mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 0.999999644039842 (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)

chr1:39340282C>TN/A show variant in all transcripts IGV

HGNC symbol

GJA9

Ensembl transcript ID

ENST00000454994

Genbank transcript ID

N/A

UniProt peptide

P57773

alteration type

single base exchange

alteration region

intron

DNA changes

g.7008G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs880303

database	homozygous (T/T)	heterozygous	allele carriers
1000G	286	985	1271
ExAC	10030	12707	22737

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.151	0.003
	-0.321	0
(flanking)	-1.982	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	7009	wt: 0.2914 / mu: 0.3037 (marginal change - not scored)	wt: TGTTTGTCCTCCAAATCACGTAGTGTCCCTAACGAACAATC mu: TGTTTGTCCTCCAAATCACATAGTGTCCCTAACGAACAATC	acgt\|AGTG
Acc increased	7005	wt: 0.22 / mu: 0.31	wt: ATCCTGTTTGTCCTCCAAATCACGTAGTGTCCCTAACGAAC mu: ATCCTGTTTGTCCTCCAAATCACATAGTGTCCCTAACGAAC	aatc\|ACGT
Donor marginally increased	7005	wt: 0.6876 / mu: 0.7541 (marginal change - not scored)	wt: CAAATCACGTAGTGT mu: CAAATCACATAGTGT	AATC\|acgt

distance from splice site

168

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
231	515	TOPO_DOM	Cytoplasmic (Potential).	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

278 / 278

chromosome

strand

-1

last intron/exon boundary

2166

theoretical NMD boundary in CDS

1838

length of CDS

1545

coding sequence (CDS) position

N/A

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

N/A

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

7008

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

39340282

original gDNA sequence snippet

CTGTTTGTCCTCCAAATCACGTAGTGTCCCTAACGAACAAT

altered gDNA sequence snippet

CTGTTTGTCCTCCAAATCACATAGTGTCCCTAACGAACAAT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MGDWNLLGDT LEEVHIHSTM IGKIWLTILF IFRMLVLGVA AEDVWNDEQS GFICNTEQPG
CRNVCYDQAF PISLIRYWVL QVIFVSSPSL VYMGHALYRL RVLEEERQRM KAQLRVELEE
VEFEMPRDRR RLEQELCQLE KRKLNKAPLR GTLLCTYVIH IFTRSVVEVG FMIGQYLLYG
FHLEPLFKCH GHPCPNIIDC FVSRPTEKTI FLLFMQSIAT ISLFLNILEI FHLGFKKIKR
GLWGKYKLKK EHNEFHANKA KQNVAKYQST SANSLKRLPS APDYNLLVEK QTHTAVYPSL
NSSSVFQPNP DNHSVNDEKC ILDEQETVLS NEISTLSTSC SHFQHISSNN NKDTHKIFGK
ELNGNQLMEK RETEGKDSKR NYYSRGHRSI PGVAIDGENN MRQSPQTVFS LPANCDWKPR
WLRATWGSST EHENRGSPPK VPGSKATASS LLLILQRPTS SQPRLKETPK IKAEAKIYDS
KHPPRLLQST VSTFSGREPR SPAPMGHHSF RGPR*

mutated AA sequence

N/A

speed

0.78 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