mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999992 (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)

chr19:51170706A>GN/A show variant in all transcripts IGV

HGNC symbol

SHANK1

Ensembl transcript ID

ENST00000359082

Genbank transcript ID

N/A

UniProt peptide

Q9Y566

alteration type

single base exchange

alteration region

CDS

DNA changes

c.4484T>C
cDNA.4503T>C
g.52002T>C

AA changes

V1495A Score: 64 explain score(s)

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

1495

frameshift

known variant

Reference ID: rs3745521

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1381	833	2214
ExAC	7702	6102	13804

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.246	0
	0.082	0
(flanking)	-0.144	0

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	52002	wt: 0.2747 / mu: 0.2802 (marginal change - not scored)	wt: CTGCCAGCCCCGGGCCCCTGTGACGAGCGGAAGGGGTCCCC mu: CTGCCAGCCCCGGGCCCCTGCGACGAGCGGAAGGGGTCCCC	ctgt\|GACG
Donor increased	52007	wt: 0.72 / mu: 0.83	wt: TGACGAGCGGAAGGG mu: CGACGAGCGGAAGGG	ACGA\|gcgg
Donor marginally increased	52002	wt: 0.9240 / mu: 0.9771 (marginal change - not scored)	wt: CCCTGTGACGAGCGG mu: CCCTGCGACGAGCGG	CTGT\|gacg
Donor marginally increased	52000	wt: 0.9904 / mu: 0.9907 (marginal change - not scored)	wt: GCCCCTGTGACGAGC mu: GCCCCTGCGACGAGC	CCCT\|gtga

distance from splice site

1258

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1495

mutated

not conserved

1495

Ptroglodytes

no homologue

Mmulatta

not conserved

ENSMMUG00000009357

1493

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000038738

1510

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000006583

1419

Drerio

no homologue

Dmelanogaster

no alignment

FBgn0040752

n/a

Celegans

no alignment

C33B4.3

n/a

Xtropicalis

not conserved

ENSXETG00000000210

1355

protein features

start (aa)	end (aa)	feature	details
1709	1717	COMPBIAS	Poly-Gly.	might get lost (downstream of altered splice site)
1832	1832	CONFLICT	S -> C (in Ref. 1; AAD45121/AAF35887).	might get lost (downstream of altered splice site)
1844	1854	COMPBIAS	Poly-Pro.	might get lost (downstream of altered splice site)
1896	1902	COMPBIAS	Poly-Gly.	might get lost (downstream of altered splice site)
1970	1979	COMPBIAS	Poly-Ser.	might get lost (downstream of altered splice site)
2098	2161	DOMAIN	SAM.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

6459 / 6459

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

2153 / 2153

position of stopcodon in wt / mu cDNA

6478 / 6478

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

20 / 20

chromosome

strand

-1

last intron/exon boundary

5761

theoretical NMD boundary in CDS

5691

length of CDS

6459

coding sequence (CDS) position

4484

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

4503

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

52002

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

51170706

original gDNA sequence snippet

CTGCCAGCCCCGGGCCCCTGTGACGAGCGGAAGGGGTCCCC

altered gDNA sequence snippet

CTGCCAGCCCCGGGCCCCTGCGACGAGCGGAAGGGGTCCCC

original cDNA sequence snippet

CTGCCAGCCCCGGGCCCCTGTGACGAGCGGAAGGGGTCCCC

altered cDNA sequence snippet

CTGCCAGCCCCGGGCCCCTGCGACGAGCGGAAGGGGTCCCC

wildtype AA sequence

MTHSPATSED EERHSASECP EGGSESDSSP DGPGRGPRGT RGQGSGAPGS LASVRGLQGR
SMSVPDDAHF SMMVFRIGIP DLHQTKCLRF NPDATIWTAK QQVLCALSES LQDVLNYGLF
QPATSGRDAN FLEEERLLRE YPQSFEKGVP YLEFRYKTRV YKQTNLDEKQ LAKLHTKTGL
KKFLEYVQLG TSDKVARLLD KGLDPNYHDS DSGETPLTLA AQTEGSVEVI RTLCLGGAHI
DFRARDGMTA LHKAACARHC LALTALLDLG GSPNYKDRRG LTPLFHTAMV GGDPRCCELL
LFNRAQLGIA DENGWQEIHQ ACQRGHSQHL EHLLFYGAEP GAQNASGNTA LHICALYNKE
TCARILLYRG ADKDVKNNNG QTPFQVAVIA GNFELGELIR NHREQDVVPF QESPKYAARR
RGPPGTGLTV PPALLRANSD TSMALPDWMV FSAPGAASSG APGPTSGSQG QSQPSAPTTK
LSSGTLRSAS SPRGARARSP SRGRHPEDAK RQPRGRPSSS GTPREGPAGG TGGSGGPGGS
LGSRGRRRKL YSAVPGRSFM AVKSYQAQAE GEISLSKGEK IKVLSIGEGG FWEGQVKGRV
GWFPSDCLEE VANRSQESKQ ESRSDKAKRL FRHYTVGSYD SFDAPSDYII KEKTVLLQKK
DSEGFGFVLR GAKAQTPIEE FTPTPAFPAL QYLESVDEGG VAWRAGLRMG DFLIEVNGQN
VVKVGHRQVV NMIRQGGNTL MVKVVMVTRH PDMDEAVHKK APQQAKRLPP PTISLRSKSM
TSELEEMEYE QQPAPVPSME KKRTVYQMAL NKLDEILAAA QQTISASESP GPGGLASLGK
HRPKGFFATE SSFDPHHRAQ PSYERPSFLP PGPGLMLRQK SIGAAEDDRP YLAPPAMKFS
RSLSVPGSED IPPPPTTSPP EPPYSTPPVP SSSGRLTPSP RGGPFNPGSG GPLPASSPAS
FDGPSPPDTR VGSREKSLYH SGPLPPAHHH PPHHHHHHAP PPQPHHHHAH PPHPPEMETG
GSPDDPPPRL ALGPQPSLRG WRGGGPSPTP GAPSPSHHGS AGGGGGSSQG PALRYFQLPP
RAASAAMYVP ARSGRGRKGP LVKQTKVEGE PQKGGGLPPA PSPTSPASPQ PPPAVAAPSE
KNSIPIPTII IKAPSTSSSG RSSQGSSTEA EPPTQPEPTG GGGGGGSSPS PAPAMSPVPP
SPSPVPTPAS PSGPATLDFT SQFGAALVGA ARREGGWQNE ARRRSTLFLS TDAGDEDGGD
GGLGTGAAPG PRLRHSKSID EGMFSAEPYL RLESAGSGAG YGGYGAGSRA YGGGGGSSAF
TSFLPPRPLV HPLTGKALDP ASPLGLALAA RERALKESSE GGGAPQPPPR PPSPRYEAPP
PTPHHHSPHA HHEPVLRLWG ASPPDPARRE LGYRAGLGSQ EKSLPASPPA ARRSLLHRLP
PTAPGVGPLL LQLGTEPPAP HPGVSKPWRS AAPEEPERLP LHVRFLENCQ PRAPVTSGRG
PPSEDGPGVP PPSPRRSVPP SPTSPRASEE NGLPLLVLPP PAPSVDVEDG EFLFVEPLPP
PLEFSNSFEK PESPLTPGPP HPLPDTPAPA TPLPPVPPPA VAAAPPTLDS TASSLTSYDS
EVATLTQGAS AAPGDPHPPG PPAPAAPAPA APQPGPDPPP GTDSGIEEVD SRSSSDHPLE
TISSASTLSS LSAEGGGSAG GGGGAGAGVA SGPELLDTYV AYLDGQAFGG SSTPGPPYPP
QLMTPSKLRG RALGASGGLR PGPSGGLRDP VTPTSPTVSV TGAGTDGLLA LRACSGPPTA
GVAGGPVAVE PEVPPVPLPT ASSLPRKLLP WEEGPGPPPP PLPGPLAQPQ ASALATVKAS
IISELSSKLQ QFGGSSAAGG ALPWARGGSG GGGDSHHGGA SYVPERTSSL QRQRLSDDSQ
SSLLSKPVSS LFQNWPKPPL PPLPTGTGVS PTAAAAPGAT SPSASSSSTS TRHLQGVEFE
MRPPLLRRAP SPSLLPASEH KVSPAPRPSS LPILPSGPLY PGLFDIRGSP TGGAGGSADP
FAPVFVPPHP GISGGLGGAL SGASRSLSPT RLLSLPPDKP FGAKPLGFWT KFDVADWLEW
LGLAEHRAQF LDHEIDGSHL PALTKEDYVD LGVTRVGHRM NIDRALKFFL ER*

mutated AA sequence

MTHSPATSED EERHSASECP EGGSESDSSP DGPGRGPRGT RGQGSGAPGS LASVRGLQGR
SMSVPDDAHF SMMVFRIGIP DLHQTKCLRF NPDATIWTAK QQVLCALSES LQDVLNYGLF
QPATSGRDAN FLEEERLLRE YPQSFEKGVP YLEFRYKTRV YKQTNLDEKQ LAKLHTKTGL
KKFLEYVQLG TSDKVARLLD KGLDPNYHDS DSGETPLTLA AQTEGSVEVI RTLCLGGAHI
DFRARDGMTA LHKAACARHC LALTALLDLG GSPNYKDRRG LTPLFHTAMV GGDPRCCELL
LFNRAQLGIA DENGWQEIHQ ACQRGHSQHL EHLLFYGAEP GAQNASGNTA LHICALYNKE
TCARILLYRG ADKDVKNNNG QTPFQVAVIA GNFELGELIR NHREQDVVPF QESPKYAARR
RGPPGTGLTV PPALLRANSD TSMALPDWMV FSAPGAASSG APGPTSGSQG QSQPSAPTTK
LSSGTLRSAS SPRGARARSP SRGRHPEDAK RQPRGRPSSS GTPREGPAGG TGGSGGPGGS
LGSRGRRRKL YSAVPGRSFM AVKSYQAQAE GEISLSKGEK IKVLSIGEGG FWEGQVKGRV
GWFPSDCLEE VANRSQESKQ ESRSDKAKRL FRHYTVGSYD SFDAPSDYII KEKTVLLQKK
DSEGFGFVLR GAKAQTPIEE FTPTPAFPAL QYLESVDEGG VAWRAGLRMG DFLIEVNGQN
VVKVGHRQVV NMIRQGGNTL MVKVVMVTRH PDMDEAVHKK APQQAKRLPP PTISLRSKSM
TSELEEMEYE QQPAPVPSME KKRTVYQMAL NKLDEILAAA QQTISASESP GPGGLASLGK
HRPKGFFATE SSFDPHHRAQ PSYERPSFLP PGPGLMLRQK SIGAAEDDRP YLAPPAMKFS
RSLSVPGSED IPPPPTTSPP EPPYSTPPVP SSSGRLTPSP RGGPFNPGSG GPLPASSPAS
FDGPSPPDTR VGSREKSLYH SGPLPPAHHH PPHHHHHHAP PPQPHHHHAH PPHPPEMETG
GSPDDPPPRL ALGPQPSLRG WRGGGPSPTP GAPSPSHHGS AGGGGGSSQG PALRYFQLPP
RAASAAMYVP ARSGRGRKGP LVKQTKVEGE PQKGGGLPPA PSPTSPASPQ PPPAVAAPSE
KNSIPIPTII IKAPSTSSSG RSSQGSSTEA EPPTQPEPTG GGGGGGSSPS PAPAMSPVPP
SPSPVPTPAS PSGPATLDFT SQFGAALVGA ARREGGWQNE ARRRSTLFLS TDAGDEDGGD
GGLGTGAAPG PRLRHSKSID EGMFSAEPYL RLESAGSGAG YGGYGAGSRA YGGGGGSSAF
TSFLPPRPLV HPLTGKALDP ASPLGLALAA RERALKESSE GGGAPQPPPR PPSPRYEAPP
PTPHHHSPHA HHEPVLRLWG ASPPDPARRE LGYRAGLGSQ EKSLPASPPA ARRSLLHRLP
PTAPGVGPLL LQLGTEPPAP HPGVSKPWRS AAPEEPERLP LHVRFLENCQ PRAPATSGRG
PPSEDGPGVP PPSPRRSVPP SPTSPRASEE NGLPLLVLPP PAPSVDVEDG EFLFVEPLPP
PLEFSNSFEK PESPLTPGPP HPLPDTPAPA TPLPPVPPPA VAAAPPTLDS TASSLTSYDS
EVATLTQGAS AAPGDPHPPG PPAPAAPAPA APQPGPDPPP GTDSGIEEVD SRSSSDHPLE
TISSASTLSS LSAEGGGSAG GGGGAGAGVA SGPELLDTYV AYLDGQAFGG SSTPGPPYPP
QLMTPSKLRG RALGASGGLR PGPSGGLRDP VTPTSPTVSV TGAGTDGLLA LRACSGPPTA
GVAGGPVAVE PEVPPVPLPT ASSLPRKLLP WEEGPGPPPP PLPGPLAQPQ ASALATVKAS
IISELSSKLQ QFGGSSAAGG ALPWARGGSG GGGDSHHGGA SYVPERTSSL QRQRLSDDSQ
SSLLSKPVSS LFQNWPKPPL PPLPTGTGVS PTAAAAPGAT SPSASSSSTS TRHLQGVEFE
MRPPLLRRAP SPSLLPASEH KVSPAPRPSS LPILPSGPLY PGLFDIRGSP TGGAGGSADP
FAPVFVPPHP GISGGLGGAL SGASRSLSPT RLLSLPPDKP FGAKPLGFWT KFDVADWLEW
LGLAEHRAQF LDHEIDGSHL PALTKEDYVD LGVTRVGHRM NIDRALKFFL ER*

speed

1.01 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