQEETEP RFSRQISTSG ELSFDSLASE FSFSKLAALN TSKYLELNSL
PSKETCENRL DWKEQESLNF LIGRLLDDGC VHEASRVCRY FHFYNPDVAL VLHCRALASG
EASMEDLHPE IHALLQSAEL LEEEAPDIPL RRVHSTSSLD SQKFVTVPSS NEVVTNLEVL
TSKCLHGKNY CRQVLCLYDL AKELGCSYTD VAAQDGEAML RKILASQQPD RCKRAQAFIS
TQGLKPDTVA ELVAEEVTRE LLTSSQGTGH KQMFNPTEES QTFLQLTTLC QDRTLVGMKL
LDKISSVPHG ELSCTTELLI LAHHCFTLTC HMEGIIRVLQ AAHMLTDNHL APSEEYGLVV
RLLTGIGRYN EMTYIFDLLH KKHYFEVLMR KKLDPSGTLK TALLDYIKRC RPGDSEKHNM
IALCFSMCRE IGENHEAAAR IQLKLIESQP WEDSLKDGHQ LKQLLLKALT LMLDAAESYA
KDSCVRQAQH CQRLTKLITL QIHFLNTGQN TMLINLGRHK LMDCILALPR FYQASIVAEA
YDFVPDWAEI LYQQVILKGD FNYLEEFKQQ RLLKSSIFEE ISKKYKQHQP TDMVMENLKK
LLTYCEDVYL YYKLAYEHKF YEIVNVLLKD PQTGCCLKDM LAG*

speed

0.96 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: 0.999999999707753 (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)

chr15:44943757A>GN/A show variant in all transcripts IGV

HGNC symbol

SPG11

Ensembl transcript ID

ENST00000535302

Genbank transcript ID

NM_001160227

UniProt peptide

Q96JI7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1388T>C
cDNA.1416T>C
g.12120T>C

AA changes

F463S Score: 155 explain score(s)

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

463

frameshift

known variant

Reference ID: rs3759871

database	homozygous (G/G)	heterozygous	allele carriers
1000G	562	1254	1816
ExAC	13393	5981	19374

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.303	0.004
	0.69	0.009
(flanking)	0.267	0.012

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	12127	wt: 0.8616 / mu: 0.8772 (marginal change - not scored)	wt: GGCATGCAGTGTTTTTCCCTTGGCACAAAGTGTATTCCTGT mu: GGCATGCAGTGTTCTTCCCTTGGCACAAAGTGTATTCCTGT	cctt\|GGCA
Donor increased	12111	wt: 0.65 / mu: 0.76	wt: GGGCATGCAGTGTTT mu: GGGCATGCAGTGTTC	GCAT\|gcag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

463

mutated

not conserved

463

Ptroglodytes

all identical

ENSPTRG00000007016

463

Mmulatta

all identical

ENSMMUG00000014291

460

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000033396

456

Ggallus

all conserved

ENSGALG00000008180

471

Trubripes

not conserved

ENSTRUG00000014452

394

Drerio

no alignment

ENSDARG00000045968

n/a

Dmelanogaster

no alignment

FBgn0034786

n/a

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000025297

341

protein features

start (aa)	end (aa)	feature	details
1	1237	TOPO_DOM	Extracellular (Potential).	lost
612	612	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1046	1046	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1205	1205	CONFLICT	N -> K (in Ref. 5; CAH10686).	might get lost (downstream of altered splice site)
1238	1258	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1259	1471	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1472	1492	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1493	2443	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
1674	1674	CONFLICT	R -> G (in Ref. 6; BAC03600).	might get lost (downstream of altered splice site)
1955	1955	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1958	1958	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1961	1961	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
2253	2253	CONFLICT	D -> G (in Ref. 4; AAH94704).	might get lost (downstream of altered splice site)
2378	2378	CONFLICT	F -> L (in Ref. 6; BAB15065).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

6993 / 6993

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

2331 / 2331

position of stopcodon in wt / mu cDNA

7021 / 7021

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

29 / 29

chromosome

strand

-1

last intron/exon boundary

6841

theoretical NMD boundary in CDS

6762

length of CDS

6993

coding sequence (CDS) position

1388

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

1416

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

12120

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

44943757

original gDNA sequence snippet

GACCCAGGGCATGCAGTGTTTTTCCCTTGGCACAAAGTGTA

altered gDNA sequence snippet

GACCCAGGGCATGCAGTGTTCTTCCCTTGGCACAAAGTGTA

original cDNA sequence snippet

GACCCAGGGCATGCAGTGTTTTTCCCTTGGCACAAAGTGTA

altered cDNA sequence snippet

GACCCAGGGCATGCAGTGTTCTTCCCTTGGCACAAAGTGTA

wildtype AA sequence

MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCFSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVEILKEKN
YFSEKEKRTI DFVHQVEKLY LGHFQENMQI QSFPRYWIKE QDFFKHKSVL DSFLKYDCKD
EFNKQDHRIV LNWALWWDQL TQESILLPRI SPEEYKSYSP EALWRYLTAR HDWLNIILWI
GEFQTQHSYA SLQQNKWPLL TVDVINQNTS CNNYMRNEIL DKLARNGVFL ASELEDFECF
LLRLSRIGGV IQDTLPVQNY KTKEGWDFHS QFILYCLEHS LQHLLYVYLD CYKLSPENCP
FLEKKELHEA HPWFEFLVQC RQVASNLTDP KLIFQASLAN AQILIPTNQA SVSSMLLEGH
TLLALATTMY SPGGVSQVVQ NEENENCLKK VDPQLLKMAL TPYPKLKTAL FPQCTPPSVL
PSDITIYHLI QSLSPFDPSR LFGWQSANTL AIGDAWSHLP HFSSPDLVNK YAIVERLNFA
YYLHNGRPSF AFGTFLVQEL IKSKTPKQLI QQVGNEAYVI GLSSFHIPSI GAACVCFLEL
LGLDSLKLRV DMKVANIILS YKCRNEDAQY SFIRESVAEK LSKLADGEKT TTEELLVLLE
EGTWNSIQQQ EIKRLSSESS SQWALVVQFC RLHNMKLSIS YLRECAKAND WLQFIIHSQL
HNYHPAEVKS LIQYFSPVIQ DHLRLAFENL PSVPTSKMDS DQVCNKCPQE LQGSKQEMTD
LFEILLQCSE EPDSWHWLLV EAVKQQAPIL SVLASCLQGA SAISCLCVWI ITSVEDNVAT
EAMGHIQDST EDHTWNLEDL SVIWRTLLTR QKSKTLIRGF QLFFKDSPLL LVMEMYELCM
FFRNYKEAEA KLLEFQKSLE TLNTAATKVH PVIPAMWLED QVCFLLKLML QQCKTQYELG
KLLQLFVERE HLFSDGPDVK KLCILCQILK DTSIAINHTI ITSYSIENLQ HECRSILERL
QTDGQFALAR RVAELAELPV DNLVIKEITQ EMQTLKHIEQ WSLKQARIDF WKKCHENFKK
NSISSKAASS FFSTQAHVAC EHPTGWSSME ERHLLLTLAG HWLAQEDVVP LDKLEELEKQ
IWLCRITQHT LGRNQEETEP RFSRQISTSG ELSFDSLASE FSFSKLAALN TSKYLELNSL
PSKETCENRL DWKEQESLNF LIGRLLDDGC VHEASRVCRY FHFYNPDVAL VLHCRALASG
EASMEDLHPE IHALLQSAEL LEEEAPDIPL RRVHSRHKQM FNPTEESQTF LQLTTLCQDR
TLVGMKLLDK ISSVPHGELS CTTELLILAH HCFTLTCHME GIIRVLQAAH MLTDNHLAPS
EEYGLVVRLL TGIGRYNEMT YIFDLLHKKH YFEVLMRKKL DPSGTLKTAL LDYIKRCRPG
DSEKHNMIAL CFSMCREIGE NHEAAARIQL KLIESQPWED SLKDGHQLKQ LLLKALTLML
DAAESYAKDS CVRQAQHCQR LTKLITLQIH FLNTGQNTML INLGRHKLMD CILALPRFYQ
ASIVAEAYDF VPDWAEILYQ QVILKGDFNY LEEFKQQRLL KSSIFEEISK KYKQHQPTDM
VMENLKKLLT YCEDVYLYYK LAYEHKFYEI VNVLLKDPQT GCCLKDMLAG *

mutated AA sequence

MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCSSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVEILKEKN
YFSEKEKRTI DFVHQVEKLY LGHFQENMQI QSFPRYWIKE QDFFKHKSVL DSFLKYDCKD
EFNKQDHRIV LNWALWWDQL TQESILLPRI SPEEYKSYSP EALWRYLTAR HDWLNIILWI
GEFQTQHSYA SLQQNKWPLL TVDVINQNTS CNNYMRNEIL DKLARNGVFL ASELEDFECF
LLRLSRIGGV IQDTLPVQNY KTKEGWDFHS QFILYCLEHS LQHLLYVYLD CYKLSPENCP
FLEKKELHEA HPWFEFLVQC RQVASNLTDP KLIFQASLAN AQILIPTNQA SVSSMLLEGH
TLLALATTMY SPGGVSQVVQ NEENENCLKK VDPQLLKMAL TPYPKLKTAL FPQCTPPSVL
PSDITIYHLI QSLSPFDPSR LFGWQSANTL AIGDAWSHLP HFSSPDLVNK YAIVERLNFA
YYLHNGRPSF AFGTFLVQEL IKSKTPKQLI QQVGNEAYVI GLSSFHIPSI GAACVCFLEL
LGLDSLKLRV DMKVANIILS YKCRNEDAQY SFIRESVAEK LSKLADGEKT TTEELLVLLE
EGTWNSIQQQ EIKRLSSESS SQWALVVQFC RLHNMKLSIS YLRECAKAND WLQFIIHSQL
HNYHPAEVKS LIQYFSPVIQ DHLRLAFENL PSVPTSKMDS DQVCNKCPQE LQGSKQEMTD
LFEILLQCSE EPDSWHWLLV EAVKQQAPIL SVLASCLQGA SAISCLCVWI ITSVEDNVAT
EAMGHIQDST EDHTWNLEDL SVIWRTLLTR QKSKTLIRGF QLFFKDSPLL LVMEMYELCM
FFRNYKEAEA KLLEFQKSLE TLNTAATKVH PVIPAMWLED QVCFLLKLML QQCKTQYELG
KLLQLFVERE HLFSDGPDVK KLCILCQILK DTSIAINHTI ITSYSIENLQ HECRSILERL
QTDGQFALAR RVAELAELPV DNLVIKEITQ EMQTLKHIEQ WSLKQARIDF WKKCHENFKK
NSISSKAASS FFSTQAHVAC EHPTGWSSME ERHLLLTLAG HWLAQEDVVP LDKLEELEKQ
IWLCRITQHT LGRNQEETEP RFSRQISTSG ELSFDSLASE FSFSKLAALN TSKYLELNSL
PSKETCENRL DWKEQESLNF LIGRLLDDGC VHEASRVCRY FHFYNPDVAL VLHCRALASG
EASMEDLHPE IHALLQSAEL LEEEAPDIPL RRVHSRHKQM FNPTEESQTF LQLTTLCQDR
TLVGMKLLDK ISSVPHGELS CTTELLILAH HCFTLTCHME GIIRVLQAAH MLTDNHLAPS
EEYGLVVRLL TGIGRYNEMT YIFDLLHKKH YFEVLMRKKL DPSGTLKTAL LDYIKRCRPG
DSEKHNMIAL CFSMCREIGE NHEAAARIQL KLIESQPWED SLKDGHQLKQ LLLKALTLML
DAAESYAKDS CVRQAQHCQR LTKLITLQIH FLNTGQNTML INLGRHKLMD CILALPRFYQ
ASIVAEAYDF VPDWAEILYQ QVILKGDFNY LEEFKQQRLL KSSIFEEISK KYKQHQPTDM
VMENLKKLLT YCEDVYLYYK LAYEHKFYEI VNVLLKDPQT GCCLKDMLAG *

speed

0.94 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999707753 (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)

chr15:44943757A>GN/A show variant in all transcripts IGV

HGNC symbol

SPG11

Ensembl transcript ID

ENST00000427534

Genbank transcript ID

N/A

UniProt peptide

Q96JI7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1388T>C
cDNA.1388T>C
g.12120T>C

AA changes

F463S Score: 155 explain score(s)

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

463

frameshift

known variant

Reference ID: rs3759871

database	homozygous (G/G)	heterozygous	allele carriers
1000G	562	1254	1816
ExAC	13393	5981	19374

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.303	0.004
	0.69	0.009
(flanking)	0.267	0.012

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	12127	wt: 0.8616 / mu: 0.8772 (marginal change - not scored)	wt: GGCATGCAGTGTTTTTCCCTTGGCACAAAGTGTATTCCTGT mu: GGCATGCAGTGTTCTTCCCTTGGCACAAAGTGTATTCCTGT	cctt\|GGCA
Donor increased	12111	wt: 0.65 / mu: 0.76	wt: GGGCATGCAGTGTTT mu: GGGCATGCAGTGTTC	GCAT\|gcag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

463

mutated

not conserved

463

Ptroglodytes

all identical

ENSPTRG00000007016

463

Mmulatta

all identical

ENSMMUG00000014291

460

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000033396

456

Ggallus

all conserved

ENSGALG00000008180

471

Trubripes

not conserved

ENSTRUG00000014452

394

Drerio

no alignment

ENSDARG00000045968

n/a

Dmelanogaster

no alignment

FBgn0034786

n/a

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000025297

341

protein features

start (aa)	end (aa)	feature	details
1	1237	TOPO_DOM	Extracellular (Potential).	lost
612	612	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1046	1046	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1205	1205	CONFLICT	N -> K (in Ref. 5; CAH10686).	might get lost (downstream of altered splice site)
1238	1258	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1259	1471	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1472	1492	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1493	2443	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
1674	1674	CONFLICT	R -> G (in Ref. 6; BAC03600).	might get lost (downstream of altered splice site)
1955	1955	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1958	1958	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1961	1961	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
2253	2253	CONFLICT	D -> G (in Ref. 4; AAH94704).	might get lost (downstream of altered splice site)
2378	2378	CONFLICT	F -> L (in Ref. 6; BAB15065).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

6798 / 6798

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

2266 / 2266

position of stopcodon in wt / mu cDNA

6798 / 6798

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

6755

theoretical NMD boundary in CDS

6704

length of CDS

6798

coding sequence (CDS) position

1388

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

1388

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

12120

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

44943757

original gDNA sequence snippet

GACCCAGGGCATGCAGTGTTTTTCCCTTGGCACAAAGTGTA

altered gDNA sequence snippet

GACCCAGGGCATGCAGTGTTCTTCCCTTGGCACAAAGTGTA

original cDNA sequence snippet

GACCCAGGGCATGCAGTGTTTTTCCCTTGGCACAAAGTGTA

altered cDNA sequence snippet

GACCCAGGGCATGCAGTGTTCTTCCCTTGGCACAAAGTGTA

wildtype AA sequence

mutated AA sequence

MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCSSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVEILKEKN
YFSEKEKRTI DFVHQVEKLY LGHFQENMQI QSFPRYWIKE QDFFKHKSVL DSFLKYDCKD
EFNKQDHRIV LNWALWWDQL TQESILLPRI SPEEYKSYSP EALWRYLTAR HDWLNIILWI
GEFQTQHSYA SLQQNKWPLL TVDVINQNTS CNNYMRNEIL DKLARNGVFL ASELEDFECF
LLRLSRIGGV IQDTLPVQNY KTKEGWDFHS QFILYCLEHS LQHLLYVYLD CYKLSPENCP
FLEKKELHEA HPWFEFLVQC RQVASNLTDP KLIFQASLAN AQILIPTNQA SVSSMLLEGH
TLLALATTMY SPGGVSQVVQ NEENENCLKK VDPQLLKMAL TPYPKLKTAL FPQCTPPSVL
PSDITIYHLI QSLSPFDPSR LFGWQSANTL AIGDAWSHLP HFSSPDLVNK YAIVERLNFA
YYLHNGRPSF AFGTFLVQEL IKSKTPKQLI QQVGNEAYVI GLSSFHIPSI GAACVCFLEL
LGLDSLKLRV DMKVANIILS YKCRNEDAQY SFIRESVAEK LSKLADGEKT TTEELLVLLE
EGTWNSIQQQ EIKRLSSESS SQWALVVQFC RLHNMKLSIS YLRECAKAND WLQFIIHSQL
HNYHPAEVKS LIQYFSPVIQ DHLRLAFENL PSVPTSKMDS DQVCNKCPQE LQGSKQEMTD
LFEILLQCSE EPDSWHWLLV EAVKQQAPIL SVLASCLQGA SAISCLCVWI ITSVEDNVAT
EAMGHIQDST EDHTWNLEDL SVIWRTLLTR QKSKTLIRGF QLFFKDSPLL LVMEMYELCM
FFRNYKEAEA KLLEFQKSLE TLNTAATKVH PVIPAMWLED QVCFLLKLML QQCKTQYELG
KLLQLFVERE HLFSDGPDVK KLCILCQILK DTSIAINHTI ITSYSIENLQ HECRSILERL
QTDGQFALAR RVAELAELPV DNLVIKEITQ EMQTLKHIEQ WSLKQARIDF WKKCHENFKK
NSISSKAASS FFSTQAHVAC EHPTGWSSME ERHLLLTLAG HWLAQEDVVP LDKLEELEKQ
IWLCRITQHT LGRNQEETEP RFSRQISTSG ELSFDSLASE FSFSKLAALN TSKYLELNSL
PSKETCENRL DWKEQESLNF LIGRLLDDGC VHEASRVCRY FHFYNPDVAL VLHCRALASG
EASMEDLHPE IHALLQSAEL LEEEAPDIPL RRVHSTSSLD SQKFVTVPSS NEVVTNLEVL
TSKCLHGKNY CRQVLCLYDL AKELGCSYTD VAAQDGEAML RKILASQQPD RCKRAQAFIS
TQGLKPDTVA ELVAEEVTRE LLTSSQGTGH KQMFNPTEES QTFLQLTTLC QDRTLVGMKL
LDKISSVPHG ELSCTTELLI LAHHCFTLTC HMEGIIRVLQ AAHMLTDNHL APSEEYGLVV
RLLTGIGRYN EMTYIFDLLH KKHYFEVLMR KKLDPSGTLK TALLDYIKRC RPGDSEKHNM
IALCFSMCRE IGENHEAAAR IQLKLIESQP WDINNISLLT WSWKT*

speed

0.80 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999707753 (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)

chr15:44943757A>GN/A show variant in all transcripts IGV

HGNC symbol

SPG11

Ensembl transcript ID

ENST00000558319

Genbank transcript ID

N/A

UniProt peptide

Q96JI7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1388T>C
cDNA.1419T>C
g.12120T>C

AA changes

F463S Score: 155 explain score(s)

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

463

frameshift

known variant

Reference ID: rs3759871

database	homozygous (G/G)	heterozygous	allele carriers
1000G	562	1254	1816
ExAC	13393	5981	19374

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.303	0.004
	0.69	0.009
(flanking)	0.267	0.012

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	12127	wt: 0.8616 / mu: 0.8772 (marginal change - not scored)	wt: GGCATGCAGTGTTTTTCCCTTGGCACAAAGTGTATTCCTGT mu: GGCATGCAGTGTTCTTCCCTTGGCACAAAGTGTATTCCTGT	cctt\|GGCA
Donor increased	12111	wt: 0.65 / mu: 0.76	wt: GGGCATGCAGTGTTT mu: GGGCATGCAGTGTTC	GCAT\|gcag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

463

mutated

not conserved

463

Ptroglodytes

all identical

ENSPTRG00000007016

463

Mmulatta

all identical

ENSMMUG00000014291

460

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000033396

456

Ggallus

all conserved

ENSGALG00000008180

471

Trubripes

not conserved

ENSTRUG00000014452

394

Drerio

no alignment

ENSDARG00000045968

n/a

Dmelanogaster

no alignment

FBgn0034786

n/a

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000025297

341

protein features

start (aa)	end (aa)	feature	details
1	1237	TOPO_DOM	Extracellular (Potential).	lost
612	612	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1046	1046	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1205	1205	CONFLICT	N -> K (in Ref. 5; CAH10686).	might get lost (downstream of altered splice site)
1238	1258	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1259	1471	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1472	1492	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1493	2443	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
1674	1674	CONFLICT	R -> G (in Ref. 6; BAC03600).	might get lost (downstream of altered splice site)
1955	1955	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1958	1958	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1961	1961	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
2253	2253	CONFLICT	D -> G (in Ref. 4; AAH94704).	might get lost (downstream of altered splice site)
2378	2378	CONFLICT	F -> L (in Ref. 6; BAB15065).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

6240 / 6240

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

2080 / 2080

position of stopcodon in wt / mu cDNA

6271 / 6271

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

32 / 32

chromosome

strand

-1

last intron/exon boundary

6038

theoretical NMD boundary in CDS

5956

length of CDS

6240

coding sequence (CDS) position

1388

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

1419

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

12120

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

44943757

original gDNA sequence snippet

GACCCAGGGCATGCAGTGTTTTTCCCTTGGCACAAAGTGTA

altered gDNA sequence snippet

GACCCAGGGCATGCAGTGTTCTTCCCTTGGCACAAAGTGTA

original cDNA sequence snippet

GACCCAGGGCATGCAGTGTTTTTCCCTTGGCACAAAGTGTA

altered cDNA sequence snippet

GACCCAGGGCATGCAGTGTTCTTCCCTTGGCACAAAGTGTA

wildtype AA sequence

mutated AA sequence

MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCSSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVEILKEKN
YFSEKEKRTI DFVHQVEKLY LGHFQENMQI QSFPRYWIKE QDFFKHKSVL DSFLKYDCKD
EFNKQDHRIV LNWALWWDQL TQESILLPRI SPEEYKSYSP EALWRYLTAR HDWLNIILWI
GEFQTQHSYA SLQQNKWPLL TVDVINQNTS CNNYMRNEIL DKLARNGVFL ASELEDFECF
LLRLSRIGGV IQDTLPVQNY KTKEGWDFHS QFILYCLEHS LQHLLYVYLD CYKLSPENCP
FLEKKELHEA HPWFEFLVQC RQVASNLTDP KLIFQASLAN AQILIPTNQA SVSSMLLEGH
TLLALATTMY SPGGVSQVVQ NEENENCLKK VDPQLLKMAL TPYPKLKTAL FPQCTPPSVL
PSDITIYHLI QSLSPFDPSR LFGWQSANTL AIGDAWSHLP HFSSPDLVNK YAIVERLNFA
YYLHNGRPSF AFGTFLVQEL IKSKTPKQLI QQVGNEAYVI GLSSFHIPSI GAACVCFLEL
LGLDSLKLRV DMKVANIILS YKCRNEDAQY SFIRESVAEK LSKLADGEKT TTEELLVLLE
EGTWNSIQQQ EIKRLSSESS SQWALVVQFC RLHNMKLSIS YLRECAKAND WLQFIIHSQL
HNYHPAEVKS LIQYFSPVIQ DHLRLAFENL PSVPTSKMDS DQVCNKCPQE LQGSKQEMTD
LFEILLQCSE EPDSWHWLLV EAVKQQAPIL SVLASCLQGA SAISCLCVWI ITSVEDNVAT
EAMGHIQDST EDHTWNLEDL SVIWRTLLTR QKSKTLIRGF QLFFKDSPLL LVMEMYELCM
FFRNYKEAEA KLLEFQKSLE TLNTAATKVH PVIPAMWLED QVCFLLKLML QQCKTQYELG
KLLQLFVERE HLFSDGPDVK KLCILCQILK DTSIAINHTI ITSYSIENLQ HECRSILERL
QTDGQFALAR RVAELAELPV DNLVIKEITQ EMQTLKHIEQ WSLKQARIDF WKKCHENFKK
NSISSKAASS FFSTQAHVAC EHPTGWSSME ERHLLLTLAG HWLAQEDVVP LDKLEELEKQ
IWLCRITQHT LGRNQEETEP RFSRQISTSG ELSFDSLASE FSFSKLAALN TSKYLELNSL
PSKETCENRL DWKEQESLNF LIGRLLDDGC VHEASRVCRY FHFYNPDVAL VLHCRALASG
EASMEDLHPE IHALLQSAEL LEEEAPDIPL RRVHSTSSLD SQKFVTVPSS NEVVTNLEVL
TSKCLHGKNY CRQVLCLYDL AKELGCSYTD VAAQDGEAML RKILASQQPD RCKRAQAFIS
TQGLKPDTVA ELVAEEVTRE LLTSSQGTGA LPPGDSQPL*

speed

1.02 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999707753 (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)

chr15:44943757A>GN/A show variant in all transcripts IGV

HGNC symbol

SPG11

Ensembl transcript ID

ENST00000559193

Genbank transcript ID

N/A

UniProt peptide

Q96JI7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1388T>C
cDNA.1399T>C
g.12120T>C

AA changes

F463S Score: 155 explain score(s)

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

463

frameshift

known variant

Reference ID: rs3759871

database	homozygous (G/G)	heterozygous	allele carriers
1000G	562	1254	1816
ExAC	13393	5981	19374

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.303	0.004
	0.69	0.009
(flanking)	0.267	0.012

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	12127	wt: 0.8616 / mu: 0.8772 (marginal change - not scored)	wt: GGCATGCAGTGTTTTTCCCTTGGCACAAAGTGTATTCCTGT mu: GGCATGCAGTGTTCTTCCCTTGGCACAAAGTGTATTCCTGT	cctt\|GGCA
Donor increased	12111	wt: 0.65 / mu: 0.76	wt: GGGCATGCAGTGTTT mu: GGGCATGCAGTGTTC	GCAT\|gcag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

463

mutated

not conserved

463

Ptroglodytes

all identical

ENSPTRG00000007016

463

Mmulatta

all identical

ENSMMUG00000014291

460

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000033396

456

Ggallus

all conserved

ENSGALG00000008180

471

Trubripes

not conserved

ENSTRUG00000014452

394

Drerio

no alignment

ENSDARG00000045968

n/a

Dmelanogaster

no alignment

FBgn0034786

n/a

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000025297

341

protein features

start (aa)	end (aa)	feature	details
1	1237	TOPO_DOM	Extracellular (Potential).	lost
612	612	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1046	1046	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1205	1205	CONFLICT	N -> K (in Ref. 5; CAH10686).	might get lost (downstream of altered splice site)
1238	1258	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1259	1471	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1472	1492	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1493	2443	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
1674	1674	CONFLICT	R -> G (in Ref. 6; BAC03600).	might get lost (downstream of altered splice site)
1955	1955	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1958	1958	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1961	1961	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
2253	2253	CONFLICT	D -> G (in Ref. 4; AAH94704).	might get lost (downstream of altered splice site)
2378	2378	CONFLICT	F -> L (in Ref. 6; BAB15065).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2340 / 2340

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

780 / 780

position of stopcodon in wt / mu cDNA

2351 / 2351

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

12 / 12

chromosome

strand

-1

last intron/exon boundary

2256

theoretical NMD boundary in CDS

2194

length of CDS

2340

coding sequence (CDS) position

1388

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

1399

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

12120

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

44943757

original gDNA sequence snippet

GACCCAGGGCATGCAGTGTTTTTCCCTTGGCACAAAGTGTA

altered gDNA sequence snippet

GACCCAGGGCATGCAGTGTTCTTCCCTTGGCACAAAGTGTA

original cDNA sequence snippet

GACCCAGGGCATGCAGTGTTTTTCCCTTGGCACAAAGTGTA

altered cDNA sequence snippet

GACCCAGGGCATGCAGTGTTCTTCCCTTGGCACAAAGTGTA

wildtype AA sequence

mutated AA sequence

speed

0.98 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

Problems