mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 7.27879177863274e-12 (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)

chr10:124189197A>GN/A show variant in all transcripts IGV

HGNC symbol

PLEKHA1

Ensembl transcript ID

ENST00000368989

Genbank transcript ID

N/A

UniProt peptide

Q9HB21

alteration type

single base exchange

alteration region

CDS

DNA changes

c.999A>G
cDNA.1139A>G
g.55025A>G

AA changes

no AA changes

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

N/A

frameshift

known variant

Reference ID: rs1045216

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1423	894	2317
ExAC	28316	-23865	4451

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.003	0.953
	0.689	0.974
(flanking)	3.117	0.996

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 increased	55017	wt: 0.22 / mu: 0.41	wt: ACACGCTTTCCGTCCTACCAACGCAGCCACCGCCACCTCAC mu: ACACGCTTTCCGTCCTACCAACGCAGCCGCCGCCACCTCAC	ccaa\|CGCA
Acc marginally increased	55016	wt: 0.8713 / mu: 0.8969 (marginal change - not scored)	wt: AACACGCTTTCCGTCCTACCAACGCAGCCACCGCCACCTCA mu: AACACGCTTTCCGTCCTACCAACGCAGCCGCCGCCACCTCA	acca\|ACGC
Donor marginally increased	55016	wt: 0.2899 / mu: 0.3017 (marginal change - not scored)	wt: CTACCAACGCAGCCA mu: CTACCAACGCAGCCG	ACCA\|acgc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
332	332	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
362	362	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

position of stopcodon in wt / mu CDS

1152 / 1152

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

384 / 384

position of stopcodon in wt / mu cDNA

1292 / 1292

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

141 / 141

chromosome

strand

last intron/exon boundary

1082

theoretical NMD boundary in CDS

891

length of CDS

1152

coding sequence (CDS) position

999

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

1139

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

55025

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

124189197

original gDNA sequence snippet

TCCGTCCTACCAACGCAGCCACCGCCACCTCACATTCCACA

altered gDNA sequence snippet

TCCGTCCTACCAACGCAGCCGCCGCCACCTCACATTCCACA

original cDNA sequence snippet

TCCGTCCTACCAACGCAGCCACCGCCACCTCACATTCCACA

altered cDNA sequence snippet

TCCGTCCTACCAACGCAGCCGCCGCCACCTCACATTCCACA

wildtype AA sequence

MPYVDRQNRI CGFLDIEENE NSGKFLRRYF ILDTREDSFV WYMDNPQNLP SGSSRVGAIK
LTYISKVSDA TKLRPKAEFC FVMNAGMRKY FLQANDQQDL VEWVNVLNKA IKITVPKQSD
SQPNSDNLSR HGECGKKQVS YRTDIVGGVP IITPTQKEEV NECGESIDRN NLKRSQSHLP
YFTPKPPQDS AVIKAGYCVK QGAVMKNWKR RYFQLDENTI GYFKSELEKE PLRVIPLKEV
HKVQECKQSD IMMRDNLFEI VTTSRTFYVQ ADSPEEMHSW IKAVSGAIVA QRGPGRSASS
MRQARRLSNP CIQRSIPPVL QNPNTLSVLP TQPPPPHIPQ PLAATLWSQP LPWRSEDFTS
LLPRSSQGTS RSRLSLQENQ LPK*

mutated AA sequence

speed

0.23 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