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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000249837
Querying Taster for transcript #2: ENST00000261517
Querying Taster for transcript #3: ENST00000395896
Querying Taster for transcript #4: ENST00000395898
MT speed 0 s - this script 5.114228 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
VPS13C	polymorphism_automatic	1.33197957600251e-05	simple_aae		affected		S2870N	single base exchange	rs10851704		show file
VPS13C	polymorphism_automatic	1.33197957600251e-05	simple_aae		affected		S2913N	single base exchange	rs10851704		show file
VPS13C	polymorphism_automatic	1.33197957600251e-05	simple_aae		affected		S2913N	single base exchange	rs10851704		show file
VPS13C	polymorphism_automatic	1.33197957600251e-05	simple_aae		affected		S2870N	single base exchange	rs10851704		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99998668020424 (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)

chr15:62202482C>TN/A show variant in all transcripts IGV

HGNC symbol

VPS13C

Ensembl transcript ID

ENST00000249837

Genbank transcript ID

NM_017684

UniProt peptide

Q709C8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.8609G>A
cDNA.8708G>A
g.150191G>A

AA changes

S2870N Score: 46 explain score(s)

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

2870

frameshift

known variant

Reference ID: rs10851704

database	homozygous (T/T)	heterozygous	allele carriers
1000G	687	1212	1899
ExAC	18513	-4259	14254

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.255	0.934
	0.808	0.976
(flanking)	2.758	1

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	150182	wt: 0.9295 / mu: 0.9383 (marginal change - not scored)	wt: TTTTTAGTGCCTTCCATTTTGGCCAGAAAGTTTGTCAGGCA mu: TTTTTAGTGCCTTCCATTTTGGCCAGAAAATTTGTCAGGCA	tttg\|GCCA
Acc marginally increased	150186	wt: 0.4747 / mu: 0.4913 (marginal change - not scored)	wt: TAGTGCCTTCCATTTTGGCCAGAAAGTTTGTCAGGCAAACT mu: TAGTGCCTTCCATTTTGGCCAGAAAATTTGTCAGGCAAACT	gcca\|GAAA
Acc marginally increased	150181	wt: 0.9502 / mu: 0.9519 (marginal change - not scored)	wt: ATTTTTAGTGCCTTCCATTTTGGCCAGAAAGTTTGTCAGGC mu: ATTTTTAGTGCCTTCCATTTTGGCCAGAAAATTTGTCAGGC	tttt\|GGCC
Donor increased	150186	wt: 0.44 / mu: 0.98	wt: TGGCCAGAAAGTTTG mu: TGGCCAGAAAATTTG	GCCA\|gaaa
Donor increased	150194	wt: 0.84 / mu: 0.94	wt: AAGTTTGTCAGGCAA mu: AAATTTGTCAGGCAA	GTTT\|gtca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

2870

mutated

all conserved

2870

Ptroglodytes

all conserved

ENSPTRG00000007135

2914

Mmulatta

all conserved

ENSMMUG00000001362

2913

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000035284

2908

Ggallus

all conserved

ENSGALG00000003705

2910

Trubripes

all conserved

ENSTRUG00000003978

2891

Drerio

all identical

ENSDARG00000074465

2912

Dmelanogaster

not conserved

FBgn0033194

2501

Celegans

not conserved

T08G11.1

2398

RKL

Xtropicalis

all conserved

ENSXETG00000005221

2917

protein features

start (aa)	end (aa)	feature	details
3538	3538	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

