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

ENST00000395896

Genbank transcript ID

NM_001018088

UniProt peptide

Q709C8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2921G>A
cDNA.2995G>A
g.93036G>A

AA changes

R974K Score: 26 explain score(s)

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

974

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

974

mutated

all conserved

974

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

905

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

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

2921

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

2995

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
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 GSKKKPLHLI 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*

speed

1.03 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