mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999925039994761 (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)

chr22:50878196G>AN/A show variant in all transcripts IGV

HGNC symbol

PPP6R2

Ensembl transcript ID

ENST00000395741

Genbank transcript ID

NM_001242899

UniProt peptide

O75170

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2117G>A
cDNA.2492G>A
g.96464G>A

AA changes

R706K Score: 26 explain score(s)

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

706

frameshift

known variant

Reference ID: rs13057311

database	homozygous (A/A)	heterozygous	allele carriers
1000G	111	748	859
ExAC	3657	21546	25203

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.162	0.009
	0.555	0.326
(flanking)	0.829	0.666

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	96459	wt: 0.54 / mu: 0.96	wt: GGAGTGGTGAGGGAC mu: GGAGTGGTGAAGGAC	AGTG\|gtga
Donor marginally increased	96456	wt: 0.8364 / mu: 0.9181 (marginal change - not scored)	wt: CCAGGAGTGGTGAGG mu: CCAGGAGTGGTGAAG	AGGA\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

706

mutated

all conserved

706

Ptroglodytes

all identical

ENSPTRG00000014540

642

Mmulatta

all identical

ENSMMUG00000009075

728

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000036561

707

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000006924

723

Drerio

not conserved

ENSDARG00000045540

730

Dmelanogaster

no alignment

FBgn0035688

n/a

Celegans

no alignment

C47G2.5

n/a

Xtropicalis

not conserved

ENSXETG00000023068

738

APIT

protein features

start (aa)	end (aa)	feature	details
770	770	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
806	806	CONFLICT	A -> T (in Ref. 2; BAH13719).	might get lost (downstream of altered splice site)
820	825	COMPBIAS	Poly-Ser.	might get lost (downstream of altered splice site)
835	835	CONFLICT	Q -> H (in Ref. 4; AAH52995).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2802 / 2802

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

934 / 934

position of stopcodon in wt / mu cDNA

3177 / 3177

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

376 / 376

chromosome

strand

last intron/exon boundary

3129

theoretical NMD boundary in CDS

2703

length of CDS

2802

coding sequence (CDS) position

2117

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

2492

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

96464

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

50878196

original gDNA sequence snippet

CACAGCCCCAGGAGTGGTGAGGGACGTGGGTTCCAGTGTGT

altered gDNA sequence snippet

CACAGCCCCAGGAGTGGTGAAGGACGTGGGTTCCAGTGTGT

original cDNA sequence snippet

CACAGCCCCAGGAGTGGTGAGGGACGTGGGTTCCAGTGTGT

altered cDNA sequence snippet

CACAGCCCCAGGAGTGGTGAAGGACGTGGGTTCCAGTGTGT

wildtype AA sequence

MFWKFDLNTT SHVDKLLDKE HVTLQELMDE DDILQECKAQ NQKLLDFLCR QQCMEELVSL
ITQDPPLDME EKVRFKYPNT ACELLTCDVP QISDRLGGDE SLLSLLYDFL DHEPPLNPLL
ASFFSKTIGN LIARKTEQVI TFLKKKDKFI SLVLKHIGTS ALMDLLLRLV SCVEPAGLRQ
DVLHWLNEEK VIQRLVELIH PSQDEDRQSN ASQTLCDIVR LGRDQGSQLQ EALEPDPLLT
ALESRQDCVE QLLKNMFDGD RTESCLVSGT QVLLTLLETR RVGTEGLVDS FSQGLERSYA
VSSSVLHGIE PRLKDFHQLL LNPPKKKAIL TTIGVLEEPL GNARLHGARL MAALLHTNTP
SINQELCRLN TMDLLLDLFF KYTWNNFLHF QVELCIAAIL SHAAREERTE ASGSESRVEP
PHENGNRSLE TPQPAASLPD NTMVTHLFQK CCLVQRILEA WEANDHTQAA GGMRRGNMGH
LTRIANAVVQ NLERGPVQTH ISEVIRGLPA DCRGRWESFV EETLTETNRR NTVDLAFSDY
QIQQMTANFV DQFGFNDEEF ADQDDNINAP FDRIAEINFN IDADEDSPSA ALFEACCSDR
IQPFDDDEDE DIWEDSDTRC AARVMARPRF GAPHASESCS KNGPERGGQD GKASLEAHRD
APGAGAPPAP GKKEAPPVEG DSEGAMWTAV FDEPANSTPT APGVVRDVGS SVWAAGTSAP
EEKGWAKFTD FQPFCCSESG PRCSSPVDTE CSHAEGSRSQ GPEKAFSPAS PCAWNVCVTR
KAPLLASDSS SSGGSHSEDG DQKAASAMDA VSRGPGREAP PLPTVARTEE AVGRVGCADS
RLLSPACPAP KEVTAAPAVA VPPEATVAIT TALSKAGPAI PTPAVSSALA VAVPLGPIMA
VTAAPAMVAT LGTVTKDGKT DAPPEGAALN GPV*

mutated AA sequence

MFWKFDLNTT SHVDKLLDKE HVTLQELMDE DDILQECKAQ NQKLLDFLCR QQCMEELVSL
ITQDPPLDME EKVRFKYPNT ACELLTCDVP QISDRLGGDE SLLSLLYDFL DHEPPLNPLL
ASFFSKTIGN LIARKTEQVI TFLKKKDKFI SLVLKHIGTS ALMDLLLRLV SCVEPAGLRQ
DVLHWLNEEK VIQRLVELIH PSQDEDRQSN ASQTLCDIVR LGRDQGSQLQ EALEPDPLLT
ALESRQDCVE QLLKNMFDGD RTESCLVSGT QVLLTLLETR RVGTEGLVDS FSQGLERSYA
VSSSVLHGIE PRLKDFHQLL LNPPKKKAIL TTIGVLEEPL GNARLHGARL MAALLHTNTP
SINQELCRLN TMDLLLDLFF KYTWNNFLHF QVELCIAAIL SHAAREERTE ASGSESRVEP
PHENGNRSLE TPQPAASLPD NTMVTHLFQK CCLVQRILEA WEANDHTQAA GGMRRGNMGH
LTRIANAVVQ NLERGPVQTH ISEVIRGLPA DCRGRWESFV EETLTETNRR NTVDLAFSDY
QIQQMTANFV DQFGFNDEEF ADQDDNINAP FDRIAEINFN IDADEDSPSA ALFEACCSDR
IQPFDDDEDE DIWEDSDTRC AARVMARPRF GAPHASESCS KNGPERGGQD GKASLEAHRD
APGAGAPPAP GKKEAPPVEG DSEGAMWTAV FDEPANSTPT APGVVKDVGS SVWAAGTSAP
EEKGWAKFTD FQPFCCSESG PRCSSPVDTE CSHAEGSRSQ GPEKAFSPAS PCAWNVCVTR
KAPLLASDSS SSGGSHSEDG DQKAASAMDA VSRGPGREAP PLPTVARTEE AVGRVGCADS
RLLSPACPAP KEVTAAPAVA VPPEATVAIT TALSKAGPAI PTPAVSSALA VAVPLGPIMA
VTAAPAMVAT LGTVTKDGKT DAPPEGAALN GPV*

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