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 CM920021)
known disease mutation: rs13664 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:21900176A>CN/A show variant in all transcripts IGV

HGNC symbol

ALPL

Ensembl transcript ID

ENST00000374830

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.64319A>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121918002

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

known disease mutation: rs13664 (pathogenic for Infantile hypophosphatasia|Adult hypophosphatasia|Childhood hypophosphatasia|Hypophosphatasia|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920021)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920021)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920021)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.679	1
	3.878	1
(flanking)	0.965	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	64314	wt: 0.2939 / mu: 0.3341 (marginal change - not scored)	wt: TCCTCAGGTCTCTTCGAGCCAGGGGACATGCAGTACGAGCT mu: TCCTCAGGTCTCTTCGAGCCAGGGGCCATGCAGTACGAGCT	gcca\|GGGG
Donor marginally increased	64310	wt: 0.9845 / mu: 0.9945 (marginal change - not scored)	wt: CTTCGAGCCAGGGGA mu: CTTCGAGCCAGGGGC	TCGA\|gcca
Donor marginally increased	64317	wt: 0.9286 / mu: 0.9491 (marginal change - not scored)	wt: CCAGGGGACATGCAG mu: CCAGGGGCCATGCAG	AGGG\|gaca

distance from splice site

2050

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

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)

64319

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

21900176

original gDNA sequence snippet

AGGTCTCTTCGAGCCAGGGGACATGCAGTACGAGCTGAACA

altered gDNA sequence snippet

AGGTCTCTTCGAGCCAGGGGCCATGCAGTACGAGCTGAACA

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

0.59 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