MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 4 transcript(s)...
Querying Taster for transcript #1: ENST00000552636
Querying Taster for transcript #2: ENST00000308664
Querying Taster for transcript #3: ENST00000539276
Querying Taster for transcript #4: ENST00000395494
MT speed 0 s - this script 4.116558 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ATP2A2	disease_causing_automatic	0.99999931522037	simple_aae		affected	0	G23E	single base exchange	rs28929478		show file
ATP2A2	disease_causing_automatic	0.99999931522037	simple_aae		affected	0	G23E	single base exchange	rs28929478		show file
ATP2A2	disease_causing_automatic	0.99999931522037	simple_aae		affected	0	G23E	single base exchange	rs28929478		show file
ATP2A2	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs28929478		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99999931522037 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM990225)
known disease mutation: rs17789 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:110719662G>AN/A show variant in all transcripts IGV

HGNC symbol

ATP2A2

Ensembl transcript ID

ENST00000308664

Genbank transcript ID

NM_001681

UniProt peptide

P16615

alteration type

single base exchange

alteration region

CDS

DNA changes

c.68G>A
cDNA.742G>A
g.1102G>A

AA changes

G23E Score: 98 explain score(s)

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

frameshift

known variant

Reference ID: rs28929478
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs17789 (pathogenic for Keratosis follicularis|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM990225)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990225)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990225)

regulatory features

Cmyc, Transcription Factor, Cmyc TF binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K5ac, Histone, Histone 4 Lysine 5 Acetylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.224	1
	3.278	1
(flanking)	0.832	1

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	1102	wt: 0.86 / mu: 0.98	wt: TACGGGGCTGAGCCT mu: TACGGAGCTGAGCCT	CGGG\|gctg
Donor increased	1107	wt: 0.22 / mu: 0.40	wt: GGCTGAGCCTGGAAC mu: AGCTGAGCCTGGAAC	CTGA\|gcct

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000005437

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000029467

Ggallus

all identical

ENSGALG00000003835

Trubripes

all identical

ENSTRUG00000015616

Drerio

all identical

ENSDARG00000029439

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000002512

protein features

start (aa)	end (aa)	feature	details
1	48	TOPO_DOM	Cytoplasmic (By similarity).	lost
49	69	TRANSMEM	Helical; Name=1; (By similarity).	might get lost (downstream of altered splice site)
70	89	TOPO_DOM	Lumenal (By similarity).	might get lost (downstream of altered splice site)
90	110	TRANSMEM	Helical; Name=2; (By similarity).	might get lost (downstream of altered splice site)
111	253	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)
143	143	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) (By similarity).	might get lost (downstream of altered splice site)
254	273	TRANSMEM	Helical; Name=3; (By similarity).	might get lost (downstream of altered splice site)
274	295	TOPO_DOM	Lumenal (By similarity).	might get lost (downstream of altered splice site)
294	294	MOD_RES	Nitrated tyrosine.	might get lost (downstream of altered splice site)
295	295	MOD_RES	Nitrated tyrosine.	might get lost (downstream of altered splice site)
296	313	TRANSMEM	Helical; Name=4; (By similarity).	might get lost (downstream of altered splice site)
304	304	METAL	Calcium 2; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
305	305	METAL	Calcium 2; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
307	307	METAL	Calcium 2; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
309	309	METAL	Calcium 2 (By similarity).	might get lost (downstream of altered splice site)
314	756	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)
351	351	ACT_SITE	4-aspartylphosphate intermediate (By similarity).	might get lost (downstream of altered splice site)
370	400	REGION	Interacts with phospholamban 1 (By similarity).	might get lost (downstream of altered splice site)
464	464	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
537	537	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
575	594	REGION	Interacts with HAX1.	might get lost (downstream of altered splice site)
663	663	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
702	702	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
706	706	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
757	776	TRANSMEM	Helical; Name=5; (By similarity).	might get lost (downstream of altered splice site)
767	767	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
770	770	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
777	786	TOPO_DOM	Lumenal (By similarity).	might get lost (downstream of altered splice site)
787	807	REGION	Interacts with phospholamban 2 (By similarity).	might get lost (downstream of altered splice site)
787	807	TRANSMEM	Helical; Name=6; (By similarity).	might get lost (downstream of altered splice site)
795	795	METAL	Calcium 2 (By similarity).	might get lost (downstream of altered splice site)
798	798	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
799	799	METAL	Calcium 2 (By similarity).	might get lost (downstream of altered splice site)
799	799	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
808	827	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)
828	850	TRANSMEM	Helical; Name=7; (By similarity).	might get lost (downstream of altered splice site)
851	896	TOPO_DOM	Lumenal (By similarity).	might get lost (downstream of altered splice site)
897	916	TRANSMEM	Helical; Name=8; (By similarity).	might get lost (downstream of altered splice site)
907	907	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
917	929	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)
930	948	TRANSMEM	Helical; Name=9; (By similarity).	might get lost (downstream of altered splice site)
949	963	TOPO_DOM	Lumenal (By similarity).	might get lost (downstream of altered splice site)
964	984	TRANSMEM	Helical; Name=10; (By similarity).	might get lost (downstream of altered splice site)
985	1042	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2994 / 2994

