mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999994872631366 (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)

chr15:62259637C>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.2792G>A
cDNA.2891G>A
g.93036G>A

AA changes

R931K Score: 26 explain score(s)

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

931

frameshift

known variant

Reference ID: rs3784634

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1481	821	2302
ExAC	24644	-16521	8123

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.136	0.875
	0.657	0.904
(flanking)	4.095	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	93027	wt: 0.6161 / mu: 0.6487 (marginal change - not scored)	wt: TTCCTTTTTCTTTAATCTAGGATCCAAAAGGAAGCCCCTTC mu: TTCCTTTTTCTTTAATCTAGGATCCAAAAAGAAGCCCCTTC	tagg\|ATCC
Donor marginally increased	93034	wt: 0.9949 / mu: 0.9951 (marginal change - not scored)	wt: TCCAAAAGGAAGCCC mu: TCCAAAAAGAAGCCC	CAAA\|agga
Donor marginally increased	93033	wt: 0.2068 / mu: 0.2307 (marginal change - not scored)	wt: ATCCAAAAGGAAGCC mu: ATCCAAAAAGAAGCC	CCAA\|aagg
Donor gained	93036	0.77	mu: CAAAAAGAAGCCCCT	AAAA\|gaag
Donor gained	93031	0.89	mu: GGATCCAAAAAGAAG	ATCC\|aaaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

931

mutated

all conserved

931

Ptroglodytes

all conserved

ENSPTRG00000007135

974

Mmulatta

all conserved

ENSMMUG00000001362

974

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000035284

973

Ggallus

all conserved

ENSGALG00000003705

977

Trubripes

not conserved

ENSTRUG00000003978

962

Drerio

not conserved

ENSDARG00000074465

982

Dmelanogaster

not conserved

FBgn0033194

965

Celegans

all identical

T08G11.1

908

SLD

Xtropicalis

not conserved

ENSXETG00000005221

982

protein features

start (aa)	end (aa)	feature	details
1437	1437	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
1442	1442	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1979	1979	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
2357	2357	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin).	might get lost (downstream of altered splice site)
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

2792

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

2891

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

93036

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

62259637

original gDNA sequence snippet

CTTTAATCTAGGATCCAAAAGGAAGCCCCTTCACTTGATTA

altered gDNA sequence snippet

CTTTAATCTAGGATCCAAAAAGAAGCCCCTTCACTTGATTA

original cDNA sequence snippet

TGAAATTGAAGGATCCAAAAGGAAGCCCCTTCACTTGATTA

altered cDNA sequence snippet

TGAAATTGAAGGATCCAAAAAGAAGCCCCTTCACTTGATTA

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 KKPLHLISSS 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 *

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