mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (explain)

Summary

known as potential disease variant: rs13663 (probable pathogenic)
known disease mutation at this position (HGMD CM172367)
known disease mutation at this position (HGMD CM920018)
known disease mutation at this position (HGMD CM921023)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:21887619C>TN/A show variant in all transcripts IGV

HGNC symbol

ALPL

Ensembl transcript ID

ENST00000539907

Genbank transcript ID

NM_001177520

UniProt peptide

P05186

alteration type

single base exchange

alteration region

intron

DNA changes

g.51762C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121918001
Allele 'T' was neither found in ExAC nor 1000G.
known as potential disease variant: rs13663 (probable pathogenic for Infantile hypophosphatasia) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM172367)

known disease mutation at this position, please check HGMD for details (HGMD ID CM172367)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920018)

known disease mutation at this position, please check HGMD for details (HGMD ID CM172367)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920018)
known disease mutation at this position, please check HGMD for details (HGMD ID CM921023)

known disease mutation at this position, please check HGMD for details (HGMD ID CM172367)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920018)
known disease mutation at this position, please check HGMD for details (HGMD ID CM921023)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920018)

known disease mutation at this position, please check HGMD for details (HGMD ID CM172367)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920018)
known disease mutation at this position, please check HGMD for details (HGMD ID CM921023)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920018)
known disease mutation at this position, please check HGMD for details (HGMD ID CM921023)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.2	0.998
	5.234	1
(flanking)	5.234	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 increased	51771	wt: 0.47 / mu: 0.58	wt: TGACGGCTGCCCGCATCCTCAAGGGTCAGCTCCACCACAAC mu: TGACGGCTGCCTGCATCCTCAAGGGTCAGCTCCACCACAAC	ctca\|AGGG
Acc increased	51772	wt: 0.31 / mu: 0.38	wt: GACGGCTGCCCGCATCCTCAAGGGTCAGCTCCACCACAACC mu: GACGGCTGCCTGCATCCTCAAGGGTCAGCTCCACCACAACC	tcaa\|GGGT

distance from splice site

381

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
29	29	CONFLICT	W -> A (in Ref. 10; AA sequence).	might get lost (downstream of altered splice site)
60	60	METAL	Zinc 2 (Potential).	might get lost (downstream of altered splice site)
60	60	METAL	Magnesium (Potential).	might get lost (downstream of altered splice site)
104	104	CONFLICT	N -> K (in Ref. 3; CAA32376).	might get lost (downstream of altered splice site)
110	110	ACT_SITE	Phosphoserine intermediate.	might get lost (downstream of altered splice site)
140	140	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
173	173	METAL	Magnesium (Potential).	might get lost (downstream of altered splice site)
230	230	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
271	271	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
303	303	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
332	332	METAL	Magnesium (Potential).	might get lost (downstream of altered splice site)
337	337	METAL	Zinc 1 (Potential).	might get lost (downstream of altered splice site)
341	341	METAL	Zinc 1 (Potential).	might get lost (downstream of altered splice site)
361	361	CONFLICT	Q -> H (in Ref. 1; BAA32129).	might get lost (downstream of altered splice site)
378	378	METAL	Zinc 2 (Potential).	might get lost (downstream of altered splice site)
379	379	METAL	Zinc 2 (Potential).	might get lost (downstream of altered splice site)
430	430	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
446	446	CONFLICT	A -> P (in Ref. 1; BAA32129).	might get lost (downstream of altered splice site)
454	454	METAL	Zinc 1 (Potential).	might get lost (downstream of altered splice site)
502	502	LIPID	GPI-anchor amidated serine (Probable).	might get lost (downstream of altered splice site)
503	524	PROPEP	Removed in mature form (Probable). /FTId=PRO_0000024024.	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

208 / 208

chromosome

strand

last intron/exon boundary

1286

theoretical NMD boundary in CDS

1028

length of CDS

1344

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)

51762

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

21887619

original gDNA sequence snippet

TCTCCACAGTGACGGCTGCCCGCATCCTCAAGGGTCAGCTC

altered gDNA sequence snippet

TCTCCACAGTGACGGCTGCCTGCATCCTCAAGGGTCAGCTC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MPWSFRSSTP TWLRMSSCSW EMTYNTNAQV PDSAGTATAY LCGVKANEGT VGVSAATERS
RCNTTQGNEV TSILRWAKDA GKSVGIVTTT RVNHATPSAA YAHSADRDWY SDNEMPPEAL
SQGCKDIAYQ LMHNIRDIDV IMGGGRKYMY PKNKTDVEYE SDEKARGTRL DGLDLVDTWK
SFKPRYKHSH FIWNRTELLT LDPHNVDYLL GLFEPGDMQY ELNRNNVTDP SLSEMVVVAI
QILRKNPKGF FLLVEGGRID HGHHEGKAKQ ALHEAVEMDR AIGQAGSLTS SEDTLTVVTA
DHSHVFTFGG YTPRGNSIFG LAPMLSDTDK KPFTAILYGN GPGYKVVGGE RENVSMVDYA
HNNYQAQSAV PLRHETHGGE DVAVFSKGPM AHLLHGVHEQ NYVPHVMAYA ACIGANLGHC
APASSAGSLA AGPLLLALAL YPLSVLF*

mutated AA sequence

N/A

speed

0.55 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