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: ENST00000261448
Querying Taster for transcript #2: ENST00000456138
MT speed 0.79 s - this script 2.774658 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CASQ2	disease_causing_automatic	0.999999253758074	simple_aae			0	L167H	single base exchange	rs121434550		show file
CASQ2	disease_causing_automatic	1	without_aae			0		single base exchange	rs121434550		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999253758074 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM063884)
known disease mutation: rs17612 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:116280877A>TN/A show variant in all transcripts IGV

HGNC symbol

CASQ2

Ensembl transcript ID

ENST00000261448

Genbank transcript ID

NM_001232

UniProt peptide

O14958

alteration type

single base exchange

alteration region

CDS

DNA changes

c.500T>A
cDNA.740T>A
g.30526T>A

AA changes

L167H Score: 99 explain score(s)

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

167

frameshift

known variant

Reference ID: rs121434550
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs17612 (pathogenic for Ventricular tachycardia, catecholaminergic polymorphic, 2) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM063884)

known disease mutation at this position, please check HGMD for details (HGMD ID CM063884)
known disease mutation at this position, please check HGMD for details (HGMD ID CM063884)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.411	1
	3.758	1
(flanking)	4.52	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

167

mutated

not conserved

167

Ptroglodytes

all identical

ENSPTRG00000001148

167

Mmulatta

all identical

ENSMMUG00000008970

167

Fcatus

all identical

ENSFCAG00000010496

Mmusculus

all identical

ENSMUSG00000027861

167

Ggallus

all identical

ENSGALG00000015018

167

Trubripes

no homologue

Drerio

all identical

ENSDARG00000008982

168

Dmelanogaster

no homologue

Celegans

all conserved

F40E10.3

175

Xtropicalis

not conserved

ENSXETG00000023738

protein features

start (aa)	end (aa)	feature	details
159	176	STRAND		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1200 / 1200

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

400 / 400

position of stopcodon in wt / mu cDNA

1440 / 1440

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

241 / 241

chromosome

strand

-1

last intron/exon boundary

1255

theoretical NMD boundary in CDS

964

length of CDS

1200

coding sequence (CDS) position

500

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

740

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

30526

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

116280877

original gDNA sequence snippet

CATTGAAGACTACATCAAACTCATTGGCTTTTTCAAGAGTG

altered gDNA sequence snippet

CATTGAAGACTACATCAAACACATTGGCTTTTTCAAGAGTG

original cDNA sequence snippet

CATTGAAGACTACATCAAACTCATTGGCTTTTTCAAGAGTG

altered cDNA sequence snippet

CATTGAAGACTACATCAAACACATTGGCTTTTTCAAGAGTG

wildtype AA sequence

MKRTHLFIVG IYFLSSCRAE EGLNFPTYDG KDRVVSLSEK NFKQVLKKYD LLCLYYHEPV
SSDKVTQKQF QLKEIVLELV AQVLEHKAIG FVMVDAKKEA KLAKKLGFDE EGSLYILKGD
RTIEFDGEFA ADVLVEFLLD LIEDPVEIIS SKLEVQAFER IEDYIKLIGF FKSEDSEYYK
AFEEAAEHFQ PYIKFFATFD KGVAKKLSLK MNEVDFYEPF MDEPIAIPNK PYTEEELVEF
VKEHQRPTLR RLRPEEMFET WEDDLNGIHI VAFAEKSDPD GYEFLEILKQ VARDNTDNPD
LSILWIDPDD FPLLVAYWEK TFKIDLFRPQ IGVVNVTDAD SVWMEIPDDD DLPTAEELED
WIEDVLSGKI NTEDDDEDDD DDDNSDEEDN DDSDDDDDE*

mutated AA sequence

MKRTHLFIVG IYFLSSCRAE EGLNFPTYDG KDRVVSLSEK NFKQVLKKYD LLCLYYHEPV
SSDKVTQKQF QLKEIVLELV AQVLEHKAIG FVMVDAKKEA KLAKKLGFDE EGSLYILKGD
RTIEFDGEFA ADVLVEFLLD LIEDPVEIIS SKLEVQAFER IEDYIKHIGF FKSEDSEYYK
AFEEAAEHFQ PYIKFFATFD KGVAKKLSLK MNEVDFYEPF MDEPIAIPNK PYTEEELVEF
VKEHQRPTLR RLRPEEMFET WEDDLNGIHI VAFAEKSDPD GYEFLEILKQ VARDNTDNPD
LSILWIDPDD FPLLVAYWEK TFKIDLFRPQ IGVVNVTDAD SVWMEIPDDD DLPTAEELED
WIEDVLSGKI NTEDDDEDDD DDDNSDEEDN DDSDDDDDE*

speed

0.20 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

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM063884)
known disease mutation: rs17612 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:116280877A>TN/A show variant in all transcripts IGV

HGNC symbol

CASQ2

Ensembl transcript ID

ENST00000456138

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.30526T>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.411	1
	3.758	1
(flanking)	4.52	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

5282

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

N/A

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

N/A

position of start ATG in wt / mu cDNA

174 / 174

chromosome

strand

-1

last intron/exon boundary

975

theoretical NMD boundary in CDS

751

length of CDS

987

coding sequence (CDS) position

N/A

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

N/A

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

30526

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

116280877

original gDNA sequence snippet

CATTGAAGACTACATCAAACTCATTGGCTTTTTCAAGAGTG

altered gDNA sequence snippet

CATTGAAGACTACATCAAACACATTGGCTTTTTCAAGAGTG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MKRTHLFIVG IYFLSSCRAE EGLNFPTYDG KDRVVSLSEK NFKQVLKKYD LLCLYYHEPV
SSDKVTQKQF QLKEIVLELV AQVLEHKAIG FVMVDAKKEA KLAKKLDYKA FEEAAEHFQP
YIKFFATFDK GVAKKLSLKM NEVDFYEPFM DEPIAIPNKP YTEEELVEFV KEHQRPTLRR
LRPEEMFETW EDDLNGIHIV AFAEKSDPDG YEFLEILKQV ARDNTDNPDL SILWIDPDDF
PLLVAYWEKT FKIDLFRPQI GVVNVTDADS VWMEIPDDDD LPTAEELEDW IEDVLSGKIN
TEDDDEDDDD DDNSDEEDND DSDDDDDE*

mutated AA sequence

N/A

speed

0.59 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems