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: ENST00000433211
Querying Taster for transcript #2: ENST00000373744
MT speed 1.72 s - this script 3.916336 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CTNNA3	polymorphism_automatic	7.55098152005473e-07	simple_aae		affected		S596N	single base exchange	rs4548513		show file
CTNNA3	polymorphism_automatic	7.55098152005473e-07	simple_aae		affected		S596N	single base exchange	rs4548513		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999244901848 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM074765)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:68040325C>TN/A show variant in all transcripts IGV

HGNC symbol

CTNNA3

Ensembl transcript ID

ENST00000433211

Genbank transcript ID

NM_001127384

UniProt peptide

Q9UI47

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1787G>A
cDNA.1962G>A
g.1415603G>A

AA changes

S596N Score: 46 explain score(s)

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

596

frameshift

known variant

Reference ID: rs4548513

database	homozygous (T/T)	heterozygous	allele carriers
1000G	641	1147	1788
ExAC	10742	11283	22025

known disease mutation at this position, please check HGMD for details (HGMD ID CM074765)

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.287	0.361
	0.354	0.523
(flanking)	2.716	0.76

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	1415608	wt: 0.23 / mu: 0.38	wt: GCTCATTGAATGTGT mu: ACTCATTGAATGTGT	TCAT\|tgaa
Donor gained	1415598	0.44	mu: TTAAGCAAAAACTCA	AAGC\|aaaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

596

mutated

all conserved

596

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000016902

596

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000060843

596

Ggallus

all conserved

ENSGALG00000002845

247

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all conserved

FBgn0010215

604

Celegans

not conserved

R13H4.4

604

LTWDPKT

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
637	637	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
867	867	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2688 / 2688

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

896 / 896

position of stopcodon in wt / mu cDNA

2863 / 2863

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

176 / 176

chromosome

strand

-1

last intron/exon boundary

2576

theoretical NMD boundary in CDS

2350

length of CDS

2688

coding sequence (CDS) position

1787

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

1962

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

1415603

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

68040325

original gDNA sequence snippet

CTTGGAAGCCTTAAGCAAAAGCTCATTGAATGTGTTGGATG

altered gDNA sequence snippet

CTTGGAAGCCTTAAGCAAAAACTCATTGAATGTGTTGGATG

original cDNA sequence snippet

CTTGGAAGCCTTAAGCAAAAGCTCATTGAATGTGTTGGATG

altered cDNA sequence snippet

CTTGGAAGCCTTAAGCAAAAACTCATTGAATGTGTTGGATG

wildtype AA sequence

MSAETPITLN IDPQDLQVQT FTVEKLLEPL IIQVTTLVNC PQNPSSRKKG RSKRASVLLA
SVEEATWNLL DKGEKIAQEA TVLKDELTAS LEEVRKESEA LKVSAERFTD DPCFLPKREA
VVQAARALLA AVTRLLILAD MIDVMCLLQH VSAFQRTFES LKNVANKSDL QKTYQKLGKE
LENLDYLAFK RQQDLKSPNQ RDEIAGARAS LKENSPLLHS ICSACLEHSD VASLKASKDT
VCEEIQNALN VISNASQGIQ NMTTPPEPQA ATLGSALDEL ENLIVLNPLT VTEEEIRPSL
EKRLEAIISG AALLADSSCT RDLHRERIIA ECNAIRQALQ DLLSEYMNNA GKKERSNTLN
IALDNMCKKT RDLRRQLRKA IIDHVSDSFL DTTVPLLVLI EAAKNGREKE IKEYAAIFHE
HTSRLVEVAN LACSMSTNED GIKIVKIAAN HLETLCPQII NAALALAARP KSQAVKNTME
MYKRTWENHI HVLTEAVDDI TSIDDFLAVS ESHILEDVNK CIIALRDQDA DNLDRAAGAI
RGRAARVAHI VTGEMDSYEP GAYTEGVMRN VNFLTSTVIP EFVTQVNVAL EALSKSSLNV
LDDNQFVDIS KKIYDTIHDI RCSVMMIRTP EELEDVSDLE EEHEVRSHTS IQTEGKTDRA
KMTQLPEAEK EKIAEQVADF KKVKSKLDAE IEIWDDTSND IIVLAKNMCM IMMEMTDFTR
GKGPLKHTTD VIYAAKMISE SGSRMDVLAR QIANQCPDPS CKQDLLAYLE QIKFYSHQLK
ICSQVKAEIQ NLGGELIMSA LDSVTSLIQA AKNLMNAVVQ TVKMSYIAST KIIRIQSPAG
PRHPVVMWRM KAPAKKPLIK REKPEETCAA VRRGSAKKKI HPLQVMSEFR GRQIY*

mutated AA sequence

MSAETPITLN IDPQDLQVQT FTVEKLLEPL IIQVTTLVNC PQNPSSRKKG RSKRASVLLA
SVEEATWNLL DKGEKIAQEA TVLKDELTAS LEEVRKESEA LKVSAERFTD DPCFLPKREA
VVQAARALLA AVTRLLILAD MIDVMCLLQH VSAFQRTFES LKNVANKSDL QKTYQKLGKE
LENLDYLAFK RQQDLKSPNQ RDEIAGARAS LKENSPLLHS ICSACLEHSD VASLKASKDT
VCEEIQNALN VISNASQGIQ NMTTPPEPQA ATLGSALDEL ENLIVLNPLT VTEEEIRPSL
EKRLEAIISG AALLADSSCT RDLHRERIIA ECNAIRQALQ DLLSEYMNNA GKKERSNTLN
IALDNMCKKT RDLRRQLRKA IIDHVSDSFL DTTVPLLVLI EAAKNGREKE IKEYAAIFHE
HTSRLVEVAN LACSMSTNED GIKIVKIAAN HLETLCPQII NAALALAARP KSQAVKNTME
MYKRTWENHI HVLTEAVDDI TSIDDFLAVS ESHILEDVNK CIIALRDQDA DNLDRAAGAI
RGRAARVAHI VTGEMDSYEP GAYTEGVMRN VNFLTSTVIP EFVTQVNVAL EALSKNSLNV
LDDNQFVDIS KKIYDTIHDI RCSVMMIRTP EELEDVSDLE EEHEVRSHTS IQTEGKTDRA
KMTQLPEAEK EKIAEQVADF KKVKSKLDAE IEIWDDTSND IIVLAKNMCM IMMEMTDFTR
GKGPLKHTTD VIYAAKMISE SGSRMDVLAR QIANQCPDPS CKQDLLAYLE QIKFYSHQLK
ICSQVKAEIQ NLGGELIMSA LDSVTSLIQA AKNLMNAVVQ TVKMSYIAST KIIRIQSPAG
PRHPVVMWRM KAPAKKPLIK REKPEETCAA VRRGSAKKKI HPLQVMSEFR GRQIY*

speed

1.10 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: 0.999999244901848 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM074765)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:68040325C>TN/A show variant in all transcripts IGV

HGNC symbol

CTNNA3

Ensembl transcript ID

ENST00000373744

Genbank transcript ID

N/A

UniProt peptide

Q9UI47

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1787G>A
cDNA.1787G>A
g.1415603G>A

AA changes

S596N Score: 46 explain score(s)

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

596

frameshift

known variant

Reference ID: rs4548513

database	homozygous (T/T)	heterozygous	allele carriers
1000G	641	1147	1788
ExAC	10742	11283	22025

known disease mutation at this position, please check HGMD for details (HGMD ID CM074765)

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.287	0.361
	0.354	0.523
(flanking)	2.716	0.76

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	1415608	wt: 0.23 / mu: 0.38	wt: GCTCATTGAATGTGT mu: ACTCATTGAATGTGT	TCAT\|tgaa
Donor gained	1415598	0.44	mu: TTAAGCAAAAACTCA	AAGC\|aaaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

596

mutated

all conserved

596

Ptroglodytes

no homologue

Mmulatta

all conserved

ENSMMUG00000016902

596

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000060843

596

Ggallus

all conserved

ENSGALG00000002845

247

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all conserved

FBgn0010215

604

Celegans

not conserved

R13H4.4

604

LTWDPKT

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
637	637	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
867	867	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2688 / 2688

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

896 / 896

position of stopcodon in wt / mu cDNA

2688 / 2688

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

1 / 1

chromosome

strand

-1

last intron/exon boundary

2401

theoretical NMD boundary in CDS

2350

length of CDS

2688

coding sequence (CDS) position

1787

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

1787

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

1415603

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

68040325

original gDNA sequence snippet

CTTGGAAGCCTTAAGCAAAAGCTCATTGAATGTGTTGGATG

altered gDNA sequence snippet

CTTGGAAGCCTTAAGCAAAAACTCATTGAATGTGTTGGATG

original cDNA sequence snippet

CTTGGAAGCCTTAAGCAAAAGCTCATTGAATGTGTTGGATG

altered cDNA sequence snippet

CTTGGAAGCCTTAAGCAAAAACTCATTGAATGTGTTGGATG

wildtype AA sequence

mutated AA sequence

MSAETPITLN IDPQDLQVQT FTVEKLLEPL IIQVTTLVNC PQNPSSRKKG RSKRASVLLA
SVEEATWNLL DKGEKIAQEA TVLKDELTAS LEEVRKESEA LKVSAERFTD DPCFLPKREA
VVQAARALLA AVTRLLILAD MIDVMCLLQH VSAFQRTFES LKNVANKSDL QKTYQKLGKE
LENLDYLAFK RQQDLKSPNQ RDEIAGARAS LKENSPLLHS ICSACLEHSD VASLKASKDT
VCEEIQNALN VISNASQGIQ NMTTPPEPQA ATLGSALDEL ENLIVLNPLT VTEEEIRPSL
EKRLEAIISG AALLADSSCT RDLHRERIIA ECNAIRQALQ DLLSEYMNNA GKKERSNTLN
IALDNMCKKT RDLRRQLRKA IIDHVSDSFL DTTVPLLVLI EAAKNGREKE IKEYAAIFHE
HTSRLVEVAN LACSMSTNED GIKIVKIAAN HLETLCPQII NAALALAARP KSQAVKNTME
MYKRTWENHI HVLTEAVDDI TSIDDFLAVS ESHILEDVNK CIIALRDQDA DNLDRAAGAI
RGRAARVAHI VTGEMDSYEP GAYTEGVMRN VNFLTSTVIP EFVTQVNVAL EALSKNSLNV
LDDNQFVDIS KKIYDTIHDI RCSVMMIRTP EELEDVSDLE EEHEVRSHTS IQTEGKTDRA
KMTQLPEAEK EKIAEQVADF KKVKSKLDAE IEIWDDTSND IIVLAKNMCM IMMEMTDFTR
GKGPLKHTTD VIYAAKMISE SGSRMDVLAR QIANQCPDPS CKQDLLAYLE QIKFYSHQLK
ICSQVKAEIQ NLGGELIMSA LDSVTSLIQA AKNLMNAVVQ TVKMSYIAST KIIRIQSPAG
PRHPVVMWRM KAPAKKPLIK REKPEETCAA VRRGSAKKKI HPLQVMSEFR GRQIY*

speed

0.62 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems