mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.998905949641069 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM940043)
known disease mutation: rs13669 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:21900187G>AN/A show variant in all transcripts IGV

HGNC symbol

ALPL

Ensembl transcript ID

ENST00000374840

Genbank transcript ID

NM_000478

UniProt peptide

P05186

alteration type

single base exchange

alteration region

CDS

DNA changes

c.892G>A
cDNA.1142G>A
g.64330G>A

AA changes

E298K Score: 56 explain score(s)

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

298

frameshift

known variant

Reference ID: rs121918017

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

known disease mutation: rs13669 (pathogenic for Infantile hypophosphatasia) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940043)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940043)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940043)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.178	0.998
	3.111	1
(flanking)	3.878	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
Donor increased	64334	wt: 0.25 / mu: 0.59	wt: CGAGCTGAACAGGAA mu: CAAGCTGAACAGGAA	AGCT\|gaac
Donor increased	64326	wt: 0.47 / mu: 0.96	wt: ATGCAGTACGAGCTG mu: ATGCAGTACAAGCTG	GCAG\|tacg
Donor increased	64331	wt: 0.83 / mu: 0.93	wt: GTACGAGCTGAACAG mu: GTACAAGCTGAACAG	ACGA\|gctg
Donor gained	64325	0.33	mu: CATGCAGTACAAGCT	TGCA\|gtac

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

298

mutated

all conserved

298

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000002217

298

Fcatus

all identical

ENSFCAG00000002960

298

Mmusculus

all identical

ENSMUSG00000028766

298

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000004463

299

Drerio

all identical

ENSDARG00000015546

335

Dmelanogaster

not conserved

FBgn0043791

333

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
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

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1575 / 1575

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

525 / 525

position of stopcodon in wt / mu cDNA

1825 / 1825

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

251 / 251

chromosome

strand

last intron/exon boundary

1560

theoretical NMD boundary in CDS

1259

length of CDS

1575

coding sequence (CDS) position

892

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

1142

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

64330

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

21900187

original gDNA sequence snippet

AGCCAGGGGACATGCAGTACGAGCTGAACAGGAACAACGTG

altered gDNA sequence snippet

AGCCAGGGGACATGCAGTACAAGCTGAACAGGAACAACGTG

original cDNA sequence snippet

AGCCAGGGGACATGCAGTACGAGCTGAACAGGAACAACGTG

altered cDNA sequence snippet

AGCCAGGGGACATGCAGTACAAGCTGAACAGGAACAACGTG

wildtype AA sequence

MISPFLVLAI GTCLTNSLVP EKEKDPKYWR DQAQETLKYA LELQKLNTNV AKNVIMFLGD
GMGVSTVTAA RILKGQLHHN PGEETRLEMD KFPFVALSKT YNTNAQVPDS AGTATAYLCG
VKANEGTVGV SAATERSRCN TTQGNEVTSI LRWAKDAGKS VGIVTTTRVN HATPSAAYAH
SADRDWYSDN EMPPEALSQG CKDIAYQLMH NIRDIDVIMG GGRKYMYPKN KTDVEYESDE
KARGTRLDGL DLVDTWKSFK PRYKHSHFIW NRTELLTLDP HNVDYLLGLF EPGDMQYELN
RNNVTDPSLS EMVVVAIQIL RKNPKGFFLL VEGGRIDHGH HEGKAKQALH EAVEMDRAIG
QAGSLTSSED TLTVVTADHS HVFTFGGYTP RGNSIFGLAP MLSDTDKKPF TAILYGNGPG
YKVVGGEREN VSMVDYAHNN YQAQSAVPLR HETHGGEDVA VFSKGPMAHL LHGVHEQNYV
PHVMAYAACI GANLGHCAPA SSAGSLAAGP LLLALALYPL SVLF*

mutated AA sequence

MISPFLVLAI GTCLTNSLVP EKEKDPKYWR DQAQETLKYA LELQKLNTNV AKNVIMFLGD
GMGVSTVTAA RILKGQLHHN PGEETRLEMD KFPFVALSKT YNTNAQVPDS AGTATAYLCG
VKANEGTVGV SAATERSRCN TTQGNEVTSI LRWAKDAGKS VGIVTTTRVN HATPSAAYAH
SADRDWYSDN EMPPEALSQG CKDIAYQLMH NIRDIDVIMG GGRKYMYPKN KTDVEYESDE
KARGTRLDGL DLVDTWKSFK PRYKHSHFIW NRTELLTLDP HNVDYLLGLF EPGDMQYKLN
RNNVTDPSLS EMVVVAIQIL RKNPKGFFLL VEGGRIDHGH HEGKAKQALH EAVEMDRAIG
QAGSLTSSED TLTVVTADHS HVFTFGGYTP RGNSIFGLAP MLSDTDKKPF TAILYGNGPG
YKVVGGEREN VSMVDYAHNN YQAQSAVPLR HETHGGEDVA VFSKGPMAHL LHGVHEQNYV
PHVMAYAACI GANLGHCAPA SSAGSLAAGP LLLALALYPL SVLF*

speed

1.32 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