mutation t@sting

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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 CM920016)
known disease mutation: rs13667 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:21887155C>TN/A show variant in all transcripts IGV

HGNC symbol

ALPL

Ensembl transcript ID

ENST00000539907

Genbank transcript ID

NM_001177520

UniProt peptide

N/A

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.190C>T
g.51298C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121918005

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

known disease mutation: rs13667 (pathogenic for Infantile hypophosphatasia|Childhood hypophosphatasia|Hypophosphatasia|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920016)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920016)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.863	1
	3.863	0.998
(flanking)	-1.566	0.187

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	51291	wt: 0.9088 / mu: 0.9923 (marginal change - not scored)	wt: GGCGAGACCAAGCGC mu: GGCGAGACCAAGTGC	CGAG\|acca
Donor marginally increased	51302	wt: 0.8397 / mu: 0.8869 (marginal change - not scored)	wt: GCGCAAGAGACACTG mu: GTGCAAGAGACACTG	GCAA\|gaga
Donor marginally increased	51296	wt: 0.3412 / mu: 0.3481 (marginal change - not scored)	wt: GACCAAGCGCAAGAG mu: GACCAAGTGCAAGAG	CCAA\|gcgc

distance from splice site

Kozak consensus sequence altered?

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

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)

190

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

51298

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

21887155

original gDNA sequence snippet

CAAGTACTGGCGAGACCAAGCGCAAGAGACACTGAAATATG

altered gDNA sequence snippet

CAAGTACTGGCGAGACCAAGTGCAAGAGACACTGAAATATG

original cDNA sequence snippet

CAAGTACTGGCGAGACCAAGCGCAAGAGACACTGAAATATG

altered cDNA sequence snippet

CAAGTACTGGCGAGACCAAGTGCAAGAGACACTGAAATATG

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

0.53 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