MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000308664
Querying Taster for transcript #2: ENST00000539276
Querying Taster for transcript #3: ENST00000395494
MT speed 0 s - this script 2.494988 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ATP2A2	disease_causing_automatic	0.999999999778069	simple_aae		affected	0	G742R	single base exchange	rs121912736		show file
ATP2A2	disease_causing_automatic	0.999999999873954	simple_aae		affected	0	G769R	single base exchange	rs121912736		show file
ATP2A2	disease_causing_automatic	0.999999999873954	simple_aae		affected	0	G769R	single base exchange	rs121912736		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999778069 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM003130)
known disease mutation at this position (HGMD CM990254)
known disease mutation: rs17798 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:110780240G>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.2224G>A
cDNA.2787G>A
g.61680G>A

AA changes

G742R Score: 125 explain score(s)

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

742

frameshift

known variant

Reference ID: rs121912736
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs17798 (pathogenic for Darier disease, segmental|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM990254)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990254)
known disease mutation at this position, please check HGMD for details (HGMD ID CM003130)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990254)
known disease mutation at this position, please check HGMD for details (HGMD ID CM003130)
known disease mutation at this position, please check HGMD for details (HGMD ID CM003130)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990254)
known disease mutation at this position, please check HGMD for details (HGMD ID CM003130)
known disease mutation at this position, please check HGMD for details (HGMD ID CM003130)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990254)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.171	0.967
	6.108	1
(flanking)	6.108	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
Acc marginally increased	61680	wt: 0.4187 / mu: 0.4540 (marginal change - not scored)	wt: ACCTCATCTCGTCCAACGTCGGGGAAGTTGTCTGGTAGGTC mu: ACCTCATCTCGTCCAACGTCAGGGAAGTTGTCTGGTAGGTC	gtcg\|GGGA
Acc marginally increased	61681	wt: 0.3364 / mu: 0.3523 (marginal change - not scored)	wt: CCTCATCTCGTCCAACGTCGGGGAAGTTGTCTGGTAGGTCT mu: CCTCATCTCGTCCAACGTCAGGGAAGTTGTCTGGTAGGTCT	tcgg\|GGAA
Acc marginally increased	61678	wt: 0.2872 / mu: 0.3045 (marginal change - not scored)	wt: CTACCTCATCTCGTCCAACGTCGGGGAAGTTGTCTGGTAGG mu: CTACCTCATCTCGTCCAACGTCAGGGAAGTTGTCTGGTAGG	acgt\|CGGG
Acc marginally increased	61671	wt: 0.5229 / mu: 0.5322 (marginal change - not scored)	wt: TCATCCGCTACCTCATCTCGTCCAACGTCGGGGAAGTTGTC mu: TCATCCGCTACCTCATCTCGTCCAACGTCAGGGAAGTTGTC	tcgt\|CCAA
Donor marginally increased	61680	wt: 0.9820 / mu: 0.9980 (marginal change - not scored)	wt: ACGTCGGGGAAGTTG mu: ACGTCAGGGAAGTTG	GTCG\|ggga
Donor increased	61676	wt: 0.66 / mu: 0.98	wt: TCCAACGTCGGGGAA mu: TCCAACGTCAGGGAA	CAAC\|gtcg
Donor increased	61671	wt: 0.63 / mu: 0.73	wt: TCTCGTCCAACGTCG mu: TCTCGTCCAACGTCA	TCGT\|ccaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

742

mutated

not conserved

742

Ptroglodytes

all identical

ENSPTRG00000005437

769

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000029467

769

Ggallus

all identical

ENSGALG00000003835

769

Trubripes

all identical

ENSTRUG00000015616

767

Drerio

all identical

ENSDARG00000029439

768

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000002512

785

protein features

start (aa)	end (aa)	feature	details
314	756	TOPO_DOM	Cytoplasmic (By similarity).	lost
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

2224

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

2787

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

61680

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

110780240

original gDNA sequence snippet

ACCTCATCTCGTCCAACGTCGGGGAAGTTGTCTGGTAGGTC

altered gDNA sequence snippet

ACCTCATCTCGTCCAACGTCAGGGAAGTTGTCTGGTAGGTC

original cDNA sequence snippet

ACCTCATCTCGTCCAACGTCGGGGAAGTTGTCTGTATTTTC

altered cDNA sequence snippet

ACCTCATCTCGTCCAACGTCAGGGAAGTTGTCTGTATTTTC

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 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 VREVVCIFLT 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

0.14 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: 0.999999999873954 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM003130)
known disease mutation at this position (HGMD CM990254)
known disease mutation: rs17798 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:110780240G>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.2305G>A
cDNA.2979G>A
g.61680G>A

AA changes

G769R Score: 125 explain score(s)

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

769

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.171	0.967
	6.108	1
(flanking)	6.108	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
Acc marginally increased	61680	wt: 0.4187 / mu: 0.4540 (marginal change - not scored)	wt: ACCTCATCTCGTCCAACGTCGGGGAAGTTGTCTGGTAGGTC mu: ACCTCATCTCGTCCAACGTCAGGGAAGTTGTCTGGTAGGTC	gtcg\|GGGA
Acc marginally increased	61681	wt: 0.3364 / mu: 0.3523 (marginal change - not scored)	wt: CCTCATCTCGTCCAACGTCGGGGAAGTTGTCTGGTAGGTCT mu: CCTCATCTCGTCCAACGTCAGGGAAGTTGTCTGGTAGGTCT	tcgg\|GGAA
Acc marginally increased	61678	wt: 0.2872 / mu: 0.3045 (marginal change - not scored)	wt: CTACCTCATCTCGTCCAACGTCGGGGAAGTTGTCTGGTAGG mu: CTACCTCATCTCGTCCAACGTCAGGGAAGTTGTCTGGTAGG	acgt\|CGGG
Acc marginally increased	61671	wt: 0.5229 / mu: 0.5322 (marginal change - not scored)	wt: TCATCCGCTACCTCATCTCGTCCAACGTCGGGGAAGTTGTC mu: TCATCCGCTACCTCATCTCGTCCAACGTCAGGGAAGTTGTC	tcgt\|CCAA
Donor marginally increased	61680	wt: 0.9820 / mu: 0.9980 (marginal change - not scored)	wt: ACGTCGGGGAAGTTG mu: ACGTCAGGGAAGTTG	GTCG\|ggga
Donor increased	61676	wt: 0.66 / mu: 0.98	wt: TCCAACGTCGGGGAA mu: TCCAACGTCAGGGAA	CAAC\|gtcg
Donor increased	61671	wt: 0.63 / mu: 0.73	wt: TCTCGTCCAACGTCG mu: TCTCGTCCAACGTCA	TCGT\|ccaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

769

mutated

not conserved

769

Ptroglodytes

all identical

ENSPTRG00000005437

769

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000029467

769

Ggallus

all identical

ENSGALG00000003835

769

Trubripes

all identical

ENSTRUG00000015616

767

Drerio

all identical

ENSDARG00000029439

768

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000002512

785

protein features

start (aa)	end (aa)	feature	details
757	776	TRANSMEM	Helical; Name=5; (By similarity).	lost
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	TRANSMEM	Helical; Name=6; (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)
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

2305

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

2979

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

61680

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

110780240

original gDNA sequence snippet

ACCTCATCTCGTCCAACGTCGGGGAAGTTGTCTGGTAGGTC

altered gDNA sequence snippet

ACCTCATCTCGTCCAACGTCAGGGAAGTTGTCTGGTAGGTC

original cDNA sequence snippet

ACCTCATCTCGTCCAACGTCGGGGAAGTTGTCTGTATTTTC

altered cDNA sequence snippet

ACCTCATCTCGTCCAACGTCAGGGAAGTTGTCTGTATTTTC

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 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 RYLISSNVRE VVCIFLTAAL
GFPEALIPVQ LLWVNLVTDG LPATALGFNP PDLDIMNKPP RNPKEPLISG WLFFRYLAIG
CYVGAATVGA AAWWFIAADG GPRVSFYQLS HFLQCKEDNP DFEGVDCAIF ESPYPMTMAL
SVLVTIEMCN ALNSLSENQS LLRMPPWENI WLVGSICLSM SLHFLILYVE PLPLIFQITP
LNVTQWLMVL KISLPVILMD ETLKFVARNY LEPAILE*

speed

0.19 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999873954 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM003130)
known disease mutation at this position (HGMD CM990254)
known disease mutation: rs17798 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:110780240G>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.2305G>A
cDNA.2414G>A
g.61680G>A

AA changes

G769R Score: 125 explain score(s)

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

769

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.171	0.967
	6.108	1
(flanking)	6.108	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
Acc marginally increased	61680	wt: 0.4187 / mu: 0.4540 (marginal change - not scored)	wt: ACCTCATCTCGTCCAACGTCGGGGAAGTTGTCTGGTAGGTC mu: ACCTCATCTCGTCCAACGTCAGGGAAGTTGTCTGGTAGGTC	gtcg\|GGGA
Acc marginally increased	61681	wt: 0.3364 / mu: 0.3523 (marginal change - not scored)	wt: CCTCATCTCGTCCAACGTCGGGGAAGTTGTCTGGTAGGTCT mu: CCTCATCTCGTCCAACGTCAGGGAAGTTGTCTGGTAGGTCT	tcgg\|GGAA
Acc marginally increased	61678	wt: 0.2872 / mu: 0.3045 (marginal change - not scored)	wt: CTACCTCATCTCGTCCAACGTCGGGGAAGTTGTCTGGTAGG mu: CTACCTCATCTCGTCCAACGTCAGGGAAGTTGTCTGGTAGG	acgt\|CGGG
Acc marginally increased	61671	wt: 0.5229 / mu: 0.5322 (marginal change - not scored)	wt: TCATCCGCTACCTCATCTCGTCCAACGTCGGGGAAGTTGTC mu: TCATCCGCTACCTCATCTCGTCCAACGTCAGGGAAGTTGTC	tcgt\|CCAA
Donor marginally increased	61680	wt: 0.9820 / mu: 0.9980 (marginal change - not scored)	wt: ACGTCGGGGAAGTTG mu: ACGTCAGGGAAGTTG	GTCG\|ggga
Donor increased	61676	wt: 0.66 / mu: 0.98	wt: TCCAACGTCGGGGAA mu: TCCAACGTCAGGGAA	CAAC\|gtcg
Donor increased	61671	wt: 0.63 / mu: 0.73	wt: TCTCGTCCAACGTCG mu: TCTCGTCCAACGTCA	TCGT\|ccaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

769

mutated

not conserved

769

Ptroglodytes

all identical

ENSPTRG00000005437

769

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000029467

769

Ggallus

all identical

ENSGALG00000003835

769

Trubripes

all identical

ENSTRUG00000015616

767

Drerio

all identical

ENSDARG00000029439

768

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000002512

785

protein features

start (aa)	end (aa)	feature	details
757	776	TRANSMEM	Helical; Name=5; (By similarity).	lost
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	TRANSMEM	Helical; Name=6; (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)
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

2305

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

2414

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

61680

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

110780240

original gDNA sequence snippet

ACCTCATCTCGTCCAACGTCGGGGAAGTTGTCTGGTAGGTC

altered gDNA sequence snippet

ACCTCATCTCGTCCAACGTCAGGGAAGTTGTCTGGTAGGTC

original cDNA sequence snippet

ACCTCATCTCGTCCAACGTCGGGGAAGTTGTCTGTATTTTC

altered cDNA sequence snippet

ACCTCATCTCGTCCAACGTCAGGGAAGTTGTCTGTATTTTC

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 LEPGKECVQP ATKSCSFSAC TDGISWPFVL
LIMPLVIWVY STDTNFSDMF WS*

mutated 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 RYLISSNVRE VVCIFLTAAL
GFPEALIPVQ LLWVNLVTDG LPATALGFNP PDLDIMNKPP RNPKEPLISG WLFFRYLAIG
CYVGAATVGA AAWWFIAADG GPRVSFYQLS HFLQCKEDNP DFEGVDCAIF ESPYPMTMAL
SVLVTIEMCN ALNSLSENQS LLRMPPWENI WLVGSICLSM SLHFLILYVE PLPLIFQITP
LNVTQWLMVL KISLPVILMD ETLKFVARNY LEPGKECVQP ATKSCSFSAC TDGISWPFVL
LIMPLVIWVY STDTNFSDMF WS*

speed

0.21 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

Problems