mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 6.78175424591092e-19 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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)

chr19:3728609G>AN/A show variant in all transcripts IGV

HGNC symbol

TJP3

Ensembl transcript ID

ENST00000539908

Genbank transcript ID

N/A

UniProt peptide

O95049

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.67G>A
g.20503G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs2067019

database	homozygous (A/A)	heterozygous	allele carriers
1000G	242	956	1198
ExAC	3941	20713	24654

regulatory features

Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Max, Transcription Factor, Max TF binding
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.827	0.995
	2.017	0.992
(flanking)	-0.117	0.909

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

splice site change before start ATG (at aa -17) | splice site change before start ATG (at aa -16) |

effect	gDNA position	score	detection sequence	exon-intron border
Acc increased	20506	wt: 0.52 / mu: 0.59	wt: CCTCTCTCAGGACCCCCGCCGGGGCTTTGGCATTGCGATCT mu: CCTCTCTCAGGACCCCCACCGGGGCTTTGGCATTGCGATCT	gccg\|GGGC
Acc marginally decreased	20495	wt: 0.9733 / mu: 0.9640 (marginal change - not scored)	wt: CTTCCCCTCATCCTCTCTCAGGACCCCCGCCGGGGCTTTGG mu: CTTCCCCTCATCCTCTCTCAGGACCCCCACCGGGGCTTTGG	tcag\|GACC
Donor gained	20503	0.31	mu: CCCCCACCGGGGCTT	CCCA\|ccgg

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
11	93	DOMAIN	PDZ 1.	might get lost (downstream of altered splice site)
19	19	CONFLICT	R -> H (in Ref. 3; AAI08907).	might get lost (downstream of altered splice site)
112	112	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
159	159	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
164	164	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
169	169	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
195	272	DOMAIN	PDZ 2.	might get lost (downstream of altered splice site)
203	203	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
394	460	DOMAIN	PDZ 3.	might get lost (downstream of altered splice site)
489	563	DOMAIN	SH3.	might get lost (downstream of altered splice site)
492	496	STRAND		might get lost (downstream of altered splice site)
504	507	STRAND		might get lost (downstream of altered splice site)
515	520	STRAND		might get lost (downstream of altered splice site)
536	541	STRAND		might get lost (downstream of altered splice site)
547	553	STRAND		might get lost (downstream of altered splice site)
556	569	HELIX		might get lost (downstream of altered splice site)
579	579	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
594	775	DOMAIN	Guanylate kinase-like.	might get lost (downstream of altered splice site)
605	605	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
610	616	HELIX		might get lost (downstream of altered splice site)
620	628	STRAND		might get lost (downstream of altered splice site)
635	639	STRAND		might get lost (downstream of altered splice site)
642	652	HELIX		might get lost (downstream of altered splice site)
654	656	TURN		might get lost (downstream of altered splice site)
657	659	STRAND		might get lost (downstream of altered splice site)
675	683	HELIX		might get lost (downstream of altered splice site)
687	690	STRAND		might get lost (downstream of altered splice site)
694	702	HELIX		might get lost (downstream of altered splice site)
708	715	STRAND		might get lost (downstream of altered splice site)
717	727	HELIX		might get lost (downstream of altered splice site)
735	749	HELIX		might get lost (downstream of altered splice site)
750	752	HELIX		might get lost (downstream of altered splice site)
754	759	STRAND		might get lost (downstream of altered splice site)
761	763	STRAND		might get lost (downstream of altered splice site)
765	777	HELIX		might get lost (downstream of altered splice site)
780	785	STRAND		might get lost (downstream of altered splice site)
919	919	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
920	920	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

120 / 120

chromosome

strand

last intron/exon boundary

2669

theoretical NMD boundary in CDS

2499

length of CDS

2652

coding sequence (CDS) position

N/A

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

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

20503

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

3728609

original gDNA sequence snippet

CATCCTCTCTCAGGACCCCCGCCGGGGCTTTGGCATTGCGA

altered gDNA sequence snippet

CATCCTCTCTCAGGACCCCCACCGGGGCTTTGGCATTGCGA

original cDNA sequence snippet

GCCTCCTAGACAGGACCCCCGCCGGGGCTTTGGCATTGCGA

altered cDNA sequence snippet

GCCTCCTAGACAGGACCCCCACCGGGGCTTTGGCATTGCGA

wildtype AA sequence

MVVSDVVPGG PAEGRLQTGD HIVMVNGVSM ENATSAFAIQ ILKTCTKMAN ITVKRPRRIH
LPATKASPSS PGRQDSDEDD GPQRVEEVDQ GRGYDGDSSS GSGRSWDERS RRPRPGRRGR
AGSHGRRSPG GGSEANGLAL VSGFKRLPRQ DVQMKPVKSV LVKRRDSEEF GVKLGSQIFI
KHITDSGLAA RHRGLQEGDL ILQINGVSSQ NLSLNDTRRL IEKSEGKLSL LVLRDRGQFL
VNIPPAVSDS DSSPLEDISD LASELSQAPP SHIPPPPRHA QRSPEASQTD SPVESPRLRR
ESSVDSRTIS EPDEQRSELP RESSYDIYRV PSSQSMEDRG YSPDTRVVRF LKGKSIGLRL
AGGNDVGIFV SGVQAGSPAD GQGIQEGDQI LQVNDVPFQN LTREEAVQFL LGLPPGEEME
LVTQRKQDIF WKMVQSRVGD SFYIRTHFEL EPSPPSGLGF TRGDVFHVLD TLHPGPGQSH
ARGGHWLAVR MGRDLREQER GIIPNQSRAE QLASLEAAQR AVGVGPGSSA GSNARAEFWR
LRGLRRGAKK TTQRSREDLS ALTRQGRYPP YERVVLREAS FKRPVVILGP VADIAMQKLT
AEMPDQFEIA ETVSRTDSPS KIIKLDTVRV IAEKDKHALL DVTPSAIERL NYVQYYPIVV
FFIPESRPAL KALRQWLAPA SRRSTRRLYA QAQKLRKHSS HLFTATIPLN GTSDTWYQEL
KAIIREQQTR PIWTAEDQLD GSLEDNLDLP HHGLADSSAD LSCDSRVNSD YETDGEGGAY
TDGEGYTDGE GGPYTDVDDE PPAPALARSS EPVQADESQS PRDRGRISAH QGAQVDSRHP
QGQWRQDSMR TYEREALKKK FMRVHDAESS DEDGYDWGPA TDL*

mutated AA sequence

N/A

speed

0.72 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