MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000323830
Querying Taster for transcript #2: ENST00000429275
MT speed 0 s - this script 3.705833 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CPN2	polymorphism_automatic	7.26396720551747e-12	simple_aae		affected		A305T	single base exchange	rs3732477		show file
CPN2	polymorphism_automatic	7.26396720551747e-12	simple_aae		affected		A305T	single base exchange	rs3732477		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999992736 (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)

chr3:194062519C>TN/A show variant in all transcripts IGV

HGNC symbol

CPN2

Ensembl transcript ID

ENST00000323830

Genbank transcript ID

NM_001080513

UniProt peptide

P22792

alteration type

single base exchange

alteration region

CDS

DNA changes

c.913G>A
cDNA.1003G>A
g.9539G>A

AA changes

A305T Score: 58 explain score(s)

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

305

frameshift

known variant

Reference ID: rs3732477

database	homozygous (T/T)	heterozygous	allele carriers
1000G	332	1171	1503
ExAC	6341	20085	26426

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.786	0.004
	-0.818	0
(flanking)	-0.571	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
Donor gained	9539	0.49	mu: CTGTCACTGAGGGCA	GTCA\|ctga

distance from splice site

916

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

305

mutated

not conserved

305

Ptroglodytes

all identical

ENSPTRG00000030017

305

Mmulatta

all identical

ENSMMUG00000007865

305

Fcatus

not conserved

ENSFCAG00000015345

305

Mmusculus

not conserved

ENSMUSG00000023176

305

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000063518

304

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
290	311	REPEAT	LRR 9.	lost
314	335	REPEAT	LRR 10.	might get lost (downstream of altered splice site)
338	359	REPEAT	LRR 11.	might get lost (downstream of altered splice site)
348	348	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
359	359	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
362	383	REPEAT	LRR 12.	might get lost (downstream of altered splice site)
395	447	DOMAIN	LRRCT.	might get lost (downstream of altered splice site)
509	509	CONFLICT	Q -> W (in Ref. 4; AAH31569/AAH42334/ AAI37399/AAI37404).	might get lost (downstream of altered splice site)
518	518	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1638 / 1638

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

546 / 546

position of stopcodon in wt / mu cDNA

1728 / 1728

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

91 / 91

chromosome

strand

-1

last intron/exon boundary

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

1638

coding sequence (CDS) position

913

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

1003

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

9539

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

194062519

original gDNA sequence snippet

ATAACCAGCTGGAGACTGTCGCTGAGGGCACCTTTGCCCAC

altered gDNA sequence snippet

ATAACCAGCTGGAGACTGTCACTGAGGGCACCTTTGCCCAC

original cDNA sequence snippet

ATAACCAGCTGGAGACTGTCGCTGAGGGCACCTTTGCCCAC

altered cDNA sequence snippet

ATAACCAGCTGGAGACTGTCACTGAGGGCACCTTTGCCCAC

wildtype AA sequence

MLPGAWLLWT SLLLLARPAQ PCPMGCDCFV QEVFCSDEEL ATVPLDIPPY TKNIIFVETS
FTTLETRAFG SNPNLTKVVF LNTQLCQFRP DAFGGLPRLE DLEVTGSSFL NLSTNIFSNL
TSLGKLTLNF NMLEALPEGL FQHLAALESL HLQGNQLQAL PRRLFQPLTH LKTLNLAQNL
LAQLPEELFH PLTSLQTLKL SNNALSGLPQ GVFGKLGSLQ ELFLDSNNIS ELPPQVFSQL
FCLERLWLQR NAITHLPLSI FASLGNLTFL SLQWNMLRVL PAGLFAHTPC LVGLSLTHNQ
LETVAEGTFA HLSNLRSLML SYNAITHLPA GIFRDLEELV KLYLGSNNLT ALHPALFQNL
SKLELLSLSK NQLTTLPEGI FDTNYNLFNL ALHGNPWQCD CHLAYLFNWL QQYTDRLLNI
QTYCAGPAYL KGQVVPALNE KQLVCPVTRD HLGFQVTWPD ESKAGGSWDL AVQERAARSQ
CTYSNPEGTV VLACDQAQCR WLNVQLSPQQ GSLGLQYNAS QEWDLRSSCG SLRLTVSIEA
RAAGP*

mutated AA sequence

MLPGAWLLWT SLLLLARPAQ PCPMGCDCFV QEVFCSDEEL ATVPLDIPPY TKNIIFVETS
FTTLETRAFG SNPNLTKVVF LNTQLCQFRP DAFGGLPRLE DLEVTGSSFL NLSTNIFSNL
TSLGKLTLNF NMLEALPEGL FQHLAALESL HLQGNQLQAL PRRLFQPLTH LKTLNLAQNL
LAQLPEELFH PLTSLQTLKL SNNALSGLPQ GVFGKLGSLQ ELFLDSNNIS ELPPQVFSQL
FCLERLWLQR NAITHLPLSI FASLGNLTFL SLQWNMLRVL PAGLFAHTPC LVGLSLTHNQ
LETVTEGTFA HLSNLRSLML SYNAITHLPA GIFRDLEELV KLYLGSNNLT ALHPALFQNL
SKLELLSLSK NQLTTLPEGI FDTNYNLFNL ALHGNPWQCD CHLAYLFNWL QQYTDRLLNI
QTYCAGPAYL KGQVVPALNE KQLVCPVTRD HLGFQVTWPD ESKAGGSWDL AVQERAARSQ
CTYSNPEGTV VLACDQAQCR WLNVQLSPQQ GSLGLQYNAS QEWDLRSSCG SLRLTVSIEA
RAAGP*

speed

0.82 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: 0.999999999992736 (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)

chr3:194062519C>TN/A show variant in all transcripts IGV

HGNC symbol

CPN2

Ensembl transcript ID

ENST00000429275

Genbank transcript ID

N/A

UniProt peptide

P22792

alteration type

single base exchange

alteration region

CDS

DNA changes

c.913G>A
cDNA.990G>A
g.9539G>A

AA changes

A305T Score: 58 explain score(s)

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

305

frameshift

known variant

Reference ID: rs3732477

database	homozygous (T/T)	heterozygous	allele carriers
1000G	332	1171	1503
ExAC	6341	20085	26426

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.786	0.004
	-0.818	0
(flanking)	-0.571	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
Donor gained	9539	0.49	mu: CTGTCACTGAGGGCA	GTCA\|ctga

distance from splice site

913

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

305

mutated

not conserved

305

Ptroglodytes

all identical

ENSPTRG00000030017

305

Mmulatta

all identical

ENSMMUG00000007865

305

Fcatus

not conserved

ENSFCAG00000015345

305

Mmusculus

not conserved

ENSMUSG00000023176

305

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000063518

304

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
290	311	REPEAT	LRR 9.	lost
314	335	REPEAT	LRR 10.	might get lost (downstream of altered splice site)
338	359	REPEAT	LRR 11.	might get lost (downstream of altered splice site)
348	348	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
359	359	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
362	383	REPEAT	LRR 12.	might get lost (downstream of altered splice site)
395	447	DOMAIN	LRRCT.	might get lost (downstream of altered splice site)
509	509	CONFLICT	Q -> W (in Ref. 4; AAH31569/AAH42334/ AAI37399/AAI37404).	might get lost (downstream of altered splice site)
518	518	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1638 / 1638

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

546 / 546

position of stopcodon in wt / mu cDNA

1715 / 1715

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

78 / 78

chromosome

strand

-1

last intron/exon boundary

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

1638

coding sequence (CDS) position

913

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

990

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

9539

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

194062519

original gDNA sequence snippet

ATAACCAGCTGGAGACTGTCGCTGAGGGCACCTTTGCCCAC

altered gDNA sequence snippet

ATAACCAGCTGGAGACTGTCACTGAGGGCACCTTTGCCCAC

original cDNA sequence snippet

ATAACCAGCTGGAGACTGTCGCTGAGGGCACCTTTGCCCAC

altered cDNA sequence snippet

ATAACCAGCTGGAGACTGTCACTGAGGGCACCTTTGCCCAC

wildtype AA sequence

mutated AA sequence

MLPGAWLLWT SLLLLARPAQ PCPMGCDCFV QEVFCSDEEL ATVPLDIPPY TKNIIFVETS
FTTLETRAFG SNPNLTKVVF LNTQLCQFRP DAFGGLPRLE DLEVTGSSFL NLSTNIFSNL
TSLGKLTLNF NMLEALPEGL FQHLAALESL HLQGNQLQAL PRRLFQPLTH LKTLNLAQNL
LAQLPEELFH PLTSLQTLKL SNNALSGLPQ GVFGKLGSLQ ELFLDSNNIS ELPPQVFSQL
FCLERLWLQR NAITHLPLSI FASLGNLTFL SLQWNMLRVL PAGLFAHTPC LVGLSLTHNQ
LETVTEGTFA HLSNLRSLML SYNAITHLPA GIFRDLEELV KLYLGSNNLT ALHPALFQNL
SKLELLSLSK NQLTTLPEGI FDTNYNLFNL ALHGNPWQCD CHLAYLFNWL QQYTDRLLNI
QTYCAGPAYL KGQVVPALNE KQLVCPVTRD HLGFQVTWPD ESKAGGSWDL AVQERAARSQ
CTYSNPEGTV VLACDQAQCR WLNVQLSPQQ GSLGLQYNAS QEWDLRSSCG SLRLTVSIEA
RAAGP*

speed

0.88 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems