mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999992777 (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)

chr15:56152729T>CN/A show variant in all transcripts IGV

HGNC symbol

NEDD4

Ensembl transcript ID

ENST00000338963

Genbank transcript ID

NM_198400

UniProt peptide

P46934

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1877A>G
cDNA.2177A>G
g.133216A>G

AA changes

N626S Score: 46 explain score(s)

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

626

frameshift

known variant

Reference ID: rs2303579

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1147	1085	2232
ExAC	-	-	-

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.403	0.199
	-1.37	0.012
(flanking)	0.245	0.03

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
Donor increased	133215	wt: 0.58 / mu: 0.99	wt: ATAGCAACCAGGCCT mu: ATAGCAGCCAGGCCT	AGCA\|acca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

626

mutated

all conserved

626

Ptroglodytes

all conserved

ENSPTRG00000007102

626

Mmulatta

all conserved

ENSMMUG00000008112

626

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000032216

337

Ggallus

all identical

ENSGALG00000004347

280

Trubripes

all conserved

ENSTRUG00000017899

275

HSP

Drerio

all conserved

ENSDARG00000039778

281

Dmelanogaster

all conserved

FBgn0259174

335

Celegans

no alignment

Y92H12A.2

n/a

Xtropicalis

all identical

ENSXETG00000016554

279

protein features

start (aa)	end (aa)	feature	details
578	981	REGION	Mediates interaction with TNIK (By similarity).	lost
610	643	DOMAIN	WW 1.	lost
648	648	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
670	670	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
747	747	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
767	800	DOMAIN	WW 2.	might get lost (downstream of altered splice site)
840	873	DOMAIN	WW 3.	might get lost (downstream of altered splice site)
846	850	STRAND		might get lost (downstream of altered splice site)
852	854	TURN		might get lost (downstream of altered splice site)
856	860	STRAND		might get lost (downstream of altered splice site)
861	864	TURN		might get lost (downstream of altered splice site)
863	863	CONFLICT	T -> I (in Ref. 8; AAI36606/AAI44285).	might get lost (downstream of altered splice site)
865	869	STRAND		might get lost (downstream of altered splice site)
871	873	TURN		might get lost (downstream of altered splice site)
892	925	DOMAIN	WW 4.	might get lost (downstream of altered splice site)
941	951	HELIX		might get lost (downstream of altered splice site)
956	958	STRAND		might get lost (downstream of altered splice site)
960	966	STRAND		might get lost (downstream of altered splice site)
968	970	HELIX		might get lost (downstream of altered splice site)
971	979	HELIX		might get lost (downstream of altered splice site)
984	1318	DOMAIN	HECT.	might get lost (downstream of altered splice site)
985	989	HELIX		might get lost (downstream of altered splice site)
990	996	STRAND		might get lost (downstream of altered splice site)
1004	1019	HELIX		might get lost (downstream of altered splice site)
1022	1024	HELIX		might get lost (downstream of altered splice site)
1025	1031	STRAND		might get lost (downstream of altered splice site)
1037	1039	STRAND		might get lost (downstream of altered splice site)
1043	1046	HELIX		might get lost (downstream of altered splice site)
1050	1066	HELIX		might get lost (downstream of altered splice site)
1071	1073	STRAND		might get lost (downstream of altered splice site)
1077	1083	HELIX		might get lost (downstream of altered splice site)
1090	1094	HELIX		might get lost (downstream of altered splice site)
1098	1109	HELIX		might get lost (downstream of altered splice site)
1113	1115	HELIX		might get lost (downstream of altered splice site)
1118	1125	STRAND		might get lost (downstream of altered splice site)
1128	1135	STRAND		might get lost (downstream of altered splice site)
1138	1140	HELIX		might get lost (downstream of altered splice site)
1145	1147	TURN		might get lost (downstream of altered splice site)
1148	1160	HELIX		might get lost (downstream of altered splice site)
1162	1164	HELIX		might get lost (downstream of altered splice site)
1165	1175	HELIX		might get lost (downstream of altered splice site)
1176	1178	TURN		might get lost (downstream of altered splice site)
1181	1184	HELIX		might get lost (downstream of altered splice site)
1189	1197	HELIX		might get lost (downstream of altered splice site)
1199	1199	CONFLICT	L -> P (in Ref. 3; BAG65229).	might get lost (downstream of altered splice site)
1204	1209	HELIX		might get lost (downstream of altered splice site)
1211	1214	STRAND		might get lost (downstream of altered splice site)
1219	1221	STRAND		might get lost (downstream of altered splice site)
1222	1233	HELIX		might get lost (downstream of altered splice site)
1236	1247	HELIX		might get lost (downstream of altered splice site)
1248	1250	STRAND		might get lost (downstream of altered splice site)
1257	1259	HELIX		might get lost (downstream of altered splice site)
1263	1266	STRAND		might get lost (downstream of altered splice site)
1268	1268	CONFLICT	S -> L (in Ref. 5; AL832063).	might get lost (downstream of altered splice site)
1269	1273	STRAND		might get lost (downstream of altered splice site)
1282	1284	STRAND		might get lost (downstream of altered splice site)
1285	1287	HELIX		might get lost (downstream of altered splice site)
1286	1286	ACT_SITE	Glycyl thioester intermediate (By similarity).	might get lost (downstream of altered splice site)
1289	1292	STRAND		might get lost (downstream of altered splice site)
1298	1310	HELIX		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3744 / 3744

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

1248 / 1248

position of stopcodon in wt / mu cDNA

4044 / 4044

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

301 / 301

chromosome

strand

-1

last intron/exon boundary

3942

theoretical NMD boundary in CDS

3591

length of CDS

3744

coding sequence (CDS) position

1877

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

2177

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

133216

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

56152729

original gDNA sequence snippet

TGAAGCCACCATGTATAGCAACCAGGCCTTCCCATCACCTC

altered gDNA sequence snippet

TGAAGCCACCATGTATAGCAGCCAGGCCTTCCCATCACCTC

original cDNA sequence snippet

TGAAGCCACCATGTATAGCAACCAGGCCTTCCCATCACCTC

altered cDNA sequence snippet

TGAAGCCACCATGTATAGCAGCCAGGCCTTCCCATCACCTC

wildtype AA sequence

MAQSLRLHFA ARRSNTYPLS ETSGDDLDSH VHMCFKRPTR ISTSNVVQMK LTPRQTALAP
LIKENVQSQE RSSVPSSENV NKKSSCLQIS LQPTRYSGYL QSSNVLADSD DASFTCILKD
GIYSSAVVDN ELNAVNDGHL VSSPAICSGS LSNFSTSDNG SYSSNGSDFG SCASITSGGS
YTNSVISDSS SYTFPPSDDT FLGGNLPSDS TSNRSVPNRN TTPCEIFSRS TSTDPFVQDD
LEHGLEIMKL PVSRNTKIPL KRYSSLVIFP RSPSTTRPTS PTSLCTLLSK GSYQTSHQFI
ISPSEIAHNE DGTSAKGFLS TAVNGLRLSK TICTPGEVRD IRPLHRKGSL QKKIVLSNNT
PRQTVCEKSS EGYSCVSVHF TQRKAATLDC ETTNGDCKPE MSEIKLNSDS EYIKLMHRTS
ACLPSSQNVD CQININGELE RPHSQMNKNH GILRRSISLG GAYPNISCLS SLKHNCSKGG
PSQLLIKFAS GNEGKVDNLS RDSNRDCTNE LSNSCKPGWV VLDQPDAACH LQQQQEPSPL
PPGWEERQDI LGRTYYVNHE SRRTQWKRPT PQDNLTDAEN GNIQLQAQRA FTTRRQISEE
TESVDNRESS ENWEIIREDE ATMYSNQAFP SPPPSSNLDV PTHLAEELNA RLTIFGNSAV
SQPASSSNHS SRRGSLQAYT FEEQPTLPVL LPTSSGLPPG WEEKQDERGR SYYVDHNSRT
TTWTKPTVQA TVETSQLTSS QSSAGPQSQA STSDSGQQVT QPSEIEQGFL PKGWEVRHAP
NGRPFFIDHN TKTTTWEDPR LKIPAHLRGK TSLDTSNDLG PLPPGWEERT HTDGRIFYIN
HNIKRTQWED PRLENVAITG PAVPYSRDYK RKYEFFRRKL KKQNDIPNKF EMKLRRATVL
EDSYRRIMGV KRADFLKARL WIEFDGEKGL DYGGVAREWF FLISKEMFNP YYGLFEYSAT
DNYTLQINPN SGLCNEDHLS YFKFIGRVAG MAVYHGKLLD GFFIRPFYKM MLHKPITLHD
MESVDSEYYN SLRWILENDP TELDLRFIID EELFGQTHQH ELKNGGSEIV VTNKNKKEYI
YLVIQWRFVN RIQKQMAAFK EGFFELIPQD LIKIFDENEL ELLMCGLGDV DVNDWREHTK
YKNGYSANHQ VIQWFWKAVL MMDSEKRIRL LQFVTGTSRV PMNGFAELYG SNGPQSFTVE
QWGTPEKLPR AHTCFNRLDL PPYESFEELW DKLQMAIENT QGFDGVD*

mutated AA sequence

MAQSLRLHFA ARRSNTYPLS ETSGDDLDSH VHMCFKRPTR ISTSNVVQMK LTPRQTALAP
LIKENVQSQE RSSVPSSENV NKKSSCLQIS LQPTRYSGYL QSSNVLADSD DASFTCILKD
GIYSSAVVDN ELNAVNDGHL VSSPAICSGS LSNFSTSDNG SYSSNGSDFG SCASITSGGS
YTNSVISDSS SYTFPPSDDT FLGGNLPSDS TSNRSVPNRN TTPCEIFSRS TSTDPFVQDD
LEHGLEIMKL PVSRNTKIPL KRYSSLVIFP RSPSTTRPTS PTSLCTLLSK GSYQTSHQFI
ISPSEIAHNE DGTSAKGFLS TAVNGLRLSK TICTPGEVRD IRPLHRKGSL QKKIVLSNNT
PRQTVCEKSS EGYSCVSVHF TQRKAATLDC ETTNGDCKPE MSEIKLNSDS EYIKLMHRTS
ACLPSSQNVD CQININGELE RPHSQMNKNH GILRRSISLG GAYPNISCLS SLKHNCSKGG
PSQLLIKFAS GNEGKVDNLS RDSNRDCTNE LSNSCKPGWV VLDQPDAACH LQQQQEPSPL
PPGWEERQDI LGRTYYVNHE SRRTQWKRPT PQDNLTDAEN GNIQLQAQRA FTTRRQISEE
TESVDNRESS ENWEIIREDE ATMYSSQAFP SPPPSSNLDV PTHLAEELNA RLTIFGNSAV
SQPASSSNHS SRRGSLQAYT FEEQPTLPVL LPTSSGLPPG WEEKQDERGR SYYVDHNSRT
TTWTKPTVQA TVETSQLTSS QSSAGPQSQA STSDSGQQVT QPSEIEQGFL PKGWEVRHAP
NGRPFFIDHN TKTTTWEDPR LKIPAHLRGK TSLDTSNDLG PLPPGWEERT HTDGRIFYIN
HNIKRTQWED PRLENVAITG PAVPYSRDYK RKYEFFRRKL KKQNDIPNKF EMKLRRATVL
EDSYRRIMGV KRADFLKARL WIEFDGEKGL DYGGVAREWF FLISKEMFNP YYGLFEYSAT
DNYTLQINPN SGLCNEDHLS YFKFIGRVAG MAVYHGKLLD GFFIRPFYKM MLHKPITLHD
MESVDSEYYN SLRWILENDP TELDLRFIID EELFGQTHQH ELKNGGSEIV VTNKNKKEYI
YLVIQWRFVN RIQKQMAAFK EGFFELIPQD LIKIFDENEL ELLMCGLGDV DVNDWREHTK
YKNGYSANHQ VIQWFWKAVL MMDSEKRIRL LQFVTGTSRV PMNGFAELYG SNGPQSFTVE
QWGTPEKLPR AHTCFNRLDL PPYESFEELW DKLQMAIENT QGFDGVD*

speed

1.08 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