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: ENST00000372836
Querying Taster for transcript #2: ENST00000394142
MT speed 0 s - this script 2.229736 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CNPY3	polymorphism_automatic	0.879888719647226	simple_aae				S231I	single base exchange	rs9471969		show file
CNPY3	polymorphism_automatic	1	without_aae					single base exchange	rs9471969		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.120111280352774 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:42906384G>TN/A show variant in all transcripts IGV

HGNC symbol

CNPY3

Ensembl transcript ID

ENST00000372836

Genbank transcript ID

NM_006586

UniProt peptide

Q9BT09

alteration type

single base exchange

alteration region

CDS

DNA changes

c.692G>T
cDNA.1063G>T
g.9447G>T

AA changes

S231I Score: 142 explain score(s)

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

231

frameshift

known variant

Reference ID: rs9471969

database	homozygous (T/T)	heterozygous	allele carriers
1000G	144	783	927
ExAC	3088	19789	22877

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.124	0.914
	3.902	0.961
(flanking)	2.234	0.937

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 marginally increased	9451	wt: 0.9973 / mu: 0.9984 (marginal change - not scored)	wt: AGCAGGGCCAAGGCA mu: ATCAGGGCCAAGGCA	CAGG\|gcca
Donor marginally increased	9438	wt: 0.9954 / mu: 0.9955 (marginal change - not scored)	wt: CAAGAAGAAGAGCAG mu: CAAGAAGAAGAGCAT	AGAA\|gaag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

231

mutated

not conserved

231

Ptroglodytes

all identical

ENSPTRG00000018177

231

Mmulatta

all identical

ENSMMUG00000000461

230

Fcatus

not conserved

ENSFCAG00000009710

177

Mmusculus

all identical

ENSMUSG00000023973

231

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000013389

215

Drerio

not conserved

ENSDARG00000070512

215

EDGQKKEKKVKKKKKKSKISD

Dmelanogaster

not conserved

FBgn0036847

221

Celegans

no alignment

C11H1.7

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
47	271	DOMAIN	Saposin B-type.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

837 / 837

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

279 / 279

position of stopcodon in wt / mu cDNA

1208 / 1208

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

372 / 372

chromosome

strand

last intron/exon boundary

985

theoretical NMD boundary in CDS

563

length of CDS

837

coding sequence (CDS) position

692

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

1063

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

9447

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

42906384

original gDNA sequence snippet

GAAGTCCAAGAAGAAGAGCAGCAGGGCCAAGGCAGCAGGCG

altered gDNA sequence snippet

GAAGTCCAAGAAGAAGAGCATCAGGGCCAAGGCAGCAGGCG

original cDNA sequence snippet

GAAGTCCAAGAAGAAGAGCAGCAGGGCCAAGGCAGCAGGCG

altered cDNA sequence snippet

GAAGTCCAAGAAGAAGAGCATCAGGGCCAAGGCAGCAGGCG

wildtype AA sequence

MDSMPEPASR CLLLLPLLLL LLLLLPAPEL GPSQAGAEEN DWVRLPSKCE VCKYVAVELK
SAFEETGKTK EVIGTGYGIL DQKASGVKYT KSDLRLIEVT ETICKRLLDY SLHKERTGSN
RFAKGMSETF ETLHNLVHKG VKVVMDIPYE LWNETSAEVA DLKKQCDVLV EEFEEVIEDW
YRNHQEEDLT EFLCANHVLK GKDTSCLAEQ WSGKKGDTAA LGGKKSKKKS SRAKAAGGRS
SSSKQRKELG GLEGDPSPEE DEGIQKASPL THSPPDEL*

mutated AA sequence

MDSMPEPASR CLLLLPLLLL LLLLLPAPEL GPSQAGAEEN DWVRLPSKCE VCKYVAVELK
SAFEETGKTK EVIGTGYGIL DQKASGVKYT KSDLRLIEVT ETICKRLLDY SLHKERTGSN
RFAKGMSETF ETLHNLVHKG VKVVMDIPYE LWNETSAEVA DLKKQCDVLV EEFEEVIEDW
YRNHQEEDLT EFLCANHVLK GKDTSCLAEQ WSGKKGDTAA LGGKKSKKKS IRAKAAGGRS
SSSKQRKELG GLEGDPSPEE DEGIQKASPL THSPPDEL*

speed

0.18 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: without_aae, prob: 4.12139715393132e-32 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:42906384G>TN/A show variant in all transcripts IGV

HGNC symbol

CNPY3

Ensembl transcript ID

ENST00000394142

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

3'UTR

DNA changes

cDNA.895G>T
g.9447G>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs9471969

database	homozygous (T/T)	heterozygous	allele carriers
1000G	144	783	927
ExAC	3088	19789	22877

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.124	0.914
	3.902	0.961
(flanking)	2.234	0.937

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 marginally increased	9451	wt: 0.9973 / mu: 0.9984 (marginal change - not scored)	wt: AGCAGGGCCAAGGCA mu: ATCAGGGCCAAGGCA	CAGG\|gcca
Donor marginally increased	9438	wt: 0.9954 / mu: 0.9955 (marginal change - not scored)	wt: CAAGAAGAAGAGCAG mu: CAAGAAGAAGAGCAT	AGAA\|gaag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

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

signal is predicted to be ok

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

328 / 328

chromosome

strand

last intron/exon boundary

817

theoretical NMD boundary in CDS

439

length of CDS

165

coding sequence (CDS) position

N/A

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

895

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

9447

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

42906384

original gDNA sequence snippet

GAAGTCCAAGAAGAAGAGCAGCAGGGCCAAGGCAGCAGGCG

altered gDNA sequence snippet

GAAGTCCAAGAAGAAGAGCATCAGGGCCAAGGCAGCAGGCG

original cDNA sequence snippet

GAAGTCCAAGAAGAAGAGCAGCAGGGCCAAGGCAGCAGGCG

altered cDNA sequence snippet

GAAGTCCAAGAAGAAGAGCATCAGGGCCAAGGCAGCAGGCG

wildtype AA sequence

MDSMPEPASR CLLLLPLLLL LLLLLPAPEL GPSQAGAEEN DWVRLPSKCE GTCG*

mutated AA sequence

N/A

speed

0.16 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems