MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000205557
MT speed 0 s - this script 3.259537 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ABCC6	disease_causing_automatic	0.99999999986541	simple_aae		affected	0	G1302R	single base exchange	rs63749856		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99999999986541 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM014494)
known disease mutation: rs6579 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:16248867C>TN/A show variant in all transcripts IGV

HGNC symbol

ABCC6

Ensembl transcript ID

ENST00000205557

Genbank transcript ID

NM_001171

UniProt peptide

O95255

alteration type

single base exchange

alteration region

CDS

DNA changes

c.3904G>A
cDNA.3934G>A
g.68513G>A

AA changes

G1302R Score: 125 explain score(s)

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

1302

frameshift

known variant

Reference ID: rs63749856

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

known disease mutation: rs6579 (pathogenic for Pseudoxanthoma elasticum, forme fruste|Pseudoxanthoma elasticum|Generalized arterial calcification of infancy 2|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM014494)

known disease mutation at this position, please check HGMD for details (HGMD ID CM014494)
known disease mutation at this position, please check HGMD for details (HGMD ID CM014494)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.491	1
	3.865	0.998
(flanking)	-1.634	0.309

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 marginally increased	68518	wt: 0.9986 / mu: 0.9988 (marginal change - not scored)	wt: GGGGCAGGGAAGTCC mu: AGGGCAGGGAAGTCC	GGCA\|ggga
Donor increased	68514	wt: 0.44 / mu: 0.78	wt: GACCGGGGCAGGGAA mu: GACCAGGGCAGGGAA	CCGG\|ggca
Donor gained	68508	0.56	mu: TGGCAGGACCAGGGC	GCAG\|gacc
Donor gained	68513	0.84	mu: GGACCAGGGCAGGGA	ACCA\|gggc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1302

mutated

not conserved

1302

Ptroglodytes

all identical

ENSPTRG00000007815

1144

Mmulatta

no homologue

Fcatus

all identical

ENSFCAG00000009261

1288

Mmusculus

all identical

ENSMUSG00000030834

1297

Ggallus

all identical

ENSGALG00000006698

1333

Trubripes

all identical

ENSTRUG00000011515

1332

Drerio

all identical

ENSDARG00000016750

1306

Dmelanogaster

all identical

FBgn0032456

1347

Celegans

all identical

F57C12.5

1332

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
1220	1503	TOPO_DOM	Cytoplasmic (By similarity).	lost
1265	1499	DOMAIN	ABC transporter 2.	lost
1299	1306	NP_BIND	ATP 2 (Potential).	lost
1310	1310	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1455	1455	CONFLICT	L -> P (in Ref. 4; AAD51293).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4512 / 4512

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

1504 / 1504

position of stopcodon in wt / mu cDNA

4542 / 4542

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

31 / 31

chromosome

strand

-1

last intron/exon boundary

4434

theoretical NMD boundary in CDS

4353

length of CDS

4512

coding sequence (CDS) position

3904

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

3934

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

68513

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

16248867

original gDNA sequence snippet

TGGGCATCGTTGGCAGGACCGGGGCAGGGAAGTCCTCCCTG

altered gDNA sequence snippet

TGGGCATCGTTGGCAGGACCAGGGCAGGGAAGTCCTCCCTG

original cDNA sequence snippet

TGGGCATCGTTGGCAGGACCGGGGCAGGGAAGTCCTCCCTG

altered cDNA sequence snippet

TGGGCATCGTTGGCAGGACCAGGGCAGGGAAGTCCTCCCTG

wildtype AA sequence

MAAPAEPCAG QGVWNQTEPE PAATSLLSLC FLRTAGVWVP PMYLWVLGPI YLLFIHHHGR
GYLRMSPLFK AKMVLGFALI VLCTSSVAVA LWKIQQGTPE APEFLIHPTV WLTTMSFAVF
LIHTERKKGV QSSGVLFGYW LLCFVLPATN AAQQASGAGF QSDPVRHLST YLCLSLVVAQ
FVLSCLADQP PFFPEDPQQS NPCPETGAAF PSKATFWWVS GLVWRGYRRP LRPKDLWSLG
RENSSEELVS RLEKEWMRNR SAARRHNKAI AFKRKGGSGM KAPETEPFLR QEGSQWRPLL
KAIWQVFHST FLLGTLSLII SDVFRFTVPK LLSLFLEFIG DPKPPAWKGY LLAVLMFLSA
CLQTLFEQQN MYRLKVLQMR LRSAITGLVY RKVLALSSGS RKASAVGDVV NLVSVDVQRL
TESVLYLNGL WLPLVWIVVC FVYLWQLLGP SALTAIAVFL SLLPLNFFIS KKRNHHQEEQ
MRQKDSRARL TSSILRNSKT IKFHGWEGAF LDRVLGIRGQ ELGALRTSGL LFSVSLVSFQ
VSTFLVALVV FAVHTLVAEN AMNAEKAFVT LTVLNILNKA QAFLPFSIHS LVQARVSFDR
LVTFLCLEEV DPGVVDSSSS GSAAGKDCIT IHSATFAWSQ ESPPCLHRIN LTVPQGCLLA
VVGPVGAGKS SLLSALLGEL SKVEGFVSIE GAVAYVPQEA WVQNTSVVEN VCFGQELDPP
WLERVLEACA LQPDVDSFPE GIHTSIGEQG MNLSGGQKQR LSLARAVYRK AAVYLLDDPL
AALDAHVGQH VFNQVIGPGG LLQGTTRILV THALHILPQA DWIIVLANGA IAEMGSYQEL
LQRKGALMCL LDQARQPGDR GEGETEPGTS TKDPRGTSAG RRPELRRERS IKSVPEKDRT
TSEAQTEVPL DDPDRAGWPA GKDSIQYGRV KATVHLAYLR AVGTPLCLYA LFLFLCQQVA
SFCRGYWLSL WADDPAVGGQ QTQAALRGGI FGLLGCLQAI GLFASMAAVL LGGARASRLL
FQRLLWDVVR SPISFFERTP IGHLLNRFSK ETDTVDVDIP DKLRSLLMYA FGLLEVSLVV
AVATPLATVA ILPLFLLYAG FQSLYVVSSC QLRRLESASY SSVCSHMAET FQGSTVVRAF
RTQAPFVAQN NARVDESQRI SFPRLVADRW LAANVELLGN GLVFAAATCA VLSKAHLSAG
LVGFSVSAAL QVTQTLQWVV RNWTDLENSI VSVERMQDYA WTPKEAPWRL PTCAAQPPWP
QGGQIEFRDF GLRYRPELPL AVQGVSFKIH AGEKVGIVGR TGAGKSSLAS GLLRLQEAAE
GGIWIDGVPI AHVGLHTLRS RISIIPQDPI LFPGSLRMNL DLLQEHSDEA IWAALETVQL
KALVASLPGQ LQYKCADRGE DLSVGQKQLL CLARALLRKT QILILDEATA AVDPGTELQM
QAMLGSWFAQ CTVLLIAHRL RSVMDCARVL VMDKGQVAES GSPAQLLAQK GLFYRLAQES
GLV*

mutated AA sequence

MAAPAEPCAG QGVWNQTEPE PAATSLLSLC FLRTAGVWVP PMYLWVLGPI YLLFIHHHGR
GYLRMSPLFK AKMVLGFALI VLCTSSVAVA LWKIQQGTPE APEFLIHPTV WLTTMSFAVF
LIHTERKKGV QSSGVLFGYW LLCFVLPATN AAQQASGAGF QSDPVRHLST YLCLSLVVAQ
FVLSCLADQP PFFPEDPQQS NPCPETGAAF PSKATFWWVS GLVWRGYRRP LRPKDLWSLG
RENSSEELVS RLEKEWMRNR SAARRHNKAI AFKRKGGSGM KAPETEPFLR QEGSQWRPLL
KAIWQVFHST FLLGTLSLII SDVFRFTVPK LLSLFLEFIG DPKPPAWKGY LLAVLMFLSA
CLQTLFEQQN MYRLKVLQMR LRSAITGLVY RKVLALSSGS RKASAVGDVV NLVSVDVQRL
TESVLYLNGL WLPLVWIVVC FVYLWQLLGP SALTAIAVFL SLLPLNFFIS KKRNHHQEEQ
MRQKDSRARL TSSILRNSKT IKFHGWEGAF LDRVLGIRGQ ELGALRTSGL LFSVSLVSFQ
VSTFLVALVV FAVHTLVAEN AMNAEKAFVT LTVLNILNKA QAFLPFSIHS LVQARVSFDR
LVTFLCLEEV DPGVVDSSSS GSAAGKDCIT IHSATFAWSQ ESPPCLHRIN LTVPQGCLLA
VVGPVGAGKS SLLSALLGEL SKVEGFVSIE GAVAYVPQEA WVQNTSVVEN VCFGQELDPP
WLERVLEACA LQPDVDSFPE GIHTSIGEQG MNLSGGQKQR LSLARAVYRK AAVYLLDDPL
AALDAHVGQH VFNQVIGPGG LLQGTTRILV THALHILPQA DWIIVLANGA IAEMGSYQEL
LQRKGALMCL LDQARQPGDR GEGETEPGTS TKDPRGTSAG RRPELRRERS IKSVPEKDRT
TSEAQTEVPL DDPDRAGWPA GKDSIQYGRV KATVHLAYLR AVGTPLCLYA LFLFLCQQVA
SFCRGYWLSL WADDPAVGGQ QTQAALRGGI FGLLGCLQAI GLFASMAAVL LGGARASRLL
FQRLLWDVVR SPISFFERTP IGHLLNRFSK ETDTVDVDIP DKLRSLLMYA FGLLEVSLVV
AVATPLATVA ILPLFLLYAG FQSLYVVSSC QLRRLESASY SSVCSHMAET FQGSTVVRAF
RTQAPFVAQN NARVDESQRI SFPRLVADRW LAANVELLGN GLVFAAATCA VLSKAHLSAG
LVGFSVSAAL QVTQTLQWVV RNWTDLENSI VSVERMQDYA WTPKEAPWRL PTCAAQPPWP
QGGQIEFRDF GLRYRPELPL AVQGVSFKIH AGEKVGIVGR TRAGKSSLAS GLLRLQEAAE
GGIWIDGVPI AHVGLHTLRS RISIIPQDPI LFPGSLRMNL DLLQEHSDEA IWAALETVQL
KALVASLPGQ LQYKCADRGE DLSVGQKQLL CLARALLRKT QILILDEATA AVDPGTELQM
QAMLGSWFAQ CTVLLIAHRL RSVMDCARVL VMDKGQVAES GSPAQLLAQK GLFYRLAQES
GLV*

speed

1.20 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

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

Problems