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

998 / 998

position of stopcodon in wt / mu cDNA

3668 / 3668

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

675 / 675

chromosome

strand

last intron/exon boundary

3655

theoretical NMD boundary in CDS

2930

length of CDS

2994

coding sequence (CDS) position

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

742

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

1102

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

110719662

original gDNA sequence snippet

CGGCGTCAACGAGAGTACGGGGCTGAGCCTGGAACAGGTCA

altered gDNA sequence snippet

CGGCGTCAACGAGAGTACGGAGCTGAGCCTGGAACAGGTCA

original cDNA sequence snippet

CGGCGTCAACGAGAGTACGGGGCTGAGCCTGGAACAGGTCA

altered cDNA sequence snippet

CGGCGTCAACGAGAGTACGGAGCTGAGCCTGGAACAGGTCA

wildtype AA sequence

MENAHTKTVE EVLGHFGVNE STGLSLEQVK KLKERWGSNE LPAEEGKTLL ELVIEQFEDL
LVRILLLAAC ISFVLAWFEE GEETITAFVE PFVILLILVA NAIVGVWQER NAENAIEALK
EYEPEMGKVY RQDRKSVQRI KAKDIVPGDI VEIAVGDKVP ADIRLTSIKS TTLRVDQSIL
TGESVSVIKH TDPVPDPRAV NQDKKNMLFS GTNIAAGKAM GVVVATGVNT EIGKIRDEMV
ATEQERTPLQ QKLDEFGEQL SKVISLICIA VWIINIGHFN DPVHGGSWIR GAIYYFKIAV
ALAVAAIPEG LPAVITTCLA LGTRRMAKKN AIVRSLPSVE TLGCTSVICS DKTGTLTTNQ
MSVCRMFILD RVEGDTCSLN EFTITGSTYA PIGEVHKDDK PVNCHQYDGL VELATICALC
NDSALDYNEA KGVYEKVGEA TETALTCLVE KMNVFDTELK GLSKIERANA CNSVIKQLMK
KEFTLEFSRD RKSMSVYCTP NKPSRTSMSK MFVKGAPEGV IDRCTHIRVG STKVPMTSGV
KQKIMSVIRE WGSGSDTLRC LALATHDNPL RREEMHLEDS ANFIKYETNL TFVGCVGMLD
PPRIEVASSV KLCRQAGIRV IMITGDNKGT AVAICRRIGI FGQDEDVTSK AFTGREFDEL
NPSAQRDACL NARCFARVEP SHKSKIVEFL QSFDEITAMT GDGVNDAPAL KKAEIGIAMG
SGTAVAKTAS EMVLADDNFS TIVAAVEEGR AIYNNMKQFI RYLISSNVGE VVCIFLTAAL
GFPEALIPVQ LLWVNLVTDG LPATALGFNP PDLDIMNKPP RNPKEPLISG WLFFRYLAIG
CYVGAATVGA AAWWFIAADG GPRVSFYQLS HFLQCKEDNP DFEGVDCAIF ESPYPMTMAL
SVLVTIEMCN ALNSLSENQS LLRMPPWENI WLVGSICLSM SLHFLILYVE PLPLIFQITP
LNVTQWLMVL KISLPVILMD ETLKFVARNY LEPAILE*

