MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000242783
Querying Taster for transcript #2: ENST00000342216
MT speed 0 s - this script 3.091183 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PKN1	polymorphism_automatic	0.620795446244101	simple_aae		affected		V901I	single base exchange	rs10846		show file
PKN1	polymorphism_automatic	0.620795446244101	simple_aae		affected		V907I	single base exchange	rs10846		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.379204553755899 (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)

chr19:14582468G>AN/A show variant in all transcripts IGV

HGNC symbol

PKN1

Ensembl transcript ID

ENST00000242783

Genbank transcript ID

NM_002741

UniProt peptide

Q16512

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2701G>A
cDNA.2866G>A
g.38604G>A

AA changes

V901I Score: 29 explain score(s)

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

901

frameshift

known variant

Reference ID: rs10846

database	homozygous (A/A)	heterozygous	allele carriers
1000G	373	511	884
ExAC	3572	11333	14905

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.304	1
	1.636	1
(flanking)	3.573	1

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	38601	wt: 0.2968 / mu: 0.3352 (marginal change - not scored)	wt: CCACGCTGTCCGGCCGCACCGACGTCAGCAACTTCGACGAG mu: CCACGCTGTCCGGCCGCACCGACATCAGCAACTTCGACGAG	accg\|ACGT
Donor marginally increased	38607	wt: 0.9272 / mu: 0.9611 (marginal change - not scored)	wt: ACGTCAGCAACTTCG mu: ACATCAGCAACTTCG	GTCA\|gcaa
Donor gained	38600	0.58	mu: CGCACCGACATCAGC	CACC\|gaca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

901

mutated

all conserved

901

Ptroglodytes

all identical

ENSPTRG00000010591

900

Mmulatta

all identical

ENSMMUG00000005727

901

Fcatus

all identical

ENSFCAG00000013492

904

Mmusculus

all identical

ENSMUSG00000057672

910

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
875	942	DOMAIN	AGC-kinase C-terminal.	lost
914	914	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
916	916	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2829 / 2829

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

943 / 943

position of stopcodon in wt / mu cDNA

2994 / 2994

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

166 / 166

chromosome

strand

last intron/exon boundary

2791

theoretical NMD boundary in CDS

2575

length of CDS

2829

coding sequence (CDS) position

2701

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

2866

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

38604

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

14582468

original gDNA sequence snippet

CGCTGTCCGGCCGCACCGACGTCAGCAACTTCGACGAGGAG

altered gDNA sequence snippet

CGCTGTCCGGCCGCACCGACATCAGCAACTTCGACGAGGAG

original cDNA sequence snippet

CGCTGTCCGGCCGCACCGACGTCAGCAACTTCGACGAGGAG

altered cDNA sequence snippet

CGCTGTCCGGCCGCACCGACATCAGCAACTTCGACGAGGAG

wildtype AA sequence

MASDAVQSEP RSWSLLEQLG LAGADLAAPG VQQQLELERE RLRREIRKEL KLKEGAENLR
RATTDLGRSL GPVELLLRGS SRRLDLLHQQ LQELHAHVVL PDPAATHDGP QSPGAGGPTC
SATNLSRVAG LEKQLAIELK VKQGAENMIQ TYSNGSTKDR KLLLTAQQML QDSKTKIDII
RMQLRRALQA GQLENQAAPD DTQGSPDLGA VELRIEELRH HFRVEHAVAE GAKNVLRLLS
AAKAPDRKAV SEAQEKLTES NQKLGLLREA LERRLGELPA DHPKGRLLRE ELAAASSAAF
STRLAGPFPA THYSTLCKPA PLTGTLEVRV VGCRDLPETI PWNPTPSMGG PGTPDSRPPF
LSRPARGLYS RSGSLSGRSS LKAEAENTSE VSTVLKLDNT VVGQTSWKPC GPNAWDQSFT
LELERARELE LAVFWRDQRG LCALKFLKLE DFLDNERHEV QLDMEPQGCL VAEVTFRNPV
IERIPRLRRQ KKIFSKQQGK AFQRARQMNI DVATWVRLLR RLIPNATGTG TFSPGASPGS
EARTTGDISV EKLNLGTDSD SSPQKSSRDP PSSPSSLSSP IQESTAPELP SETQETPGPA
LCSPLRKSPL TLEDFKFLAV LGRGHFGKVL LSEFRPSGEL FAIKALKKGD IVARDEVESL
MCEKRILAAV TSAGHPFLVN LFGCFQTPEH VCFVMEYSAG GDLMLHIHSD VFSEPRAIFY
SACVVLGLQF LHEHKIVYRD LKLDNLLLDT EGYVKIADFG LCKEGMGYGD RTSTFCGTPE
FLAPEVLTDT SYTRAVDWWG LGVLLYEMLV GESPFPGDDE EEVFDSIVND EVRYPRFLSA
EAIGIMRRLL RRNPERRLGS SERDAEDVKK QPFFRTLGWE ALLARRLPPP FVPTLSGRTD
VSNFDEEFTG EAPTLSPPRD ARPLTAAEQA AFLDFDFVAG GC*

mutated AA sequence

speed

0.81 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
back to results table

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.379204553755899 (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)

chr19:14582468G>AN/A show variant in all transcripts IGV

HGNC symbol

PKN1

Ensembl transcript ID

ENST00000342216

Genbank transcript ID

NM_213560

UniProt peptide

Q16512

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2719G>A
cDNA.2750G>A
g.38604G>A

