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: ENST00000360971
MT speed 0 s - this script 2.259587 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ENPP1	disease_causing_automatic	0.971931435192148	simple_aae		affected	0	L579F	single base exchange	rs121918024		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.971931435192148 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM031970)
known disease mutation: rs13588 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:132198145G>CN/A show variant in all transcripts IGV

HGNC symbol

ENPP1

Ensembl transcript ID

ENST00000360971

Genbank transcript ID

NM_006208

UniProt peptide

P22413

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1737G>C
cDNA.1757G>C
g.68990G>C

AA changes

L579F Score: 22 explain score(s)

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

579

frameshift

known variant

Reference ID: rs121918024

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation: rs13588 (pathogenic for Arterial calcification, generalized, of infancy, 1) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM031970)

known disease mutation at this position, please check HGMD for details (HGMD ID CM031970)
known disease mutation at this position, please check HGMD for details (HGMD ID CM031970)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.976	0.997
	0.307	0.642
(flanking)	1.084	0.568

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	68981	wt: 0.62 / mu: 0.75	wt: GATTTACTGAATTTG mu: GATTTACTGAATTTC	TTTA\|ctga
Acc gained	68996	0.34	mu: GATTTACTGAATTTCACACCGGCTCCTAATAACGGAACTCA	accg\|GCTC
Acc gained	68992	0.53	mu: TGCAGATTTACTGAATTTCACACCGGCTCCTAATAACGGAA	tcac\|ACCG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

579

mutated

not conserved

579

Ptroglodytes

all identical

ENSPTRG00000018603

579

Mmulatta

all identical

ENSMMUG00000014151

579

Fcatus

not conserved

ENSFCAG00000014133

520

Mmusculus

all identical

ENSMUSG00000037370

561

Ggallus

all identical

ENSGALG00000002896

576

Trubripes

all conserved

ENSTRUG00000017715

385

Drerio

all conserved

ENSDARG00000005789

546

Dmelanogaster

no homologue

Celegans

all identical

C27A7.3

427

Xtropicalis

all conserved

ENSXETG00000030043

476

protein features

start (aa)	end (aa)	feature	details
98	925	TOPO_DOM	Extracellular (Potential).	lost
191	591	REGION	Phosphodiesterase.	lost
585	585	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
643	643	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
654	925	REGION	Nuclease.	might get lost (downstream of altered splice site)
700	700	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
731	731	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
748	748	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
868	868	DISULFID	By similarity.	might get lost (downstream of altered splice site)
915	915	SITE	Essential for catalytic activity (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

2778 / 2778

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

926 / 926

position of stopcodon in wt / mu cDNA

2798 / 2798

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

21 / 21

chromosome

strand

last intron/exon boundary

2628

theoretical NMD boundary in CDS

2557

length of CDS

2778

coding sequence (CDS) position

1737

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

1757

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

68990

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

132198145

original gDNA sequence snippet

TATGCAGATTTACTGAATTTGACACCGGCTCCTAATAACGG

altered gDNA sequence snippet

TATGCAGATTTACTGAATTTCACACCGGCTCCTAATAACGG

original cDNA sequence snippet

ATGTGTGATTTACTGAATTTGACACCGGCTCCTAATAACGG

altered cDNA sequence snippet

ATGTGTGATTTACTGAATTTCACACCGGCTCCTAATAACGG

wildtype AA sequence

MERDGCAGGG SRGGEGGRAP REGPAGNGRD RGRSHAAEAP GDPQAAASLL APMDVGEEPL
EKAARARTAK DPNTYKVLSL VLSVCVLTTI LGCIFGLKPS CAKEVKSCKG RCFERTFGNC
RCDAACVELG NCCLDYQETC IEPEHIWTCN KFRCGEKRLT RSLCACSDDC KDKGDCCINY
SSVCQGEKSW VEEPCESINE PQCPAGFETP PTLLFSLDGF RAEYLHTWGG LLPVISKLKK
CGTYTKNMRP VYPTKTFPNH YSIVTGLYPE SHGIIDNKMY DPKMNASFSL KSKEKFNPEW
YKGEPIWVTA KYQGLKSGTF FWPGSDVEIN GIFPDIYKMY NGSVPFEERI LAVLQWLQLP
KDERPHFYTL YLEEPDSSGH SYGPVSSEVI KALQRVDGMV GMLMDGLKEL NLHRCLNLIL
ISDHGMEQGS CKKYIYLNKY LGDVKNIKVI YGPAARLRPS DVPDKYYSFN YEGIARNLSC
REPNQHFKPY LKHFLPKRLH FAKSDRIEPL TFYLDPQWQL ALNPSERKYC GSGFHGSDNV
FSNMQALFVG YGPGFKHGIE ADTFENIEVY NLMCDLLNLT PAPNNGTHGS LNHLLKNPVY
TPKHPKEVHP LVQCPFTRNP RDNLGCSCNP SILPIEDFQT QFNLTVAEEK IIKHETLPYG
RPRVLQKENT ICLLSQHQFM SGYSQDILMP LWTSYTVDRN DSFSTEDFSN CLYQDFRIPL
SPVHKCSFYK NNTKVSYGFL SPPQLNKNSS GIYSEALLTT NIVPMYQSFQ VIWRYFHDTL
LRKYAEERNG VNVVSGPVFD FDYDGRCDSL ENLRQKRRVI RNQEILIPTH FFIVLTSCKD
TSQTPLHCEN LDTLAFILPH RTDNSESCVH GKHDSSWVEE LLMLHRARIT DVEHITGLSF
YQQRKEPVSD ILKLKTHLPT FSQED*

mutated AA sequence

MERDGCAGGG SRGGEGGRAP REGPAGNGRD RGRSHAAEAP GDPQAAASLL APMDVGEEPL
EKAARARTAK DPNTYKVLSL VLSVCVLTTI LGCIFGLKPS CAKEVKSCKG RCFERTFGNC
RCDAACVELG NCCLDYQETC IEPEHIWTCN KFRCGEKRLT RSLCACSDDC KDKGDCCINY
SSVCQGEKSW VEEPCESINE PQCPAGFETP PTLLFSLDGF RAEYLHTWGG LLPVISKLKK
CGTYTKNMRP VYPTKTFPNH YSIVTGLYPE SHGIIDNKMY DPKMNASFSL KSKEKFNPEW
YKGEPIWVTA KYQGLKSGTF FWPGSDVEIN GIFPDIYKMY NGSVPFEERI LAVLQWLQLP
KDERPHFYTL YLEEPDSSGH SYGPVSSEVI KALQRVDGMV GMLMDGLKEL NLHRCLNLIL
ISDHGMEQGS CKKYIYLNKY LGDVKNIKVI YGPAARLRPS DVPDKYYSFN YEGIARNLSC
REPNQHFKPY LKHFLPKRLH FAKSDRIEPL TFYLDPQWQL ALNPSERKYC GSGFHGSDNV
FSNMQALFVG YGPGFKHGIE ADTFENIEVY NLMCDLLNFT PAPNNGTHGS LNHLLKNPVY
TPKHPKEVHP LVQCPFTRNP RDNLGCSCNP SILPIEDFQT QFNLTVAEEK IIKHETLPYG
RPRVLQKENT ICLLSQHQFM SGYSQDILMP LWTSYTVDRN DSFSTEDFSN CLYQDFRIPL
SPVHKCSFYK NNTKVSYGFL SPPQLNKNSS GIYSEALLTT NIVPMYQSFQ VIWRYFHDTL
LRKYAEERNG VNVVSGPVFD FDYDGRCDSL ENLRQKRRVI RNQEILIPTH FFIVLTSCKD
TSQTPLHCEN LDTLAFILPH RTDNSESCVH GKHDSSWVEE LLMLHRARIT DVEHITGLSF
YQQRKEPVSD ILKLKTHLPT FSQED*

speed

0.15 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
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MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

Problems