mutated AA sequence

MENAHTKTVE EVLGHFGVNE STELSLEQVK KLKERWGSNE LPAEEGKTLL ELVIEQFEDL
LVRILLLAAC ISFVLAWFEE GEETITAFVE PFVILLILVA NAIVGVWQER NAENAIEALK
EYEPEMGKVY RQDRKSVQRI KAKDIVPGDI VEIAVGDKVP ADIRLTSIKS TTLRVDQSIL
TGESVSVIKH TDPVPDPRAV NQDKKNMLFS GTNIAAGKAM GVVVATGVNT EIGKIRDEMV
ATEQERTPLQ QKLDEFGEQL SKVISLICIA VWIINIGHFN DPVHGGSWIR GAIYYFKIAV
ALAVAAIPEG LPAVITTCLA LGTRRMAKKN AIVRSLPSVE TLGCTSVICS DKTGTLTTNQ
MSVCRMFILD RVEGDTCSLN EFTITGSTYA PIGEVHKDDK PVNCHQYDGL VELATICALC
NDSALDYNEA KGVYEKVGEA TETALTCLVE KMNVFDTELK GLSKIERANA CNSVIKQLMK
KEFTLEFSRD RKSMSVYCTP NKPSRTSMSK MFVKGAPEGV IDRCTHIRVG STKVPMTSGV
KQKIMSVIRE WGSGSDTLRC LALATHDNPL RREEMHLEDS ANFIKYETNL TFVGCVGMLD
PPRIEVASSV KLCRQAGIRV IMITGDNKGT AVAICRRIGI FGQDEDVTSK AFTGREFDEL
NPSAQRDACL NARCFARVEP SHKSKIVEFL QSFDEITAMT GDGVNDAPAL KKAEIGIAMG
SGTAVAKTAS EMVLADDNFS TIVAAVEEGR AIYNNMKQFI RYLISSNVGE VVCIFLTAAL
GFPEALIPVQ LLWVNLVTDG LPATALGFNP PDLDIMNKPP RNPKEPLISG WLFFRYLAIG
CYVGAATVGA AAWWFIAADG GPRVSFYQLS HFLQCKEDNP DFEGVDCAIF ESPYPMTMAL
SVLVTIEMCN ALNSLSENQS LLRMPPWENI WLVGSICLSM SLHFLILYVE PLPLIFQITP
LNVTQWLMVL KISLPVILMD ETLKFVARNY LEPAILE*

speed

0.66 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: 0.99999931522037 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM990225)
known disease mutation: rs17789 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:110719662G>AN/A show variant in all transcripts IGV

HGNC symbol

ATP2A2

Ensembl transcript ID

ENST00000539276

Genbank transcript ID

NM_170665

UniProt peptide

P16615

alteration type

single base exchange

alteration region

CDS

DNA changes

c.68G>A
cDNA.177G>A
g.1102G>A

AA changes

G23E Score: 98 explain score(s)

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

frameshift

known variant

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.224	1
	3.278	1
(flanking)	0.832	1

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	1102	wt: 0.86 / mu: 0.98	wt: TACGGGGCTGAGCCT mu: TACGGAGCTGAGCCT	CGGG\|gctg
Donor increased	1107	wt: 0.22 / mu: 0.40	wt: GGCTGAGCCTGGAAC mu: AGCTGAGCCTGGAAC	CTGA\|gcct

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000005437

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000029467

Ggallus

all identical

ENSGALG00000003835

Trubripes

all identical

ENSTRUG00000015616

Drerio

all identical

ENSDARG00000029439

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000002512

protein features

start (aa)	end (aa)	feature	details
1	48	TOPO_DOM	Cytoplasmic (By similarity).	lost
49	69	TRANSMEM	Helical; Name=1; (By similarity).	might get lost (downstream of altered splice site)
70	89	TOPO_DOM	Lumenal (By similarity).	might get lost (downstream of altered splice site)
90	110	TRANSMEM	Helical; Name=2; (By similarity).	might get lost (downstream of altered splice site)
111	253	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)
143	143	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) (By similarity).	might get lost (downstream of altered splice site)
254	273	TRANSMEM	Helical; Name=3; (By similarity).	might get lost (downstream of altered splice site)
274	295	TOPO_DOM	Lumenal (By similarity).	might get lost (downstream of altered splice site)
294	294	MOD_RES	Nitrated tyrosine.	might get lost (downstream of altered splice site)
295	295	MOD_RES	Nitrated tyrosine.	might get lost (downstream of altered splice site)
296	313	TRANSMEM	Helical; Name=4; (By similarity).	might get lost (downstream of altered splice site)
304	304	METAL	Calcium 2; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
305	305	METAL	Calcium 2; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
307	307	METAL	Calcium 2; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
309	309	METAL	Calcium 2 (By similarity).	might get lost (downstream of altered splice site)
314	756	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)
351	351	ACT_SITE	4-aspartylphosphate intermediate (By similarity).	might get lost (downstream of altered splice site)
370	400	REGION	Interacts with phospholamban 1 (By similarity).	might get lost (downstream of altered splice site)
464	464	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
537	537	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
575	594	REGION	Interacts with HAX1.	might get lost (downstream of altered splice site)
663	663	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
702	702	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
706	706	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
757	776	TRANSMEM	Helical; Name=5; (By similarity).	might get lost (downstream of altered splice site)
767	767	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
770	770	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
777	786	TOPO_DOM	Lumenal (By similarity).	might get lost (downstream of altered splice site)
787	807	REGION	Interacts with phospholamban 2 (By similarity).	might get lost (downstream of altered splice site)
787	807	TRANSMEM	Helical; Name=6; (By similarity).	might get lost (downstream of altered splice site)
795	795	METAL	Calcium 2 (By similarity).	might get lost (downstream of altered splice site)
798	798	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
799	799	METAL	Calcium 2 (By similarity).	might get lost (downstream of altered splice site)
799	799	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
808	827	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)
828	850	TRANSMEM	Helical; Name=7; (By similarity).	might get lost (downstream of altered splice site)
851	896	TOPO_DOM	Lumenal (By similarity).	might get lost (downstream of altered splice site)
897	916	TRANSMEM	Helical; Name=8; (By similarity).	might get lost (downstream of altered splice site)
907	907	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
917	929	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)
930	948	TRANSMEM	Helical; Name=9; (By similarity).	might get lost (downstream of altered splice site)
949	963	TOPO_DOM	Lumenal (By similarity).	might get lost (downstream of altered splice site)
964	984	TRANSMEM	Helical; Name=10; (By similarity).	might get lost (downstream of altered splice site)
985	1042	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3129 / 3129

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

1043 / 1043

position of stopcodon in wt / mu cDNA

3238 / 3238

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

110 / 110

chromosome

strand

last intron/exon boundary

2969

theoretical NMD boundary in CDS

2809

length of CDS

3129

coding sequence (CDS) position

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

177

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

1102

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

110719662

original gDNA sequence snippet

CGGCGTCAACGAGAGTACGGGGCTGAGCCTGGAACAGGTCA

altered gDNA sequence snippet

CGGCGTCAACGAGAGTACGGAGCTGAGCCTGGAACAGGTCA

original cDNA sequence snippet

CGGCGTCAACGAGAGTACGGGGCTGAGCCTGGAACAGGTCA

altered cDNA sequence snippet

CGGCGTCAACGAGAGTACGGAGCTGAGCCTGGAACAGGTCA

wildtype AA sequence

mutated AA sequence

speed

1.30 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99999931522037 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM990225)
known disease mutation: rs17789 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:110719662G>AN/A show variant in all transcripts IGV

HGNC symbol

ATP2A2

Ensembl transcript ID

ENST00000395494

Genbank transcript ID

N/A

UniProt peptide

P16615

alteration type

single base exchange

alteration region

CDS

DNA changes

c.68G>A
cDNA.631G>A
g.1102G>A

AA changes

G23E Score: 98 explain score(s)

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

frameshift

known variant

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.224	1
	3.278	1
(flanking)	0.832	1

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	1102	wt: 0.86 / mu: 0.98	wt: TACGGGGCTGAGCCT mu: TACGGAGCTGAGCCT	CGGG\|gctg
Donor increased	1107	wt: 0.22 / mu: 0.40	wt: GGCTGAGCCTGGAAC mu: AGCTGAGCCTGGAAC	CTGA\|gcct

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000005437

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000029467

Ggallus

all identical

ENSGALG00000003835

Trubripes

all identical

ENSTRUG00000015616

Drerio

all identical

ENSDARG00000029439

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000002512

protein features

start (aa)	end (aa)	feature	details
1	48	TOPO_DOM	Cytoplasmic (By similarity).	lost
49	69	TRANSMEM	Helical; Name=1; (By similarity).	might get lost (downstream of altered splice site)
70	89	TOPO_DOM	Lumenal (By similarity).	might get lost (downstream of altered splice site)
90	110	TRANSMEM	Helical; Name=2; (By similarity).	might get lost (downstream of altered splice site)
111	253	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)
143	143	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) (By similarity).	might get lost (downstream of altered splice site)
254	273	TRANSMEM	Helical; Name=3; (By similarity).	might get lost (downstream of altered splice site)
274	295	TOPO_DOM	Lumenal (By similarity).	might get lost (downstream of altered splice site)
294	294	MOD_RES	Nitrated tyrosine.	might get lost (downstream of altered splice site)
295	295	MOD_RES	Nitrated tyrosine.	might get lost (downstream of altered splice site)
296	313	TRANSMEM	Helical; Name=4; (By similarity).	might get lost (downstream of altered splice site)
304	304	METAL	Calcium 2; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
305	305	METAL	Calcium 2; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
307	307	METAL	Calcium 2; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
309	309	METAL	Calcium 2 (By similarity).	might get lost (downstream of altered splice site)
314	756	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)
351	351	ACT_SITE	4-aspartylphosphate intermediate (By similarity).	might get lost (downstream of altered splice site)
370	400	REGION	Interacts with phospholamban 1 (By similarity).	might get lost (downstream of altered splice site)
464	464	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
537	537	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
575	594	REGION	Interacts with HAX1.	might get lost (downstream of altered splice site)
663	663	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
702	702	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
706	706	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
757	776	TRANSMEM	Helical; Name=5; (By similarity).	might get lost (downstream of altered splice site)
767	767	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
770	770	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
777	786	TOPO_DOM	Lumenal (By similarity).	might get lost (downstream of altered splice site)
787	807	REGION	Interacts with phospholamban 2 (By similarity).	might get lost (downstream of altered splice site)
787	807	TRANSMEM	Helical; Name=6; (By similarity).	might get lost (downstream of altered splice site)
795	795	METAL	Calcium 2 (By similarity).	might get lost (downstream of altered splice site)
798	798	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
799	799	METAL	Calcium 2 (By similarity).	might get lost (downstream of altered splice site)
799	799	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
808	827	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)
828	850	TRANSMEM	Helical; Name=7; (By similarity).	might get lost (downstream of altered splice site)
851	896	TOPO_DOM	Lumenal (By similarity).	might get lost (downstream of altered splice site)
897	916	TRANSMEM	Helical; Name=8; (By similarity).	might get lost (downstream of altered splice site)
907	907	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
917	929	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)
930	948	TRANSMEM	Helical; Name=9; (By similarity).	might get lost (downstream of altered splice site)
949	963	TOPO_DOM	Lumenal (By similarity).	might get lost (downstream of altered splice site)
964	984	TRANSMEM	Helical; Name=10; (By similarity).	might get lost (downstream of altered splice site)
985	1042	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3048 / 3048

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

1016 / 1016

position of stopcodon in wt / mu cDNA

3611 / 3611

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

564 / 564

chromosome

strand

last intron/exon boundary

3342

theoretical NMD boundary in CDS

2728

length of CDS

3048

coding sequence (CDS) position

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

631

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

1102

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

110719662

original gDNA sequence snippet

CGGCGTCAACGAGAGTACGGGGCTGAGCCTGGAACAGGTCA

altered gDNA sequence snippet

CGGCGTCAACGAGAGTACGGAGCTGAGCCTGGAACAGGTCA

original cDNA sequence snippet

CGGCGTCAACGAGAGTACGGGGCTGAGCCTGGAACAGGTCA

altered cDNA sequence snippet

CGGCGTCAACGAGAGTACGGAGCTGAGCCTGGAACAGGTCA

wildtype AA sequence

MENAHTKTVE EVLGHFGVNE STGLSLEQVK KLKERWGSNE LPAEEGKTLL ELVIEQFEDL
LVRILLLAAC ISFVLAWFEE GEETITAFVE PFVILLILVA NAIVGVWQER NAENAIEALK
EYEPEMGKVY RQDRKSVQRI KAKDIVPGDI VEIAGESVSV IKHTDPVPDP RAVNQDKKNM
LFSGTNIAAG KAMGVVVATG VNTEIGKIRD EMVATEQERT PLQQKLDEFG EQLSKVISLI
CIAVWIINIG HFNDPVHGGS WIRGAIYYFK IAVALAVAAI PEGLPAVITT CLALGTRRMA
KKNAIVRSLP SVETLGCTSV ICSDKTGTLT TNQMSVCRMF ILDRVEGDTC SLNEFTITGS
TYAPIGEVHK DDKPVNCHQY DGLVELATIC ALCNDSALDY NEAKGVYEKV GEATETALTC
LVEKMNVFDT ELKGLSKIER ANACNSVIKQ LMKKEFTLEF SRDRKSMSVY CTPNKPSRTS
MSKMFVKGAP EGVIDRCTHI RVGSTKVPMT SGVKQKIMSV IREWGSGSDT LRCLALATHD
NPLRREEMHL EDSANFIKYE TNLTFVGCVG MLDPPRIEVA SSVKLCRQAG IRVIMITGDN
KGTAVAICRR IGIFGQDEDV TSKAFTGREF DELNPSAQRD ACLNARCFAR VEPSHKSKIV
EFLQSFDEIT AMTGDGVNDA PALKKAEIGI AMGSGTAVAK TASEMVLADD NFSTIVAAVE
EGRAIYNNMK QFIRYLISSN VGEVVCIFLT AALGFPEALI PVQLLWVNLV TDGLPATALG
FNPPDLDIMN KPPRNPKEPL ISGWLFFRYL AIGCYVGAAT VGAAAWWFIA ADGGPRVSFY
QLSHFLQCKE DNPDFEGVDC AIFESPYPMT MALSVLVTIE MCNALNSLSE NQSLLRMPPW
ENIWLVGSIC LSMSLHFLIL YVEPLPLIFQ ITPLNVTQWL MVLKISLPVI LMDETLKFVA
RNYLEPGKEC VQPATKSCSF SACTDGISWP FVLLIMPLVI WVYSTDTNFS DMFWS*

mutated AA sequence

MENAHTKTVE EVLGHFGVNE STELSLEQVK KLKERWGSNE LPAEEGKTLL ELVIEQFEDL
LVRILLLAAC ISFVLAWFEE GEETITAFVE PFVILLILVA NAIVGVWQER NAENAIEALK
EYEPEMGKVY RQDRKSVQRI KAKDIVPGDI VEIAGESVSV IKHTDPVPDP RAVNQDKKNM
LFSGTNIAAG KAMGVVVATG VNTEIGKIRD EMVATEQERT PLQQKLDEFG EQLSKVISLI
CIAVWIINIG HFNDPVHGGS WIRGAIYYFK IAVALAVAAI PEGLPAVITT CLALGTRRMA
KKNAIVRSLP SVETLGCTSV ICSDKTGTLT TNQMSVCRMF ILDRVEGDTC SLNEFTITGS
TYAPIGEVHK DDKPVNCHQY DGLVELATIC ALCNDSALDY NEAKGVYEKV GEATETALTC
LVEKMNVFDT ELKGLSKIER ANACNSVIKQ LMKKEFTLEF SRDRKSMSVY CTPNKPSRTS
MSKMFVKGAP EGVIDRCTHI RVGSTKVPMT SGVKQKIMSV IREWGSGSDT LRCLALATHD
NPLRREEMHL EDSANFIKYE TNLTFVGCVG MLDPPRIEVA SSVKLCRQAG IRVIMITGDN
KGTAVAICRR IGIFGQDEDV TSKAFTGREF DELNPSAQRD ACLNARCFAR VEPSHKSKIV
EFLQSFDEIT AMTGDGVNDA PALKKAEIGI AMGSGTAVAK TASEMVLADD NFSTIVAAVE
EGRAIYNNMK QFIRYLISSN VGEVVCIFLT AALGFPEALI PVQLLWVNLV TDGLPATALG
FNPPDLDIMN KPPRNPKEPL ISGWLFFRYL AIGCYVGAAT VGAAAWWFIA ADGGPRVSFY
QLSHFLQCKE DNPDFEGVDC AIFESPYPMT MALSVLVTIE MCNALNSLSE NQSLLRMPPW
ENIWLVGSIC LSMSLHFLIL YVEPLPLIFQ ITPLNVTQWL MVLKISLPVI LMDETLKFVA
RNYLEPGKEC VQPATKSCSF SACTDGISWP FVLLIMPLVI WVYSTDTNFS DMFWS*

speed

0.58 s

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 CM990225)
known disease mutation: rs17789 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:110719662G>AN/A show variant in all transcripts IGV

HGNC symbol

ATP2A2

Ensembl transcript ID

ENST00000552636

Genbank transcript ID

N/A

UniProt peptide

P16615

alteration type

single base exchange

alteration region

intron

DNA changes

g.1102G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.224	1
	3.278	1
(flanking)	0.832	1

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

splice sites

splice site change before start ATG (at aa -60) |

effect	gDNA position	score	detection sequence	exon-intron border
Donor increased	1102	wt: 0.86 / mu: 0.98	wt: TACGGGGCTGAGCCT mu: TACGGAGCTGAGCCT	CGGG\|gctg
Donor increased	1107	wt: 0.22 / mu: 0.40	wt: GGCTGAGCCTGGAAC mu: AGCTGAGCCTGGAAC	CTGA\|gcct

distance from splice site

747

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	48	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)
49	69	TRANSMEM	Helical; Name=1; (By similarity).	might get lost (downstream of altered splice site)
70	89	TOPO_DOM	Lumenal (By similarity).	might get lost (downstream of altered splice site)
90	110	TRANSMEM	Helical; Name=2; (By similarity).	might get lost (downstream of altered splice site)
111	253	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)
143	143	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) (By similarity).	might get lost (downstream of altered splice site)
254	273	TRANSMEM	Helical; Name=3; (By similarity).	might get lost (downstream of altered splice site)
274	295	TOPO_DOM	Lumenal (By similarity).	might get lost (downstream of altered splice site)
294	294	MOD_RES	Nitrated tyrosine.	might get lost (downstream of altered splice site)
295	295	MOD_RES	Nitrated tyrosine.	might get lost (downstream of altered splice site)
296	313	TRANSMEM	Helical; Name=4; (By similarity).	might get lost (downstream of altered splice site)
304	304	METAL	Calcium 2; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
305	305	METAL	Calcium 2; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
307	307	METAL	Calcium 2; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
309	309	METAL	Calcium 2 (By similarity).	might get lost (downstream of altered splice site)
314	756	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)
351	351	ACT_SITE	4-aspartylphosphate intermediate (By similarity).	might get lost (downstream of altered splice site)
370	400	REGION	Interacts with phospholamban 1 (By similarity).	might get lost (downstream of altered splice site)
464	464	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
537	537	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
575	594	REGION	Interacts with HAX1.	might get lost (downstream of altered splice site)
663	663	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
702	702	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
706	706	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
757	776	TRANSMEM	Helical; Name=5; (By similarity).	might get lost (downstream of altered splice site)
767	767	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
770	770	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
777	786	TOPO_DOM	Lumenal (By similarity).	might get lost (downstream of altered splice site)
787	807	REGION	Interacts with phospholamban 2 (By similarity).	might get lost (downstream of altered splice site)
787	807	TRANSMEM	Helical; Name=6; (By similarity).	might get lost (downstream of altered splice site)
795	795	METAL	Calcium 2 (By similarity).	might get lost (downstream of altered splice site)
798	798	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
799	799	METAL	Calcium 2 (By similarity).	might get lost (downstream of altered splice site)
799	799	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
808	827	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)
828	850	TRANSMEM	Helical; Name=7; (By similarity).	might get lost (downstream of altered splice site)
851	896	TOPO_DOM	Lumenal (By similarity).	might get lost (downstream of altered splice site)
897	916	TRANSMEM	Helical; Name=8; (By similarity).	might get lost (downstream of altered splice site)
907	907	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
917	929	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)
930	948	TRANSMEM	Helical; Name=9; (By similarity).	might get lost (downstream of altered splice site)
949	963	TOPO_DOM	Lumenal (By similarity).	might get lost (downstream of altered splice site)
964	984	TRANSMEM	Helical; Name=10; (By similarity).	might get lost (downstream of altered splice site)
985	1042	TOPO_DOM	Cytoplasmic (By similarity).	might get lost (downstream of altered splice site)

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

393 / 393

chromosome

strand

last intron/exon boundary

416

theoretical NMD boundary in CDS

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

length of CDS

135

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)

1102

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

110719662

original gDNA sequence snippet

CGGCGTCAACGAGAGTACGGGGCTGAGCCTGGAACAGGTCA

altered gDNA sequence snippet

CGGCGTCAACGAGAGTACGGAGCTGAGCCTGGAACAGGTCA

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MQLWVYGRKE MLKMPSKPLR NMSLKWAKCI DRTERVCSGL KLKT*

mutated AA sequence

N/A

speed

0.50 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems