mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999983985405 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM087940)
known disease mutation: rs2129 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:183963079C>TN/A show variant in all transcripts IGV

HGNC symbol

ALG3

Ensembl transcript ID

ENST00000397676

Genbank transcript ID

NM_005787

UniProt peptide

Q92685

alteration type

single base exchange

alteration region

CDS

DNA changes

c.512G>A
cDNA.543G>A
g.4258G>A

AA changes

R171Q Score: 43 explain score(s)

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

171

frameshift

known variant

Reference ID: rs119103236

database	homozygous (T/T)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	5	5

known disease mutation: rs2129 (pathogenic for ALG3-CDG) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM087940)

known disease mutation at this position, please check HGMD for details (HGMD ID CM087940)
known disease mutation at this position, please check HGMD for details (HGMD ID CM087940)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.092	0.981
	5.685	1
(flanking)	3.016	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	4259	wt: 0.5690 / mu: 0.5755 (marginal change - not scored)	wt: CACTCCATCTTTGTGCTGCGGCTCTTCAATGACCCAGTGGC mu: CACTCCATCTTTGTGCTGCAGCTCTTCAATGACCCAGTGGC	gcgg\|CTCT
Acc marginally increased	4248	wt: 0.8825 / mu: 0.8905 (marginal change - not scored)	wt: CTTACCGTGTCCACTCCATCTTTGTGCTGCGGCTCTTCAAT mu: CTTACCGTGTCCACTCCATCTTTGTGCTGCAGCTCTTCAAT	atct\|TTGT

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

171

mutated

all conserved

171

Ptroglodytes

no homologue

Mmulatta

no alignment

ENSMMUG00000018951

n/a

Fcatus

all identical

ENSFCAG00000016274

171

Mmusculus

all identical

ENSMUSG00000033809

171

Ggallus

all identical

ENSGALG00000008503

109

Trubripes

no homologue

Drerio

all identical

ENSDARG00000053155

165

Dmelanogaster

all identical

FBgn0011297

174

Celegans

all identical

K09E4.2

150

Xtropicalis

all identical

ENSXETG00000017280

173

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1317 / 1317

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

439 / 439

position of stopcodon in wt / mu cDNA

1348 / 1348

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

32 / 32

chromosome

strand

-1

last intron/exon boundary

1186

theoretical NMD boundary in CDS

1104

length of CDS

1317

coding sequence (CDS) position

512

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

543

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

4258

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

183963079

original gDNA sequence snippet

CCACTCCATCTTTGTGCTGCGGCTCTTCAATGACCCAGTGG

altered gDNA sequence snippet

CCACTCCATCTTTGTGCTGCAGCTCTTCAATGACCCAGTGG

original cDNA sequence snippet

CCACTCCATCTTTGTGCTGCGGCTCTTCAATGACCCAGTGG

altered cDNA sequence snippet

CCACTCCATCTTTGTGCTGCAGCTCTTCAATGACCCAGTGG

wildtype AA sequence

MAAGLRKRGR SGSAAQAEGL CKQWLQRAWQ ERRLLLREPR YTLLVAACLC LAEVGITFWV
IHRVAYTEID WKAYMAEVEG VINGTYDYTQ LQGDTGPLVY PAGFVYIFMG LYYATSRGTD
IRMAQNIFAV LYLATLLLVF LIYHQTCKVP PFVFFFMCCA SYRVHSIFVL RLFNDPVAMV
LLFLSINLLL AQRWGWGCCF FSLAVSVKMN VLLFAPGLLF LLLTQFGFRG ALPKLGICAG
LQVVLGLPFL LENPSGYLSR SFDLGRQFLF HWTVNWRFLP EALFLHRAFH LALLTAHLTL
LLLFALCRWH RTGESILSLL RDPSKRKVPP QPLTPNQIVS TLFTSNFIGI CFSRSLHYQF
YVWYFHTLPY LLWAMPARWL THLLRLLVLG LIELSWNTYP STSCSSAALH ICHAVILLQL
WLGPQPFPKS TQHSKKAH*

mutated AA sequence

MAAGLRKRGR SGSAAQAEGL CKQWLQRAWQ ERRLLLREPR YTLLVAACLC LAEVGITFWV
IHRVAYTEID WKAYMAEVEG VINGTYDYTQ LQGDTGPLVY PAGFVYIFMG LYYATSRGTD
IRMAQNIFAV LYLATLLLVF LIYHQTCKVP PFVFFFMCCA SYRVHSIFVL QLFNDPVAMV
LLFLSINLLL AQRWGWGCCF FSLAVSVKMN VLLFAPGLLF LLLTQFGFRG ALPKLGICAG
LQVVLGLPFL LENPSGYLSR SFDLGRQFLF HWTVNWRFLP EALFLHRAFH LALLTAHLTL
LLLFALCRWH RTGESILSLL RDPSKRKVPP QPLTPNQIVS TLFTSNFIGI CFSRSLHYQF
YVWYFHTLPY LLWAMPARWL THLLRLLVLG LIELSWNTYP STSCSSAALH ICHAVILLQL
WLGPQPFPKS TQHSKKAH*

speed

0.94 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