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 CM960047)
known disease mutation at this position (HGMD CP015757)
known disease mutation: rs13673 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:21900274T>CN/A show variant in all transcripts IGV

HGNC symbol

ALPL

Ensembl transcript ID

ENST00000374830

Genbank transcript ID

N/A

UniProt peptide

P05186

alteration type

single base exchange

alteration region

intron

DNA changes

g.64417T>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121918010

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	7	7

known disease mutation: rs13673 (pathogenic for Infantile hypophosphatasia|Adult hypophosphatasia|Hypophosphatasia|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960047)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960047)
known disease mutation at this position, please check HGMD for details (HGMD ID CP015757)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960047)
known disease mutation at this position, please check HGMD for details (HGMD ID CP015757)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960047)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960047)
known disease mutation at this position, please check HGMD for details (HGMD ID CP015757)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960047)
known disease mutation at this position, please check HGMD for details (HGMD ID CP015757)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Non-Gene Associated, Regulatory Feature, Non-Gene associated regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.126	1
	4.06	1
(flanking)	4.06	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 -21) |

effect	gDNA position	score	detection sequence	exon-intron border
Acc marginally increased	64424	wt: 0.4956 / mu: 0.5343 (marginal change - not scored)	wt: GAACCCCAAAGGCTTCTTCTTGCTGGTGGAAGGTAGGGACC mu: GAACCCCAAAGGCCTCTTCTTGCTGGTGGAAGGTAGGGACC	tctt\|GCTG
Donor increased	64409	wt: 0.21 / mu: 0.38	wt: GAACCCCAAAGGCTT mu: GAACCCCAAAGGCCT	ACCC\|caaa
Donor marginally increased	64408	wt: 0.9912 / mu: 0.9931 (marginal change - not scored)	wt: AGAACCCCAAAGGCT mu: AGAACCCCAAAGGCC	AACC\|ccaa

distance from splice site

1952

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	17	SIGNAL		might get lost (downstream of altered splice site)
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

138 / 138

chromosome

strand

last intron/exon boundary

385

theoretical NMD boundary in CDS

197

length of CDS

513

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)

64417

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

21900274

original gDNA sequence snippet

TGCGGAAGAACCCCAAAGGCTTCTTCTTGCTGGTGGAAGGT

altered gDNA sequence snippet

TGCGGAAGAACCCCAAAGGCCTCTTCTTGCTGGTGGAAGGT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MDRAIGQAGS LTSSEDTLTV VTADHSHVFT FGGYTPRGNS IFGLAPMLSD TDKKPFTAIL
YGNGPGYKVV GGERENVSMV DYAHNNYQAQ SAVPLRHETH GGEDVAVFSK GPMAHLLHGV
HEQNYVPHVM AYAACIGANL GHCAPASSAG SLAAGPLLLA LALYPLSVLF *

mutated AA sequence

N/A

speed

1.02 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