AA changes

V907I Score: 29 explain score(s)

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

907

frameshift

known variant

Reference ID: rs10846

database	homozygous (A/A)	heterozygous	allele carriers
1000G	373	511	884
ExAC	3572	11333	14905

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.304	1
	1.636	1
(flanking)	3.573	1

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	38601	wt: 0.2968 / mu: 0.3352 (marginal change - not scored)	wt: CCACGCTGTCCGGCCGCACCGACGTCAGCAACTTCGACGAG mu: CCACGCTGTCCGGCCGCACCGACATCAGCAACTTCGACGAG	accg\|ACGT
Donor marginally increased	38607	wt: 0.9272 / mu: 0.9611 (marginal change - not scored)	wt: ACGTCAGCAACTTCG mu: ACATCAGCAACTTCG	GTCA\|gcaa
Donor gained	38600	0.58	mu: CGCACCGACATCAGC	CACC\|gaca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

907

mutated

all conserved

907

Ptroglodytes

all identical

ENSPTRG00000010591

900

Mmulatta

all identical

ENSMMUG00000005727

901

Fcatus

all identical

ENSFCAG00000013492

904

Mmusculus

all identical

ENSMUSG00000057672

910

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
875	942	DOMAIN	AGC-kinase C-terminal.	lost
914	914	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
916	916	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2847 / 2847

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

949 / 949

position of stopcodon in wt / mu cDNA

2878 / 2878

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

32 / 32

chromosome

strand

last intron/exon boundary

2675

theoretical NMD boundary in CDS

2593

length of CDS

2847

coding sequence (CDS) position

2719

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

2750

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

38604

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

14582468

original gDNA sequence snippet

CGCTGTCCGGCCGCACCGACGTCAGCAACTTCGACGAGGAG

altered gDNA sequence snippet

CGCTGTCCGGCCGCACCGACATCAGCAACTTCGACGAGGAG

original cDNA sequence snippet

CGCTGTCCGGCCGCACCGACGTCAGCAACTTCGACGAGGAG

altered cDNA sequence snippet

CGCTGTCCGGCCGCACCGACATCAGCAACTTCGACGAGGAG

wildtype AA sequence

MAEANNPSEQ ELESEPRSWS LLEQLGLAGA DLAAPGVQQQ LELERERLRR EIRKELKLKE
GAENLRRATT DLGRSLGPVE LLLRGSSRRL DLLHQQLQEL HAHVVLPDPA ATHDGPQSPG
AGGPTCSATN LSRVAGLEKQ LAIELKVKQG AENMIQTYSN GSTKDRKLLL TAQQMLQDSK
TKIDIIRMQL RRALQAGQLE NQAAPDDTQG SPDLGAVELR IEELRHHFRV EHAVAEGAKN
VLRLLSAAKA PDRKAVSEAQ EKLTESNQKL GLLREALERR LGELPADHPK GRLLREELAA
ASSAAFSTRL AGPFPATHYS TLCKPAPLTG TLEVRVVGCR DLPETIPWNP TPSMGGPGTP
DSRPPFLSRP ARGLYSRSGS LSGRSSLKAE AENTSEVSTV LKLDNTVVGQ TSWKPCGPNA
WDQSFTLELE RARELELAVF WRDQRGLCAL KFLKLEDFLD NERHEVQLDM EPQGCLVAEV
TFRNPVIERI PRLRRQKKIF SKQQGKAFQR ARQMNIDVAT WVRLLRRLIP NATGTGTFSP
GASPGSEART TGDISVEKLN LGTDSDSSPQ KSSRDPPSSP SSLSSPIQES TAPELPSETQ
ETPGPALCSP LRKSPLTLED FKFLAVLGRG HFGKVLLSEF RPSGELFAIK ALKKGDIVAR
DEVESLMCEK RILAAVTSAG HPFLVNLFGC FQTPEHVCFV MEYSAGGDLM LHIHSDVFSE
PRAIFYSACV VLGLQFLHEH KIVYRDLKLD NLLLDTEGYV KIADFGLCKE GMGYGDRTST
FCGTPEFLAP EVLTDTSYTR AVDWWGLGVL LYEMLVGESP FPGDDEEEVF DSIVNDEVRY
PRFLSAEAIG IMRRLLRRNP ERRLGSSERD AEDVKKQPFF RTLGWEALLA RRLPPPFVPT
LSGRTDVSNF DEEFTGEAPT LSPPRDARPL TAAEQAAFLD FDFVAGGC*

mutated AA sequence

speed

0.29 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems