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 1.81 s - this script 3.804861 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CASQ2	disease_causing_automatic	0.9999999989977	simple_aae		affected	0	D307H	single base exchange	rs121434549		show file
CASQ2	disease_causing_automatic	0.999999999255148	simple_aae		affected	0	D236H	single base exchange	rs121434549		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.9999999989977 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM013693)
known disease mutation: rs17610 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:116247833C>GN/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.919G>C
cDNA.1159G>C
g.63570G>C

AA changes

D307H Score: 81 explain score(s)

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

307

frameshift

known variant

Reference ID: rs121434549
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs17610 (pathogenic for Ventricular tachycardia, catecholaminergic polymorphic, 2) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM013693)

known disease mutation at this position, please check HGMD for details (HGMD ID CM013693)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013693)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.648	1
	5.615	1
(flanking)	-0.159	0.962

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	63562	wt: 0.28 / mu: 0.55	wt: CATCCTGTGGATCGA mu: CATCCTGTGGATCCA	TCCT\|gtgg
Acc gained	63574	0.36	mu: GAGCATCCTGTGGATCCACCCGGACGACTTTCCTCTGGTGA	accc\|GGAC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

307

mutated

not conserved

307

Ptroglodytes

all identical

ENSPTRG00000001148

307

Mmulatta

all identical

ENSMMUG00000008970

306

Fcatus

all identical

ENSFCAG00000010496

167

Mmusculus

all identical

ENSMUSG00000027861

310

Ggallus

all identical

ENSGALG00000015018

307

Trubripes

no homologue

Drerio

all identical

ENSDARG00000008982

308

Dmelanogaster

no homologue

Celegans

all identical

F40E10.3

317

Xtropicalis

not conserved

ENSXETG00000023738

128

protein features

start (aa)	end (aa)	feature	details
300	307	STRAND		lost
312	320	HELIX		might get lost (downstream of altered splice site)
321	328	STRAND		might get lost (downstream of altered splice site)
330	351	STRAND		might get lost (downstream of altered splice site)
335	335	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
356	361	HELIX		might get lost (downstream of altered splice site)
356	399	COMPBIAS	Asp/Glu-rich (acidic).	might get lost (downstream of altered splice site)
362	369	STRAND		might get lost (downstream of altered splice site)
385	385	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
393	393	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

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

919

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

1159

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

63570

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

116247833

original gDNA sequence snippet

ATCTGAGCATCCTGTGGATCGACCCGGACGACTTTCCTCTG

altered gDNA sequence snippet

ATCTGAGCATCCTGTGGATCCACCCGGACGACTTTCCTCTG

original cDNA sequence snippet

ATCTGAGCATCCTGTGGATCGACCCGGACGACTTTCCTCTG

altered cDNA sequence snippet

ATCTGAGCATCCTGTGGATCCACCCGGACGACTTTCCTCTG

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 IEDYIKLIGF FKSEDSEYYK
AFEEAAEHFQ PYIKFFATFD KGVAKKLSLK MNEVDFYEPF MDEPIAIPNK PYTEEELVEF
VKEHQRPTLR RLRPEEMFET WEDDLNGIHI VAFAEKSDPD GYEFLEILKQ VARDNTDNPD
LSILWIHPDD FPLLVAYWEK TFKIDLFRPQ IGVVNVTDAD SVWMEIPDDD DLPTAEELED
WIEDVLSGKI NTEDDDEDDD DDDNSDEEDN DDSDDDDDE*

speed

0.92 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: simple_aae, prob: 0.999999999255148 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM013693)
known disease mutation: rs17610 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:116247833C>GN/A show variant in all transcripts IGV

HGNC symbol

CASQ2

Ensembl transcript ID

ENST00000456138

Genbank transcript ID

N/A

UniProt peptide

O14958

alteration type

single base exchange

alteration region

CDS

DNA changes

c.706G>C
cDNA.879G>C
g.63570G>C

AA changes

D236H Score: 81 explain score(s)

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

236

frameshift

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)	4.648	1
	5.615	1
(flanking)	-0.159	0.962

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	63562	wt: 0.28 / mu: 0.55	wt: CATCCTGTGGATCGA mu: CATCCTGTGGATCCA	TCCT\|gtgg
Acc gained	63574	0.36	mu: GAGCATCCTGTGGATCCACCCGGACGACTTTCCTCTGGTGA	accc\|GGAC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

236

mutated

not conserved

236

Ptroglodytes

all identical

ENSPTRG00000001148

307

Mmulatta

all identical

ENSMMUG00000008970

307

Fcatus

all identical

ENSFCAG00000010496

167

Mmusculus

all identical

ENSMUSG00000027861

310

Ggallus

all identical

ENSGALG00000015018

307

Trubripes

no homologue

Drerio

all identical

ENSDARG00000008982

308

Dmelanogaster

no homologue

Celegans

all identical

F40E10.3

317

Xtropicalis

not conserved

ENSXETG00000023738

128

protein features

start (aa)	end (aa)	feature	details
229	233	STRAND		might get lost (downstream of altered splice site)
234	243	HELIX		lost
248	252	STRAND		might get lost (downstream of altered splice site)
256	261	HELIX		might get lost (downstream of altered splice site)
262	278	STRAND		might get lost (downstream of altered splice site)
279	294	HELIX		might get lost (downstream of altered splice site)
295	298	STRAND		might get lost (downstream of altered splice site)
300	307	STRAND		might get lost (downstream of altered splice site)
312	320	HELIX		might get lost (downstream of altered splice site)
321	328	STRAND		might get lost (downstream of altered splice site)
330	351	STRAND		might get lost (downstream of altered splice site)
335	335	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
356	361	HELIX		might get lost (downstream of altered splice site)
356	399	COMPBIAS	Asp/Glu-rich (acidic).	might get lost (downstream of altered splice site)
362	369	STRAND		might get lost (downstream of altered splice site)
385	385	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
393	393	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

987 / 987

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

329 / 329

position of stopcodon in wt / mu cDNA

1160 / 1160

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

706

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

879

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

63570

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

116247833

original gDNA sequence snippet

ATCTGAGCATCCTGTGGATCGACCCGGACGACTTTCCTCTG

altered gDNA sequence snippet

ATCTGAGCATCCTGTGGATCCACCCGGACGACTTTCCTCTG

original cDNA sequence snippet

ATCTGAGCATCCTGTGGATCGACCCGGACGACTTTCCTCTG

altered cDNA sequence snippet

ATCTGAGCATCCTGTGGATCCACCCGGACGACTTTCCTCTG

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

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

speed

0.89 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems