mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999999998153 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM041672)
known disease mutation: rs2563 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:77823770C>TN/A show variant in all transcripts IGV

HGNC symbol

ALG8

Ensembl transcript ID

ENST00000299626

Genbank transcript ID

NM_024079

UniProt peptide

Q9BVK2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.824G>A
cDNA.896G>A
g.26937G>A

AA changes

G275D Score: 94 explain score(s)

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

275

frameshift

known variant

Reference ID: rs121908294

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation: rs2563 (pathogenic for ALG8-CDG) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM041672)

known disease mutation at this position, please check HGMD for details (HGMD ID CM041672)
known disease mutation at this position, please check HGMD for details (HGMD ID CM041672)

regulatory features

Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
PU1, Transcription Factor, PU1 Transcription Factor Binding
SP1, Transcription Factor, SP1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.141	1
	5.632	1
(flanking)	5.632	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	26931	wt: 0.9692 / mu: 0.9783 (marginal change - not scored)	wt: TTCCCGACTCTTTCCTTTCAAGAGGGGCCTCTGTCATGCAT mu: TTCCCGACTCTTTCCTTTCAAGAGGGACCTCTGTCATGCAT	tcaa\|GAGG
Donor increased	26933	wt: 0.76 / mu: 0.97	wt: TCAAGAGGGGCCTCT mu: TCAAGAGGGACCTCT	AAGA\|gggg
Donor marginally increased	26942	wt: 0.9344 / mu: 0.9702 (marginal change - not scored)	wt: GCCTCTGTCATGCAT mu: ACCTCTGTCATGCAT	CTCT\|gtca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

275

mutated

not conserved

275

Ptroglodytes

all identical

ENSPTRG00000004112

275

Mmulatta

all identical

ENSMMUG00000017472

186

Fcatus

no alignment

ENSFCAG00000007455

n/a

Mmusculus

all identical

ENSMUSG00000035704

275

Ggallus

all identical

ENSGALG00000019042

275

Trubripes

all identical

ENSTRUG00000004967

269

Drerio

all identical

ENSDARG00000044627

272

Dmelanogaster

all identical

FBgn0029906

252

Celegans

all identical

C08H9.3

265

Xtropicalis

all identical

ENSXETG00000010450

291

protein features

start (aa)	end (aa)	feature	details
334	354	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
368	388	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
389	409	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
427	449	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
461	481	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
478	478	CONFLICT	F -> Y (in Ref. 1; CAA12176).	might get lost (downstream of altered splice site)
488	508	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
503	503	CONFLICT	I -> V (in Ref. 2; AAH01133).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1581 / 1581

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

527 / 527

position of stopcodon in wt / mu cDNA

1653 / 1653

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

73 / 73

chromosome

strand

-1

last intron/exon boundary

1422

theoretical NMD boundary in CDS

1299

length of CDS

1581

coding sequence (CDS) position

824

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

896

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

26937

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

77823770

original gDNA sequence snippet

ACTCTTTCCTTTCAAGAGGGGCCTCTGTCATGCATATTGGG

altered gDNA sequence snippet

ACTCTTTCCTTTCAAGAGGGACCTCTGTCATGCATATTGGG

original cDNA sequence snippet

ACTCTTTCCTTTCAAGAGGGGCCTCTGTCATGCATATTGGG

altered cDNA sequence snippet

ACTCTTTCCTTTCAAGAGGGACCTCTGTCATGCATATTGGG

wildtype AA sequence

MAALTIATGT GNWFSALALG VTLLKCLLIP TYHSTDFEVH RNWLAITHSL PISQWYYEAT
SEWTLDYPPF FAWFEYILSH VAKYFDQEML NVHNLNYSSS RTLLFQRFSV IFMDVLFVYA
VRECCKCIDG KKVGKELTEK PKFILSVLLL WNFGLLIVDH IHFQYNGFLF GLMLLSIARL
FQKRHMEGAF LFAVLLHFKH IYLYVAPAYG VYLLRSYCFT ANKPDGSIRW KSFSFVRVIS
LGLVVFLVSA LSLGPFLALN QLPQVFSRLF PFKRGLCHAY WAPNFWALYN ALDKVLSVIG
LKLKFLDPNN IPKASMTSGL VQQFQHTVLP SVTPLATLIC TLIAILPSIF CLWFKPQGPR
GFLRCLTLCA LSSFMFGWHV HEKAILLAIL PMSLLSVGKA GDASIFLILT TTGHYSLFPL
LFTAPELPIK ILLMLLFTIY SISSLKTLFR KEKPLFNWME TFYLLGLGPL EVCCEFVFPF
TSWKVKYPFI PLLLTSVYCA VGITYAWFKL YVSVLIDSAI GKTKKQ*

mutated AA sequence

MAALTIATGT GNWFSALALG VTLLKCLLIP TYHSTDFEVH RNWLAITHSL PISQWYYEAT
SEWTLDYPPF FAWFEYILSH VAKYFDQEML NVHNLNYSSS RTLLFQRFSV IFMDVLFVYA
VRECCKCIDG KKVGKELTEK PKFILSVLLL WNFGLLIVDH IHFQYNGFLF GLMLLSIARL
FQKRHMEGAF LFAVLLHFKH IYLYVAPAYG VYLLRSYCFT ANKPDGSIRW KSFSFVRVIS
LGLVVFLVSA LSLGPFLALN QLPQVFSRLF PFKRDLCHAY WAPNFWALYN ALDKVLSVIG
LKLKFLDPNN IPKASMTSGL VQQFQHTVLP SVTPLATLIC TLIAILPSIF CLWFKPQGPR
GFLRCLTLCA LSSFMFGWHV HEKAILLAIL PMSLLSVGKA GDASIFLILT TTGHYSLFPL
LFTAPELPIK ILLMLLFTIY SISSLKTLFR KEKPLFNWME TFYLLGLGPL EVCCEFVFPF
TSWKVKYPFI PLLLTSVYCA VGITYAWFKL YVSVLIDSAI GKTKKQ*

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