11133 / 11133

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

3711 / 3711

position of stopcodon in wt / mu cDNA

11232 / 11232

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

100 / 100

chromosome

strand

-1

last intron/exon boundary

11131

theoretical NMD boundary in CDS

10981

length of CDS

11133

coding sequence (CDS) position

8609

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

8708

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

150191

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

62202482

original gDNA sequence snippet

CCTTCCATTTTGGCCAGAAAGTTTGTCAGGCAAACTTTGTG

altered gDNA sequence snippet

CCTTCCATTTTGGCCAGAAAATTTGTCAGGCAAACTTTGTG

original cDNA sequence snippet

CCTTCCATTTTGGCCAGAAAGTTTGTCAGGCAAACTTTGTG

altered cDNA sequence snippet

CCTTCCATTTTGGCCAGAAAATTTGTCAGGCAAACTTTGTG

wildtype AA sequence

MVLESVVADL LNRFLGDYVE NLNKSQLKLG IWGGNVALDN LQIKENALSE LDVPFKVKAG
QIDKLTLKIP WKNLYGEAVV ATLEGLYLLV VPGASIKYDA VKEEKSLQDV KQKELSRIEE
ALQKAAEKDK PKEAKKDTFV EKLATQVIKN VQVKITDIHI KYEDDVTDPK RPLSFGVTLG
ELSLLTANEH WTPCILNEAD KIIYKLIRLD SLSAYWNVNC SMSYQRSREQ ILDQLKNEIL
TSGNIPPNYQ YIFQPISASA KLYMNPYAES ELKTPKLDCN IEIQNIAIEL TKPQYLSMID
LLESVDYMVR NAPYRKYKPY LPLHTNGRRW WKYAIDSVLE VHIRRYTQMW SWSNIKKHRQ
LLKSYKIAYK NKLTQSKVSE EIQKEIQDLE KTLDVFNIIL ARQQAQVEVI RSGQKLRKKS
ADTGEKRGGW FSGLWGKKES KKKDEESLIP ETIDDLMTPE EKDKLFTAIG YSESTHNLTL
PKQYVAHIMT LKLVSTSVTI RENKNIPEIL KIQIIGLGTQ VSQRPGAQAL KVEAKLEHWY
ITGLRQQDIV PSLVASIGDT TSSLLKIKFE TNPEDSPADQ TLIVQSQPVE VIYDAKTVNA
VVEFFQSNKG LDLEQITSAT LMKLEEIKER TATGLTHIIE TRKVLDLRIN LKPSYLVVPQ
TGFHHEKSDL LILDFGTFQL NSKDQGLQKT TNSSLEEIMD KAYDKFDVEI KNVQLLFARA
EETWKKCRFQ HPSTMHILQP MDIHVELAKA MVEKDIRMAR FKVSGGLPLM HVRISDQKMK
DVLYLMNSIP LPQKSSAQSP ERQVSSIPII SGGTKGLLGT SLLLDTVESE SDDEYFDAED
GEPQTCKSMK GSELKKAAEV PNEELINLLL KFEIKEVILE FTKQQKEEDT ILVFNVTQLG
TEATMRTFDL TVVSYLKKIS LDYHEIEGSK RKPLHLISSS DKPGLDLLKV EYIKADKNGP
SFQTAFGKTE QTVKVAFSSL NLLLQTQALV ASINYLTTII PSDDQSISVA KEVQISTEKQ
QKNSTLPKAI VSSRDSDIID FRLFAKLNAF CVIVCNEKNN IAEIKIQGLD SSLSLQSRKQ
SLFARLENII VTDVDPKTVH KKAVSIMGNE VFRFNLDLYP DATEGDLYTD MSKVDGVLSL
NVGCIQIVYL HKFLMSLLNF LNNFQTAKES LSAATAQAAE RAATSVKDLA QRSFRVSINI
DLKAPVIVIP QSSISTNAVV VDLGLIRVHN QFSLVSDEDY LNPPVIDRMD VQLTKLTLYR
TVIQPGIYHP DIQLLHPINL EFLVNRNLAA SWYHKVPVVE IKGHLDSMNV SLNQEDLNLL
FRILTENLCE GTEDLDKVKP RVQETGEIKE PLEISISQDV HDSKNTLTTG VEEIRSVDII
NMLLNFEIKE VVVTLMKKSE KKGRPLHELN VLQLGMEAKV KTYDMTAKAY LKKISMQCFD
FTDSKGEPLH IINSSNVTDE PLLKMLLTKA DSDGPEFKTI HDSTKQRLKV SFASLDLVLH
LEALLSFMDF LSSAAPFSEP SSSEKESELK PLVGESRSIA VKAVSSNISQ KDVFDLKITA
ELNAFNVFVC DQKCNIADIK IHGMDASISV KPKQTDVFAR LKDIIVMNVD LQSIHKKAVS
ILGDEVFRFQ LTLYPDATEG EAYADMSKVD GKLSFKVGCI QIVYVHKFFM SLLNFLNNFQ
TAKEALSTAT VQAAERAASS MKDLAQKSFR LLMDINLKAP VIIIPQSSVS PNAVIADLGL
IRVENKFSLV PMEHYSLPPV IDKMNIELTQ LKLSRTILQA SLPQNDIEIL KPVNMLLSIQ
RNLAAAWYVQ IPGMEIKGKL KPMQVALSED DLTVLMKILL ENLGEASSQP SPTQSVQETV
RVRKVDVSSV PDHLKEQEDW TDSKLSMNQI VSLQFDFHFE SLSIILYNND INQESGVAFH
NDSFQLGELR LHLMASSGKM FKDGSMNVSV KLKTCTLDDL REGIERATSR MIDRKNDQDN
NSSMIDISYK QDKNGSQIDA VLDKLYVCAS VEFLMTVADF FIKAVPQSPE NVAKETQILP
RQTATGKVKI EKDDSVRPNM TLKAMITDPE VVFVASLTKA DAPALTASFQ CNLSLSTSKL
EQMMEASVRD LKVLACPFLR EKRGKNITTV LQPCSLFMEK CTWASGKQNI NIMVKEFIIK
ISPIILNTVL TIMAALSPKT KEDGSKDTSK EMENLWGIKS INDYNTWFLG VDTATEITES
FKGIEHSLIE ENCGVVVESI QVTLECGLGH RTVPLLLAES KFSGNIKNWT SLMAAVADVT
LQVHYYNEIH AVWEPLIERV EGKRQWNLRL DVKKNPVQDK SLLPGDDFIP EPQMAIHISS
GNTMNITISK SCLNVFNNLA KGFSEGTAST FDYSLKDRAP FTVKNAVGVP IKVKPNCNLR
VMGFPEKSDI FDVDAGQNLE LEYASMVPSS QGNLSILSRQ ESSFFTLTIV PHGYTEVANI
PVARPGRRLY NVRNPNASHS DSVLVQIDAT EGNKVITLRS PLQIKNHFSI AFIIYKFVKN
VKLLERIGIA RPEEEFHVPL DSYRCQLFIQ PAGILEHQYK ESTTYISWKE ELHRSREVRC
MLQCPSVEVS FLPLIVNTVA LPDELSYICT HGEDWDVAYI IHLYPSLTLR NLLPYSLRYL
LEGTAETHEL AEGSTADVLH SRISGEIMEL VLVKYQGKNW NGHFRIRDTL PEFFPVCFSS
DSTEVTTVDL SVHVRRIGSR MVLSVFSPYW LINKTTRVLQ YRSEDIHVKH PADFRDIILF
SFKKKNIFTK NKVQLKISTS AWSSSFSLDT VGSYGCVKCP ANNMEYLVGV SIKMSSFNLS
RIVTLTPFCT IANKSSLELE VGEIASDGSM PTNKWNYIAS SECLPFWPES LSGKLCVRVV
GCEGSSKPFF YNRQDNGTLL SLEDLNGGIL VDVNTAEHST VITFSDYHEG SAPALIMNHT
PWDILTYKQS GSPEEMVLLP RQARLFAWAD PTGTRKLTWT YAANVGEHDL LKDGCGQFPY
DANIQIHWVS FLDGRQRVLL FTDDVALVSK ALQAEEMEQA DYEITLSLHS LGLSLVNNES
KQEVSYIGIT SSGVVWEVKP KQKWKPFSQK QIILLEQSYQ KHQISRDHGW IKLDNNFEVN
FDKDPMEMRL PIRSPIKRDF LSGIQIEFKQ SSHQRSLRAR LYWLQVDNQL PGAMFPVVFH
PVAPPKSIAL DSEPKPFIDV SVITRFNEYS KVLQFKYFMV LIQEMALKID QGFLGAIIAL
FTPTTDPEAE RRRTKLIQQD IDALNAELME TSMTDMSILS FFEHFHISPV KLHLSLSLGS
GGEESDKEKQ EMFAVHSVNL LLKSIGATLT DVDDLIFKLA YYEIRYQFYK RDQLIWSVVR
HYSEQFLKQM YVLVLGLDVL GNPFGLIRGL SEGVEALFYE PFQGAVQGPE EFAEGLVIGV
RSLFGHTVGG AAGVVSRITG SVGKGLAAIT MDKEYQQKRR EELSRQPRDF GDSLARGGKG
FLRGVVGGVT GIITKPVEGA KKEGAAGFFK GIGKGLVGAV ARPTGGIVDM ASSTFQGIQR
AAESTEEVSS LRPPRLIHED GIIRPYDRQE SEGSDLLENH IKKLEGETYR YHCAIPGSKK
TILMVTNRRV LCIKEVEILG LMCVDWQCPF EDFVFPPSVS ENVLKISVKE QGLFHKKDSA
NQGCVRKVYL KDTATAERAC NAIEDAQSTR QQQKLMKQSS VRLLRPQLPS *

mutated AA sequence

MVLESVVADL LNRFLGDYVE NLNKSQLKLG IWGGNVALDN LQIKENALSE LDVPFKVKAG
QIDKLTLKIP WKNLYGEAVV ATLEGLYLLV VPGASIKYDA VKEEKSLQDV KQKELSRIEE
ALQKAAEKDK PKEAKKDTFV EKLATQVIKN VQVKITDIHI KYEDDVTDPK RPLSFGVTLG
ELSLLTANEH WTPCILNEAD KIIYKLIRLD SLSAYWNVNC SMSYQRSREQ ILDQLKNEIL
TSGNIPPNYQ YIFQPISASA KLYMNPYAES ELKTPKLDCN IEIQNIAIEL TKPQYLSMID
LLESVDYMVR NAPYRKYKPY LPLHTNGRRW WKYAIDSVLE VHIRRYTQMW SWSNIKKHRQ
LLKSYKIAYK NKLTQSKVSE EIQKEIQDLE KTLDVFNIIL ARQQAQVEVI RSGQKLRKKS
ADTGEKRGGW FSGLWGKKES KKKDEESLIP ETIDDLMTPE EKDKLFTAIG YSESTHNLTL
PKQYVAHIMT LKLVSTSVTI RENKNIPEIL KIQIIGLGTQ VSQRPGAQAL KVEAKLEHWY
ITGLRQQDIV PSLVASIGDT TSSLLKIKFE TNPEDSPADQ TLIVQSQPVE VIYDAKTVNA
VVEFFQSNKG LDLEQITSAT LMKLEEIKER TATGLTHIIE TRKVLDLRIN LKPSYLVVPQ
TGFHHEKSDL LILDFGTFQL NSKDQGLQKT TNSSLEEIMD KAYDKFDVEI KNVQLLFARA
EETWKKCRFQ HPSTMHILQP MDIHVELAKA MVEKDIRMAR FKVSGGLPLM HVRISDQKMK
DVLYLMNSIP LPQKSSAQSP ERQVSSIPII SGGTKGLLGT SLLLDTVESE SDDEYFDAED
GEPQTCKSMK GSELKKAAEV PNEELINLLL KFEIKEVILE FTKQQKEEDT ILVFNVTQLG
TEATMRTFDL TVVSYLKKIS LDYHEIEGSK RKPLHLISSS DKPGLDLLKV EYIKADKNGP
SFQTAFGKTE QTVKVAFSSL NLLLQTQALV ASINYLTTII PSDDQSISVA KEVQISTEKQ
QKNSTLPKAI VSSRDSDIID FRLFAKLNAF CVIVCNEKNN IAEIKIQGLD SSLSLQSRKQ
SLFARLENII VTDVDPKTVH KKAVSIMGNE VFRFNLDLYP DATEGDLYTD MSKVDGVLSL
NVGCIQIVYL HKFLMSLLNF LNNFQTAKES LSAATAQAAE RAATSVKDLA QRSFRVSINI
DLKAPVIVIP QSSISTNAVV VDLGLIRVHN QFSLVSDEDY LNPPVIDRMD VQLTKLTLYR
TVIQPGIYHP DIQLLHPINL EFLVNRNLAA SWYHKVPVVE IKGHLDSMNV SLNQEDLNLL
FRILTENLCE GTEDLDKVKP RVQETGEIKE PLEISISQDV HDSKNTLTTG VEEIRSVDII
NMLLNFEIKE VVVTLMKKSE KKGRPLHELN VLQLGMEAKV KTYDMTAKAY LKKISMQCFD
FTDSKGEPLH IINSSNVTDE PLLKMLLTKA DSDGPEFKTI HDSTKQRLKV SFASLDLVLH
LEALLSFMDF LSSAAPFSEP SSSEKESELK PLVGESRSIA VKAVSSNISQ KDVFDLKITA
ELNAFNVFVC DQKCNIADIK IHGMDASISV KPKQTDVFAR LKDIIVMNVD LQSIHKKAVS
ILGDEVFRFQ LTLYPDATEG EAYADMSKVD GKLSFKVGCI QIVYVHKFFM SLLNFLNNFQ
TAKEALSTAT VQAAERAASS MKDLAQKSFR LLMDINLKAP VIIIPQSSVS PNAVIADLGL
IRVENKFSLV PMEHYSLPPV IDKMNIELTQ LKLSRTILQA SLPQNDIEIL KPVNMLLSIQ
RNLAAAWYVQ IPGMEIKGKL KPMQVALSED DLTVLMKILL ENLGEASSQP SPTQSVQETV
RVRKVDVSSV PDHLKEQEDW TDSKLSMNQI VSLQFDFHFE SLSIILYNND INQESGVAFH
NDSFQLGELR LHLMASSGKM FKDGSMNVSV KLKTCTLDDL REGIERATSR MIDRKNDQDN
NSSMIDISYK QDKNGSQIDA VLDKLYVCAS VEFLMTVADF FIKAVPQSPE NVAKETQILP
RQTATGKVKI EKDDSVRPNM TLKAMITDPE VVFVASLTKA DAPALTASFQ CNLSLSTSKL
EQMMEASVRD LKVLACPFLR EKRGKNITTV LQPCSLFMEK CTWASGKQNI NIMVKEFIIK
ISPIILNTVL TIMAALSPKT KEDGSKDTSK EMENLWGIKS INDYNTWFLG VDTATEITES
FKGIEHSLIE ENCGVVVESI QVTLECGLGH RTVPLLLAES KFSGNIKNWT SLMAAVADVT
LQVHYYNEIH AVWEPLIERV EGKRQWNLRL DVKKNPVQDK SLLPGDDFIP EPQMAIHISS
GNTMNITISK SCLNVFNNLA KGFSEGTAST FDYSLKDRAP FTVKNAVGVP IKVKPNCNLR
VMGFPEKSDI FDVDAGQNLE LEYASMVPSS QGNLSILSRQ ESSFFTLTIV PHGYTEVANI
PVARPGRRLY NVRNPNASHS DSVLVQIDAT EGNKVITLRS PLQIKNHFSI AFIIYKFVKN
VKLLERIGIA RPEEEFHVPL DSYRCQLFIQ PAGILEHQYK ESTTYISWKE ELHRSREVRC
MLQCPSVEVS FLPLIVNTVA LPDELSYICT HGEDWDVAYI IHLYPSLTLR NLLPYSLRYL
LEGTAETHEL AEGSTADVLH SRISGEIMEL VLVKYQGKNW NGHFRIRDTL PEFFPVCFSS
DSTEVTTVDL SVHVRRIGSR MVLSVFSPYW LINKTTRVLQ YRSEDIHVKH PADFRDIILF
SFKKKNIFTK NKVQLKISTS AWSSSFSLDT VGSYGCVKCP ANNMEYLVGV SIKMSSFNLS
RIVTLTPFCT IANKSSLELE VGEIASDGSM PTNKWNYIAS SECLPFWPEN LSGKLCVRVV
GCEGSSKPFF YNRQDNGTLL SLEDLNGGIL VDVNTAEHST VITFSDYHEG SAPALIMNHT
PWDILTYKQS GSPEEMVLLP RQARLFAWAD PTGTRKLTWT YAANVGEHDL LKDGCGQFPY
DANIQIHWVS FLDGRQRVLL FTDDVALVSK ALQAEEMEQA DYEITLSLHS LGLSLVNNES
KQEVSYIGIT SSGVVWEVKP KQKWKPFSQK QIILLEQSYQ KHQISRDHGW IKLDNNFEVN
FDKDPMEMRL PIRSPIKRDF LSGIQIEFKQ SSHQRSLRAR LYWLQVDNQL PGAMFPVVFH
PVAPPKSIAL DSEPKPFIDV SVITRFNEYS KVLQFKYFMV LIQEMALKID QGFLGAIIAL
FTPTTDPEAE RRRTKLIQQD IDALNAELME TSMTDMSILS FFEHFHISPV KLHLSLSLGS
GGEESDKEKQ EMFAVHSVNL LLKSIGATLT DVDDLIFKLA YYEIRYQFYK RDQLIWSVVR
HYSEQFLKQM YVLVLGLDVL GNPFGLIRGL SEGVEALFYE PFQGAVQGPE EFAEGLVIGV
RSLFGHTVGG AAGVVSRITG SVGKGLAAIT MDKEYQQKRR EELSRQPRDF GDSLARGGKG
FLRGVVGGVT GIITKPVEGA KKEGAAGFFK GIGKGLVGAV ARPTGGIVDM ASSTFQGIQR
AAESTEEVSS LRPPRLIHED GIIRPYDRQE SEGSDLLENH IKKLEGETYR YHCAIPGSKK
TILMVTNRRV LCIKEVEILG LMCVDWQCPF EDFVFPPSVS ENVLKISVKE QGLFHKKDSA
NQGCVRKVYL KDTATAERAC NAIEDAQSTR QQQKLMKQSS VRLLRPQLPS *

speed

1.15 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: 0.99998668020424 (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)

chr15:62202482C>TN/A show variant in all transcripts IGV

HGNC symbol

VPS13C

Ensembl transcript ID

ENST00000395896

Genbank transcript ID

NM_001018088

UniProt peptide

Q709C8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.8738G>A
cDNA.8812G>A
g.150191G>A

AA changes

S2913N Score: 46 explain score(s)

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

2913

frameshift

known variant

Reference ID: rs10851704

database	homozygous (T/T)	heterozygous	allele carriers
1000G	687	1212	1899
ExAC	18513	-4259	14254

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.255	0.934
	0.808	0.976
(flanking)	2.758	1

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	150182	wt: 0.9295 / mu: 0.9383 (marginal change - not scored)	wt: TTTTTAGTGCCTTCCATTTTGGCCAGAAAGTTTGTCAGGCA mu: TTTTTAGTGCCTTCCATTTTGGCCAGAAAATTTGTCAGGCA	tttg\|GCCA
Acc marginally increased	150186	wt: 0.4747 / mu: 0.4913 (marginal change - not scored)	wt: TAGTGCCTTCCATTTTGGCCAGAAAGTTTGTCAGGCAAACT mu: TAGTGCCTTCCATTTTGGCCAGAAAATTTGTCAGGCAAACT	gcca\|GAAA
Acc marginally increased	150181	wt: 0.9502 / mu: 0.9519 (marginal change - not scored)	wt: ATTTTTAGTGCCTTCCATTTTGGCCAGAAAGTTTGTCAGGC mu: ATTTTTAGTGCCTTCCATTTTGGCCAGAAAATTTGTCAGGC	tttt\|GGCC
Donor increased	150186	wt: 0.44 / mu: 0.98	wt: TGGCCAGAAAGTTTG mu: TGGCCAGAAAATTTG	GCCA\|gaaa
Donor increased	150194	wt: 0.84 / mu: 0.94	wt: AAGTTTGTCAGGCAA mu: AAATTTGTCAGGCAA	GTTT\|gtca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

2913

mutated

all conserved

2913

Ptroglodytes

all conserved

ENSPTRG00000007135

2914

Mmulatta

all conserved

ENSMMUG00000001362

2913

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000035284

2908

Ggallus

all conserved

ENSGALG00000003705

2910

Trubripes

all conserved

ENSTRUG00000003978

2891

Drerio

all identical

ENSDARG00000074465

2912

Dmelanogaster

not conserved

FBgn0033194

2501

Celegans

not conserved

T08G11.1

2398

RKL

Xtropicalis

all conserved

ENSXETG00000005221

2917

protein features

start (aa)	end (aa)	feature	details
3538	3538	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

10887 / 10887

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

3629 / 3629

position of stopcodon in wt / mu cDNA

10961 / 10961

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

75 / 75

chromosome

strand

-1

last intron/exon boundary

10938

theoretical NMD boundary in CDS

10813

length of CDS

10887

coding sequence (CDS) position

8738

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

8812

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

150191

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

62202482

original gDNA sequence snippet

CCTTCCATTTTGGCCAGAAAGTTTGTCAGGCAAACTTTGTG

altered gDNA sequence snippet

CCTTCCATTTTGGCCAGAAAATTTGTCAGGCAAACTTTGTG

original cDNA sequence snippet

CCTTCCATTTTGGCCAGAAAGTTTGTCAGGCAAACTTTGTG

altered cDNA sequence snippet

CCTTCCATTTTGGCCAGAAAATTTGTCAGGCAAACTTTGTG

wildtype AA sequence

MVLESVVADL LNRFLGDYVE NLNKSQLKLG IWGGNVALDN LQIKENALSE LDVPFKVKAG
QIDKLTLKIP WKNLYGEAVV ATLEGLYLLV VPGASIKYDA VKEEKSLQDV KQKELSRIEE
ALQKAAEKGT HSGEFIYGLE NFVYKDIKPG RKRKKHKKHF KKPFKGLDRS KDKPKEAKKD
TFVEKLATQV IKNVQVKITD IHIKYEDDVT DPKRPLSFGV TLGELSLLTA NEHWTPCILN
EADKIIYKLI RLDSLSAYWN VNCSMSYQRS REQILDQLKN EILTSGNIPP NYQYIFQPIS
ASAKLYMNPY AESELKTPKL DCNIEIQNIA IELTKPQYLS MIDLLESVDY MVRNAPYRKY
KPYLPLHTNG RRWWKYAIDS VLEVHIRRYT QMWSWSNIKK HRQLLKSYKI AYKNKLTQSK
VSEEIQKEIQ DLEKTLDVFN IILARQQAQV EVIRSGQKLR KKSADTGEKR GGWFSGLWGK
KESKKKDEES LIPETIDDLM TPEEKDKLFT AIGYSESTHN LTLPKQYVAH IMTLKLVSTS
VTIRENKNIP EILKIQIIGL GTQVSQRPGA QALKVEAKLE HWYITGLRQQ DIVPSLVASI
GDTTSSLLKI KFETNPEDSP ADQTLIVQSQ PVEVIYDAKT VNAVVEFFQS NKGLDLEQIT
SATLMKLEEI KERTATGLTH IIETRKVLDL RINLKPSYLV VPQTGFHHEK SDLLILDFGT
FQLNSKDQGL QKTTNSSLEE IMDKAYDKFD VEIKNVQLLF ARAEETWKKC RFQHPSTMHI
LQPMDIHVEL AKAMVEKDIR MARFKVSGGL PLMHVRISDQ KMKDVLYLMN SIPLPQKSSA
QSPERQVSSI PIISGGTKGL LGTSLLLDTV ESESDDEYFD AEDGEPQTCK SMKGSELKKA
AEVPNEELIN LLLKFEIKEV ILEFTKQQKE EDTILVFNVT QLGTEATMRT FDLTVVSYLK
KISLDYHEIE GSKRKPLHLI SSSDKPGLDL LKVEYIKADK NGPSFQTAFG KTEQTVKVAF
SSLNLLLQTQ ALVASINYLT TIIPSDDQSI SVAKEVQIST EKQQKNSTLP KAIVSSRDSD
IIDFRLFAKL NAFCVIVCNE KNNIAEIKIQ GLDSSLSLQS RKQSLFARLE NIIVTDVDPK
TVHKKAVSIM GNEVFRFNLD LYPDATEGDL YTDMSKVDGV LSLNVGCIQI VYLHKFLMSL
LNFLNNFQTA KESLSAATAQ AAERAATSVK DLAQRSFRVS INIDLKAPVI VIPQSSISTN
AVVVDLGLIR VHNQFSLVSD EDYLNPPVID RMDVQLTKLT LYRTVIQPGI YHPDIQLLHP
INLEFLVNRN LAASWYHKVP VVEIKGHLDS MNVSLNQEDL NLLFRILTEN LCEGTEDLDK
VKPRVQETGE IKEPLEISIS QDVHDSKNTL TTGVEEIRSV DIINMLLNFE IKEVVVTLMK
KSEKKGRPLH ELNVLQLGME AKVKTYDMTA KAYLKKISMQ CFDFTDSKGE PLHIINSSNV
TDEPLLKMLL TKADSDGPEF KTIHDSTKQR LKVSFASLDL VLHLEALLSF MDFLSSAAPF
SEPSSSEKES ELKPLVGESR SIAVKAVSSN ISQKDVFDLK ITAELNAFNV FVCDQKCNIA
DIKIHGMDAS ISVKPKQTDV FARLKDIIVM NVDLQSIHKK AVSILGDEVF RFQLTLYPDA
TEGEAYADMS KVDGKLSFKV GCIQIVYVHK FFMSLLNFLN NFQTAKEALS TATVQAAERA
ASSMKDLAQK SFRLLMDINL KAPVIIIPQS SVSPNAVIAD LGLIRVENKF SLVPMEHYSL
PPVIDKMNIE LTQLKLSRTI LQASLPQNDI EILKPVNMLL SIQRNLAAAW YVQIPGMEIK
GKLKPMQVAL SEDDLTVLMK ILLENLGEAS SQPSPTQSVQ ETVRVRKVDV SSVPDHLKEQ
EDWTDSKLSM NQIVSLQFDF HFESLSIILY NNDINQESGV AFHNDSFQLG ELRLHLMASS
GKMFKDGSMN VSVKLKTCTL DDLREGIERA TSRMIDRKND QDNNSSMIDI SYKQDKNGSQ
IDAVLDKLYV CASVEFLMTV ADFFIKAVPQ SPENVAKETQ ILPRQTATGK VKIEKDDSVR
PNMTLKAMIT DPEVVFVASL TKADAPALTA SFQCNLSLST SKLEQMMEAS VRDLKVLACP
FLREKRGKNI TTVLQPCSLF MEKCTWASGK QNINIMVKEF IIKISPIILN TVLTIMAALS
PKTKEDGSKD TSKEMENLWG IKSINDYNTW FLGVDTATEI TESFKGIEHS LIEENCGVVV
ESIQVTLECG LGHRTVPLLL AESKFSGNIK NWTSLMAAVA DVTLQVHYYN EIHAVWEPLI
ERVEGKRQWN LRLDVKKNPV QDKSLLPGDD FIPEPQMAIH ISSGNTMNIT ISKSCLNVFN
NLAKGFSEGT ASTFDYSLKD RAPFTVKNAV GVPIKVKPNC NLRVMGFPEK SDIFDVDAGQ
NLELEYASMV PSSQGNLSIL SRQESSFFTL TIVPHGYTEV ANIPVARPGR RLYNVRNPNA
SHSDSVLVQI DATEGNKVIT LRSPLQIKNH FSIAFIIYKF VKNVKLLERI GIARPEEEFH
VPLDSYRCQL FIQPAGILEH QYKESTTYIS WKEELHRSRE VRCMLQCPSV EVSFLPLIVN
TVALPDELSY ICTHGEDWDV AYIIHLYPSL TLRNLLPYSL RYLLEGTAET HELAEGSTAD
VLHSRISGEI MELVLVKYQG KNWNGHFRIR DTLPEFFPVC FSSDSTEVTT VDLSVHVRRI
GSRMVLSVFS PYWLINKTTR VLQYRSEDIH VKHPADFRDI ILFSFKKKNI FTKNKVQLKI
STSAWSSSFS LDTVGSYGCV KCPANNMEYL VGVSIKMSSF NLSRIVTLTP FCTIANKSSL
ELEVGEIASD GSMPTNKWNY IASSECLPFW PESLSGKLCV RVVGCEGSSK PFFYNRQDNG
TLLSLEDLNG GILVDVNTAE HSTVITFSDY HEGSAPALIM NHTPWDILTY KQSGSPEEMV
LLPRQARLFA WADPTGTRKL TWTYAANVGE HDLLKDGCGQ FPYDANIQIH WVSFLDGRQR
VLLFTDDVAL VSKALQAEEM EQADYEITLS LHSLGLSLVN NESKQEVSYI GITSSGVVWE
VKPKQKWKPF SQKQIILLEQ SYQKHQISRD HGWIKLDNNF EVNFDKDPME MRLPIRSPIK
RDFLSGIQIE FKQSSHQRSL RARLYWLQVD NQLPGAMFPV VFHPVAPPKS IALDSEPKPF
IDVSVITRFN EYSKVLQFKY FMVLIQEMAL KIDQGFLGAI IALFTPTTDP EAERRRTKLI
QQDIDALNAE LMETSMTDMS ILSFFEHFHI SPVKLHLSLS LGSGGEESDK EKQEMFAVHS
VNLLLKSIGA TLTDVDDLIF KLAYYEIRYQ FYKRDQLIWS VVRHYSEQFL KQMYVLVLGL
DVLGNPFGLI RGLSEGVEAL FYEPFQGAVQ GPEEFAEGLV IGVRSLFGHT VGGAAGVVSR
ITGSVGKGLA AITMDKEYQQ KRREELSRQP RDFGDSLARG GKGFLRGVVG GVTGIITKPV
EGAKKEGAAG FFKGIGKGLV GAVARPTGGI VDMASSTFQG IQRAAESTEE VSSLRPPRLI
HEDGIIRPYD RQESEGSDLL EQELEIQE*

mutated AA sequence

MVLESVVADL LNRFLGDYVE NLNKSQLKLG IWGGNVALDN LQIKENALSE LDVPFKVKAG
QIDKLTLKIP WKNLYGEAVV ATLEGLYLLV VPGASIKYDA VKEEKSLQDV KQKELSRIEE
ALQKAAEKGT HSGEFIYGLE NFVYKDIKPG RKRKKHKKHF KKPFKGLDRS KDKPKEAKKD
TFVEKLATQV IKNVQVKITD IHIKYEDDVT DPKRPLSFGV TLGELSLLTA NEHWTPCILN
EADKIIYKLI RLDSLSAYWN VNCSMSYQRS REQILDQLKN EILTSGNIPP NYQYIFQPIS
ASAKLYMNPY AESELKTPKL DCNIEIQNIA IELTKPQYLS MIDLLESVDY MVRNAPYRKY
KPYLPLHTNG RRWWKYAIDS VLEVHIRRYT QMWSWSNIKK HRQLLKSYKI AYKNKLTQSK
VSEEIQKEIQ DLEKTLDVFN IILARQQAQV EVIRSGQKLR KKSADTGEKR GGWFSGLWGK
KESKKKDEES LIPETIDDLM TPEEKDKLFT AIGYSESTHN LTLPKQYVAH IMTLKLVSTS
VTIRENKNIP EILKIQIIGL GTQVSQRPGA QALKVEAKLE HWYITGLRQQ DIVPSLVASI
GDTTSSLLKI KFETNPEDSP ADQTLIVQSQ PVEVIYDAKT VNAVVEFFQS NKGLDLEQIT
SATLMKLEEI KERTATGLTH IIETRKVLDL RINLKPSYLV VPQTGFHHEK SDLLILDFGT
FQLNSKDQGL QKTTNSSLEE IMDKAYDKFD VEIKNVQLLF ARAEETWKKC RFQHPSTMHI
LQPMDIHVEL AKAMVEKDIR MARFKVSGGL PLMHVRISDQ KMKDVLYLMN SIPLPQKSSA
QSPERQVSSI PIISGGTKGL LGTSLLLDTV ESESDDEYFD AEDGEPQTCK SMKGSELKKA
AEVPNEELIN LLLKFEIKEV ILEFTKQQKE EDTILVFNVT QLGTEATMRT FDLTVVSYLK
KISLDYHEIE GSKRKPLHLI SSSDKPGLDL LKVEYIKADK NGPSFQTAFG KTEQTVKVAF
SSLNLLLQTQ ALVASINYLT TIIPSDDQSI SVAKEVQIST EKQQKNSTLP KAIVSSRDSD
IIDFRLFAKL NAFCVIVCNE KNNIAEIKIQ GLDSSLSLQS RKQSLFARLE NIIVTDVDPK
TVHKKAVSIM GNEVFRFNLD LYPDATEGDL YTDMSKVDGV LSLNVGCIQI VYLHKFLMSL
LNFLNNFQTA KESLSAATAQ AAERAATSVK DLAQRSFRVS INIDLKAPVI VIPQSSISTN
AVVVDLGLIR VHNQFSLVSD EDYLNPPVID RMDVQLTKLT LYRTVIQPGI YHPDIQLLHP
INLEFLVNRN LAASWYHKVP VVEIKGHLDS MNVSLNQEDL NLLFRILTEN LCEGTEDLDK
VKPRVQETGE IKEPLEISIS QDVHDSKNTL TTGVEEIRSV DIINMLLNFE IKEVVVTLMK
KSEKKGRPLH ELNVLQLGME AKVKTYDMTA KAYLKKISMQ CFDFTDSKGE PLHIINSSNV
TDEPLLKMLL TKADSDGPEF KTIHDSTKQR LKVSFASLDL VLHLEALLSF MDFLSSAAPF
SEPSSSEKES ELKPLVGESR SIAVKAVSSN ISQKDVFDLK ITAELNAFNV FVCDQKCNIA
DIKIHGMDAS ISVKPKQTDV FARLKDIIVM NVDLQSIHKK AVSILGDEVF RFQLTLYPDA
TEGEAYADMS KVDGKLSFKV GCIQIVYVHK FFMSLLNFLN NFQTAKEALS TATVQAAERA
ASSMKDLAQK SFRLLMDINL KAPVIIIPQS SVSPNAVIAD LGLIRVENKF SLVPMEHYSL
PPVIDKMNIE LTQLKLSRTI LQASLPQNDI EILKPVNMLL SIQRNLAAAW YVQIPGMEIK
GKLKPMQVAL SEDDLTVLMK ILLENLGEAS SQPSPTQSVQ ETVRVRKVDV SSVPDHLKEQ
EDWTDSKLSM NQIVSLQFDF HFESLSIILY NNDINQESGV AFHNDSFQLG ELRLHLMASS
GKMFKDGSMN VSVKLKTCTL DDLREGIERA TSRMIDRKND QDNNSSMIDI SYKQDKNGSQ
IDAVLDKLYV CASVEFLMTV ADFFIKAVPQ SPENVAKETQ ILPRQTATGK VKIEKDDSVR
PNMTLKAMIT DPEVVFVASL TKADAPALTA SFQCNLSLST SKLEQMMEAS VRDLKVLACP
FLREKRGKNI TTVLQPCSLF MEKCTWASGK QNINIMVKEF IIKISPIILN TVLTIMAALS
PKTKEDGSKD TSKEMENLWG IKSINDYNTW FLGVDTATEI TESFKGIEHS LIEENCGVVV
ESIQVTLECG LGHRTVPLLL AESKFSGNIK NWTSLMAAVA DVTLQVHYYN EIHAVWEPLI
ERVEGKRQWN LRLDVKKNPV QDKSLLPGDD FIPEPQMAIH ISSGNTMNIT ISKSCLNVFN
NLAKGFSEGT ASTFDYSLKD RAPFTVKNAV GVPIKVKPNC NLRVMGFPEK SDIFDVDAGQ
NLELEYASMV PSSQGNLSIL SRQESSFFTL TIVPHGYTEV ANIPVARPGR RLYNVRNPNA
SHSDSVLVQI DATEGNKVIT LRSPLQIKNH FSIAFIIYKF VKNVKLLERI GIARPEEEFH
VPLDSYRCQL FIQPAGILEH QYKESTTYIS WKEELHRSRE VRCMLQCPSV EVSFLPLIVN
TVALPDELSY ICTHGEDWDV AYIIHLYPSL TLRNLLPYSL RYLLEGTAET HELAEGSTAD
VLHSRISGEI MELVLVKYQG KNWNGHFRIR DTLPEFFPVC FSSDSTEVTT VDLSVHVRRI
GSRMVLSVFS PYWLINKTTR VLQYRSEDIH VKHPADFRDI ILFSFKKKNI FTKNKVQLKI
STSAWSSSFS LDTVGSYGCV KCPANNMEYL VGVSIKMSSF NLSRIVTLTP FCTIANKSSL
ELEVGEIASD GSMPTNKWNY IASSECLPFW PENLSGKLCV RVVGCEGSSK PFFYNRQDNG
TLLSLEDLNG GILVDVNTAE HSTVITFSDY HEGSAPALIM NHTPWDILTY KQSGSPEEMV
LLPRQARLFA WADPTGTRKL TWTYAANVGE HDLLKDGCGQ FPYDANIQIH WVSFLDGRQR
VLLFTDDVAL VSKALQAEEM EQADYEITLS LHSLGLSLVN NESKQEVSYI GITSSGVVWE
VKPKQKWKPF SQKQIILLEQ SYQKHQISRD HGWIKLDNNF EVNFDKDPME MRLPIRSPIK
RDFLSGIQIE FKQSSHQRSL RARLYWLQVD NQLPGAMFPV VFHPVAPPKS IALDSEPKPF
IDVSVITRFN EYSKVLQFKY FMVLIQEMAL KIDQGFLGAI IALFTPTTDP EAERRRTKLI
QQDIDALNAE LMETSMTDMS ILSFFEHFHI SPVKLHLSLS LGSGGEESDK EKQEMFAVHS
VNLLLKSIGA TLTDVDDLIF KLAYYEIRYQ FYKRDQLIWS VVRHYSEQFL KQMYVLVLGL
DVLGNPFGLI RGLSEGVEAL FYEPFQGAVQ GPEEFAEGLV IGVRSLFGHT VGGAAGVVSR
ITGSVGKGLA AITMDKEYQQ KRREELSRQP RDFGDSLARG GKGFLRGVVG GVTGIITKPV
EGAKKEGAAG FFKGIGKGLV GAVARPTGGI VDMASSTFQG IQRAAESTEE VSSLRPPRLI
HEDGIIRPYD RQESEGSDLL EQELEIQE*

speed

0.79 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99998668020424 (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)

chr15:62202482C>TN/A show variant in all transcripts IGV

HGNC symbol

VPS13C

Ensembl transcript ID

ENST00000261517

Genbank transcript ID

NM_020821

UniProt peptide

Q709C8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.8738G>A
cDNA.8812G>A
g.150191G>A

AA changes

S2913N Score: 46 explain score(s)

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

2913

frameshift

known variant

Reference ID: rs10851704

database	homozygous (T/T)	heterozygous	allele carriers
1000G	687	1212	1899
ExAC	18513	-4259	14254

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.255	0.934
	0.808	0.976
(flanking)	2.758	1

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	150182	wt: 0.9295 / mu: 0.9383 (marginal change - not scored)	wt: TTTTTAGTGCCTTCCATTTTGGCCAGAAAGTTTGTCAGGCA mu: TTTTTAGTGCCTTCCATTTTGGCCAGAAAATTTGTCAGGCA	tttg\|GCCA
Acc marginally increased	150186	wt: 0.4747 / mu: 0.4913 (marginal change - not scored)	wt: TAGTGCCTTCCATTTTGGCCAGAAAGTTTGTCAGGCAAACT mu: TAGTGCCTTCCATTTTGGCCAGAAAATTTGTCAGGCAAACT	gcca\|GAAA
Acc marginally increased	150181	wt: 0.9502 / mu: 0.9519 (marginal change - not scored)	wt: ATTTTTAGTGCCTTCCATTTTGGCCAGAAAGTTTGTCAGGC mu: ATTTTTAGTGCCTTCCATTTTGGCCAGAAAATTTGTCAGGC	tttt\|GGCC
Donor increased	150186	wt: 0.44 / mu: 0.98	wt: TGGCCAGAAAGTTTG mu: TGGCCAGAAAATTTG	GCCA\|gaaa
Donor increased	150194	wt: 0.84 / mu: 0.94	wt: AAGTTTGTCAGGCAA mu: AAATTTGTCAGGCAA	GTTT\|gtca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

2913

mutated

all conserved

2913

Ptroglodytes

all conserved

ENSPTRG00000007135

2914

Mmulatta

all conserved

ENSMMUG00000001362

2913

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000035284

2908

Ggallus

all conserved

ENSGALG00000003705

2910

Trubripes

all conserved

ENSTRUG00000003978

2891

Drerio

all identical

ENSDARG00000074465

2912

Dmelanogaster

not conserved

FBgn0033194

2501

Celegans

not conserved

T08G11.1

2398

RKL

Xtropicalis

all conserved

ENSXETG00000005221

2917

protein features

start (aa)	end (aa)	feature	details
3538	3538	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

11262 / 11262

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

3754 / 3754

position of stopcodon in wt / mu cDNA

11336 / 11336

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

75 / 75

chromosome

strand

-1

last intron/exon boundary

11235

theoretical NMD boundary in CDS

11110

length of CDS

11262

coding sequence (CDS) position

8738

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

8812

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

150191

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

62202482

original gDNA sequence snippet

CCTTCCATTTTGGCCAGAAAGTTTGTCAGGCAAACTTTGTG

altered gDNA sequence snippet

CCTTCCATTTTGGCCAGAAAATTTGTCAGGCAAACTTTGTG

original cDNA sequence snippet

CCTTCCATTTTGGCCAGAAAGTTTGTCAGGCAAACTTTGTG

altered cDNA sequence snippet

CCTTCCATTTTGGCCAGAAAATTTGTCAGGCAAACTTTGTG

wildtype AA sequence

mutated AA sequence

MVLESVVADL LNRFLGDYVE NLNKSQLKLG IWGGNVALDN LQIKENALSE LDVPFKVKAG
QIDKLTLKIP WKNLYGEAVV ATLEGLYLLV VPGASIKYDA VKEEKSLQDV KQKELSRIEE
ALQKAAEKGT HSGEFIYGLE NFVYKDIKPG RKRKKHKKHF KKPFKGLDRS KDKPKEAKKD
TFVEKLATQV IKNVQVKITD IHIKYEDDVT DPKRPLSFGV TLGELSLLTA NEHWTPCILN
EADKIIYKLI RLDSLSAYWN VNCSMSYQRS REQILDQLKN EILTSGNIPP NYQYIFQPIS
ASAKLYMNPY AESELKTPKL DCNIEIQNIA IELTKPQYLS MIDLLESVDY MVRNAPYRKY
KPYLPLHTNG RRWWKYAIDS VLEVHIRRYT QMWSWSNIKK HRQLLKSYKI AYKNKLTQSK
VSEEIQKEIQ DLEKTLDVFN IILARQQAQV EVIRSGQKLR KKSADTGEKR GGWFSGLWGK
KESKKKDEES LIPETIDDLM TPEEKDKLFT AIGYSESTHN LTLPKQYVAH IMTLKLVSTS
VTIRENKNIP EILKIQIIGL GTQVSQRPGA QALKVEAKLE HWYITGLRQQ DIVPSLVASI
GDTTSSLLKI KFETNPEDSP ADQTLIVQSQ PVEVIYDAKT VNAVVEFFQS NKGLDLEQIT
SATLMKLEEI KERTATGLTH IIETRKVLDL RINLKPSYLV VPQTGFHHEK SDLLILDFGT
FQLNSKDQGL QKTTNSSLEE IMDKAYDKFD VEIKNVQLLF ARAEETWKKC RFQHPSTMHI
LQPMDIHVEL AKAMVEKDIR MARFKVSGGL PLMHVRISDQ KMKDVLYLMN SIPLPQKSSA
QSPERQVSSI PIISGGTKGL LGTSLLLDTV ESESDDEYFD AEDGEPQTCK SMKGSELKKA
AEVPNEELIN LLLKFEIKEV ILEFTKQQKE EDTILVFNVT QLGTEATMRT FDLTVVSYLK
KISLDYHEIE GSKRKPLHLI SSSDKPGLDL LKVEYIKADK NGPSFQTAFG KTEQTVKVAF
SSLNLLLQTQ ALVASINYLT TIIPSDDQSI SVAKEVQIST EKQQKNSTLP KAIVSSRDSD
IIDFRLFAKL NAFCVIVCNE KNNIAEIKIQ GLDSSLSLQS RKQSLFARLE NIIVTDVDPK
TVHKKAVSIM GNEVFRFNLD LYPDATEGDL YTDMSKVDGV LSLNVGCIQI VYLHKFLMSL
LNFLNNFQTA KESLSAATAQ AAERAATSVK DLAQRSFRVS INIDLKAPVI VIPQSSISTN
AVVVDLGLIR VHNQFSLVSD EDYLNPPVID RMDVQLTKLT LYRTVIQPGI YHPDIQLLHP
INLEFLVNRN LAASWYHKVP VVEIKGHLDS MNVSLNQEDL NLLFRILTEN LCEGTEDLDK
VKPRVQETGE IKEPLEISIS QDVHDSKNTL TTGVEEIRSV DIINMLLNFE IKEVVVTLMK
KSEKKGRPLH ELNVLQLGME AKVKTYDMTA KAYLKKISMQ CFDFTDSKGE PLHIINSSNV
TDEPLLKMLL TKADSDGPEF KTIHDSTKQR LKVSFASLDL VLHLEALLSF MDFLSSAAPF
SEPSSSEKES ELKPLVGESR SIAVKAVSSN ISQKDVFDLK ITAELNAFNV FVCDQKCNIA
DIKIHGMDAS ISVKPKQTDV FARLKDIIVM NVDLQSIHKK AVSILGDEVF RFQLTLYPDA
TEGEAYADMS KVDGKLSFKV GCIQIVYVHK FFMSLLNFLN NFQTAKEALS TATVQAAERA
ASSMKDLAQK SFRLLMDINL KAPVIIIPQS SVSPNAVIAD LGLIRVENKF SLVPMEHYSL
PPVIDKMNIE LTQLKLSRTI LQASLPQNDI EILKPVNMLL SIQRNLAAAW YVQIPGMEIK
GKLKPMQVAL SEDDLTVLMK ILLENLGEAS SQPSPTQSVQ ETVRVRKVDV SSVPDHLKEQ
EDWTDSKLSM NQIVSLQFDF HFESLSIILY NNDINQESGV AFHNDSFQLG ELRLHLMASS
GKMFKDGSMN VSVKLKTCTL DDLREGIERA TSRMIDRKND QDNNSSMIDI SYKQDKNGSQ
IDAVLDKLYV CASVEFLMTV ADFFIKAVPQ SPENVAKETQ ILPRQTATGK VKIEKDDSVR
PNMTLKAMIT DPEVVFVASL TKADAPALTA SFQCNLSLST SKLEQMMEAS VRDLKVLACP
FLREKRGKNI TTVLQPCSLF MEKCTWASGK QNINIMVKEF IIKISPIILN TVLTIMAALS
PKTKEDGSKD TSKEMENLWG IKSINDYNTW FLGVDTATEI TESFKGIEHS LIEENCGVVV
ESIQVTLECG LGHRTVPLLL AESKFSGNIK NWTSLMAAVA DVTLQVHYYN EIHAVWEPLI
ERVEGKRQWN LRLDVKKNPV QDKSLLPGDD FIPEPQMAIH ISSGNTMNIT ISKSCLNVFN
NLAKGFSEGT ASTFDYSLKD RAPFTVKNAV GVPIKVKPNC NLRVMGFPEK SDIFDVDAGQ
NLELEYASMV PSSQGNLSIL SRQESSFFTL TIVPHGYTEV ANIPVARPGR RLYNVRNPNA
SHSDSVLVQI DATEGNKVIT LRSPLQIKNH FSIAFIIYKF VKNVKLLERI GIARPEEEFH
VPLDSYRCQL FIQPAGILEH QYKESTTYIS WKEELHRSRE VRCMLQCPSV EVSFLPLIVN
TVALPDELSY ICTHGEDWDV AYIIHLYPSL TLRNLLPYSL RYLLEGTAET HELAEGSTAD
VLHSRISGEI MELVLVKYQG KNWNGHFRIR DTLPEFFPVC FSSDSTEVTT VDLSVHVRRI
GSRMVLSVFS PYWLINKTTR VLQYRSEDIH VKHPADFRDI ILFSFKKKNI FTKNKVQLKI
STSAWSSSFS LDTVGSYGCV KCPANNMEYL VGVSIKMSSF NLSRIVTLTP FCTIANKSSL
ELEVGEIASD GSMPTNKWNY IASSECLPFW PENLSGKLCV RVVGCEGSSK PFFYNRQDNG
TLLSLEDLNG GILVDVNTAE HSTVITFSDY HEGSAPALIM NHTPWDILTY KQSGSPEEMV
LLPRQARLFA WADPTGTRKL TWTYAANVGE HDLLKDGCGQ FPYDANIQIH WVSFLDGRQR
VLLFTDDVAL VSKALQAEEM EQADYEITLS LHSLGLSLVN NESKQEVSYI GITSSGVVWE
VKPKQKWKPF SQKQIILLEQ SYQKHQISRD HGWIKLDNNF EVNFDKDPME MRLPIRSPIK
RDFLSGIQIE FKQSSHQRSL RARLYWLQVD NQLPGAMFPV VFHPVAPPKS IALDSEPKPF
IDVSVITRFN EYSKVLQFKY FMVLIQEMAL KIDQGFLGAI IALFTPTTDP EAERRRTKLI
QQDIDALNAE LMETSMTDMS ILSFFEHFHI SPVKLHLSLS LGSGGEESDK EKQEMFAVHS
VNLLLKSIGA TLTDVDDLIF KLAYYEIRYQ FYKRDQLIWS VVRHYSEQFL KQMYVLVLGL
DVLGNPFGLI RGLSEGVEAL FYEPFQGAVQ GPEEFAEGLV IGVRSLFGHT VGGAAGVVSR
ITGSVGKGLA AITMDKEYQQ KRREELSRQP RDFGDSLARG GKGFLRGVVG GVTGIITKPV
EGAKKEGAAG FFKGIGKGLV GAVARPTGGI VDMASSTFQG IQRAAESTEE VSSLRPPRLI
HEDGIIRPYD RQESEGSDLL ENHIKKLEGE TYRYHCAIPG SKKTILMVTN RRVLCIKEVE
ILGLMCVDWQ CPFEDFVFPP SVSENVLKIS VKEQGLFHKK DSANQGCVRK VYLKDTATAE
RACNAIEDAQ STRQQQKLMK QSSVRLLRPQ LPS*

speed

0.58 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99998668020424 (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)

chr15:62202482C>TN/A show variant in all transcripts IGV

HGNC symbol

VPS13C

Ensembl transcript ID

ENST00000395898

Genbank transcript ID

N/A

UniProt peptide

Q709C8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.8609G>A
cDNA.8683G>A
g.150191G>A

AA changes

S2870N Score: 46 explain score(s)

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

2870

frameshift

known variant

Reference ID: rs10851704

database	homozygous (T/T)	heterozygous	allele carriers
1000G	687	1212	1899
ExAC	18513	-4259	14254

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.255	0.934
	0.808	0.976
(flanking)	2.758	1

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	150182	wt: 0.9295 / mu: 0.9383 (marginal change - not scored)	wt: TTTTTAGTGCCTTCCATTTTGGCCAGAAAGTTTGTCAGGCA mu: TTTTTAGTGCCTTCCATTTTGGCCAGAAAATTTGTCAGGCA	tttg\|GCCA
Acc marginally increased	150186	wt: 0.4747 / mu: 0.4913 (marginal change - not scored)	wt: TAGTGCCTTCCATTTTGGCCAGAAAGTTTGTCAGGCAAACT mu: TAGTGCCTTCCATTTTGGCCAGAAAATTTGTCAGGCAAACT	gcca\|GAAA
Acc marginally increased	150181	wt: 0.9502 / mu: 0.9519 (marginal change - not scored)	wt: ATTTTTAGTGCCTTCCATTTTGGCCAGAAAGTTTGTCAGGC mu: ATTTTTAGTGCCTTCCATTTTGGCCAGAAAATTTGTCAGGC	tttt\|GGCC
Donor increased	150186	wt: 0.44 / mu: 0.98	wt: TGGCCAGAAAGTTTG mu: TGGCCAGAAAATTTG	GCCA\|gaaa
Donor increased	150194	wt: 0.84 / mu: 0.94	wt: AAGTTTGTCAGGCAA mu: AAATTTGTCAGGCAA	GTTT\|gtca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

2870

mutated

all conserved

2870

Ptroglodytes

all conserved

ENSPTRG00000007135

2914

Mmulatta

all conserved

ENSMMUG00000001362

2913

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000035284

2908

Ggallus

all conserved

ENSGALG00000003705

2910

Trubripes

all conserved

ENSTRUG00000003978

2891

Drerio

all identical

ENSDARG00000074465

2912

Dmelanogaster

not conserved

FBgn0033194

2501

Celegans

not conserved

T08G11.1

2398

RKL

Xtropicalis

all conserved

ENSXETG00000005221

2917

protein features

start (aa)	end (aa)	feature	details
3538	3538	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

10758 / 10758

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

3586 / 3586

position of stopcodon in wt / mu cDNA

10832 / 10832

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

75 / 75

chromosome

strand

-1

last intron/exon boundary

10809

theoretical NMD boundary in CDS

10684

length of CDS

10758

coding sequence (CDS) position

8609

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

8683

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

150191

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

62202482

original gDNA sequence snippet

CCTTCCATTTTGGCCAGAAAGTTTGTCAGGCAAACTTTGTG

altered gDNA sequence snippet

CCTTCCATTTTGGCCAGAAAATTTGTCAGGCAAACTTTGTG

original cDNA sequence snippet

CCTTCCATTTTGGCCAGAAAGTTTGTCAGGCAAACTTTGTG

altered cDNA sequence snippet

CCTTCCATTTTGGCCAGAAAATTTGTCAGGCAAACTTTGTG

wildtype AA sequence

mutated AA sequence

MVLESVVADL LNRFLGDYVE NLNKSQLKLG IWGGNVALDN LQIKENALSE LDVPFKVKAG
QIDKLTLKIP WKNLYGEAVV ATLEGLYLLV VPGASIKYDA VKEEKSLQDV KQKELSRIEE
ALQKAAEKDK PKEAKKDTFV EKLATQVIKN VQVKITDIHI KYEDDVTDPK RPLSFGVTLG
ELSLLTANEH WTPCILNEAD KIIYKLIRLD SLSAYWNVNC SMSYQRSREQ ILDQLKNEIL
TSGNIPPNYQ YIFQPISASA KLYMNPYAES ELKTPKLDCN IEIQNIAIEL TKPQYLSMID
LLESVDYMVR NAPYRKYKPY LPLHTNGRRW WKYAIDSVLE VHIRRYTQMW SWSNIKKHRQ
LLKSYKIAYK NKLTQSKVSE EIQKEIQDLE KTLDVFNIIL ARQQAQVEVI RSGQKLRKKS
ADTGEKRGGW FSGLWGKKES KKKDEESLIP ETIDDLMTPE EKDKLFTAIG YSESTHNLTL
PKQYVAHIMT LKLVSTSVTI RENKNIPEIL KIQIIGLGTQ VSQRPGAQAL KVEAKLEHWY
ITGLRQQDIV PSLVASIGDT TSSLLKIKFE TNPEDSPADQ TLIVQSQPVE VIYDAKTVNA
VVEFFQSNKG LDLEQITSAT LMKLEEIKER TATGLTHIIE TRKVLDLRIN LKPSYLVVPQ
TGFHHEKSDL LILDFGTFQL NSKDQGLQKT TNSSLEEIMD KAYDKFDVEI KNVQLLFARA
EETWKKCRFQ HPSTMHILQP MDIHVELAKA MVEKDIRMAR FKVSGGLPLM HVRISDQKMK
DVLYLMNSIP LPQKSSAQSP ERQVSSIPII SGGTKGLLGT SLLLDTVESE SDDEYFDAED
GEPQTCKSMK GSELKKAAEV PNEELINLLL KFEIKEVILE FTKQQKEEDT ILVFNVTQLG
TEATMRTFDL TVVSYLKKIS LDYHEIEGSK RKPLHLISSS DKPGLDLLKV EYIKADKNGP
SFQTAFGKTE QTVKVAFSSL NLLLQTQALV ASINYLTTII PSDDQSISVA KEVQISTEKQ
QKNSTLPKAI VSSRDSDIID FRLFAKLNAF CVIVCNEKNN IAEIKIQGLD SSLSLQSRKQ
SLFARLENII VTDVDPKTVH KKAVSIMGNE VFRFNLDLYP DATEGDLYTD MSKVDGVLSL
NVGCIQIVYL HKFLMSLLNF LNNFQTAKES LSAATAQAAE RAATSVKDLA QRSFRVSINI
DLKAPVIVIP QSSISTNAVV VDLGLIRVHN QFSLVSDEDY LNPPVIDRMD VQLTKLTLYR
TVIQPGIYHP DIQLLHPINL EFLVNRNLAA SWYHKVPVVE IKGHLDSMNV SLNQEDLNLL
FRILTENLCE GTEDLDKVKP RVQETGEIKE PLEISISQDV HDSKNTLTTG VEEIRSVDII
NMLLNFEIKE VVVTLMKKSE KKGRPLHELN VLQLGMEAKV KTYDMTAKAY LKKISMQCFD
FTDSKGEPLH IINSSNVTDE PLLKMLLTKA DSDGPEFKTI HDSTKQRLKV SFASLDLVLH
LEALLSFMDF LSSAAPFSEP SSSEKESELK PLVGESRSIA VKAVSSNISQ KDVFDLKITA
ELNAFNVFVC DQKCNIADIK IHGMDASISV KPKQTDVFAR LKDIIVMNVD LQSIHKKAVS
ILGDEVFRFQ LTLYPDATEG EAYADMSKVD GKLSFKVGCI QIVYVHKFFM SLLNFLNNFQ
TAKEALSTAT VQAAERAASS MKDLAQKSFR LLMDINLKAP VIIIPQSSVS PNAVIADLGL
IRVENKFSLV PMEHYSLPPV IDKMNIELTQ LKLSRTILQA SLPQNDIEIL KPVNMLLSIQ
RNLAAAWYVQ IPGMEIKGKL KPMQVALSED DLTVLMKILL ENLGEASSQP SPTQSVQETV
RVRKVDVSSV PDHLKEQEDW TDSKLSMNQI VSLQFDFHFE SLSIILYNND INQESGVAFH
NDSFQLGELR LHLMASSGKM FKDGSMNVSV KLKTCTLDDL REGIERATSR MIDRKNDQDN
NSSMIDISYK QDKNGSQIDA VLDKLYVCAS VEFLMTVADF FIKAVPQSPE NVAKETQILP
RQTATGKVKI EKDDSVRPNM TLKAMITDPE VVFVASLTKA DAPALTASFQ CNLSLSTSKL
EQMMEASVRD LKVLACPFLR EKRGKNITTV LQPCSLFMEK CTWASGKQNI NIMVKEFIIK
ISPIILNTVL TIMAALSPKT KEDGSKDTSK EMENLWGIKS INDYNTWFLG VDTATEITES
FKGIEHSLIE ENCGVVVESI QVTLECGLGH RTVPLLLAES KFSGNIKNWT SLMAAVADVT
LQVHYYNEIH AVWEPLIERV EGKRQWNLRL DVKKNPVQDK SLLPGDDFIP EPQMAIHISS
GNTMNITISK SCLNVFNNLA KGFSEGTAST FDYSLKDRAP FTVKNAVGVP IKVKPNCNLR
VMGFPEKSDI FDVDAGQNLE LEYASMVPSS QGNLSILSRQ ESSFFTLTIV PHGYTEVANI
PVARPGRRLY NVRNPNASHS DSVLVQIDAT EGNKVITLRS PLQIKNHFSI AFIIYKFVKN
VKLLERIGIA RPEEEFHVPL DSYRCQLFIQ PAGILEHQYK ESTTYISWKE ELHRSREVRC
MLQCPSVEVS FLPLIVNTVA LPDELSYICT HGEDWDVAYI IHLYPSLTLR NLLPYSLRYL
LEGTAETHEL AEGSTADVLH SRISGEIMEL VLVKYQGKNW NGHFRIRDTL PEFFPVCFSS
DSTEVTTVDL SVHVRRIGSR MVLSVFSPYW LINKTTRVLQ YRSEDIHVKH PADFRDIILF
SFKKKNIFTK NKVQLKISTS AWSSSFSLDT VGSYGCVKCP ANNMEYLVGV SIKMSSFNLS
RIVTLTPFCT IANKSSLELE VGEIASDGSM PTNKWNYIAS SECLPFWPEN LSGKLCVRVV
GCEGSSKPFF YNRQDNGTLL SLEDLNGGIL VDVNTAEHST VITFSDYHEG SAPALIMNHT
PWDILTYKQS GSPEEMVLLP RQARLFAWAD PTGTRKLTWT YAANVGEHDL LKDGCGQFPY
DANIQIHWVS FLDGRQRVLL FTDDVALVSK ALQAEEMEQA DYEITLSLHS LGLSLVNNES
KQEVSYIGIT SSGVVWEVKP KQKWKPFSQK QIILLEQSYQ KHQISRDHGW IKLDNNFEVN
FDKDPMEMRL PIRSPIKRDF LSGIQIEFKQ SSHQRSLRAR LYWLQVDNQL PGAMFPVVFH
PVAPPKSIAL DSEPKPFIDV SVITRFNEYS KVLQFKYFMV LIQEMALKID QGFLGAIIAL
FTPTTDPEAE RRRTKLIQQD IDALNAELME TSMTDMSILS FFEHFHISPV KLHLSLSLGS
GGEESDKEKQ EMFAVHSVNL LLKSIGATLT DVDDLIFKLA YYEIRYQFYK RDQLIWSVVR
HYSEQFLKQM YVLVLGLDVL GNPFGLIRGL SEGVEALFYE PFQGAVQGPE EFAEGLVIGV
RSLFGHTVGG AAGVVSRITG SVGKGLAAIT MDKEYQQKRR EELSRQPRDF GDSLARGGKG
FLRGVVGGVT GIITKPVEGA KKEGAAGFFK GIGKGLVGAV ARPTGGIVDM ASSTFQGIQR
AAESTEEVSS LRPPRLIHED GIIRPYDRQE SEGSDLLEQE LEIQE*

speed

1.13 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

Problems