mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.99999999963628 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM001057)
known disease mutation: rs1644 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:19568310A>GN/A show variant in all transcripts IGV

HGNC symbol

ALDH3A2

Ensembl transcript ID

ENST00000571163

Genbank transcript ID

N/A

UniProt peptide

P51648

alteration type

single base exchange

alteration region

CDS

DNA changes

c.176A>G
cDNA.176A>G
g.16862A>G

AA changes

N59S Score: 46 explain score(s)

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

frameshift

known variant

Reference ID: rs72547575

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

known disease mutation: rs1644 (pathogenic for Sjögren-Larsson syndrome|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM001057)

known disease mutation at this position, please check HGMD for details (HGMD ID CM001057)
known disease mutation at this position, please check HGMD for details (HGMD ID CM001057)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.546	1
	4.546	1
(flanking)	0.271	0.999

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	16861	wt: 0.9724 / mu: 0.9984 (marginal change - not scored)	wt: CAGGCAATGACGTCA mu: CAGGCAGTGACGTCA	GGCA\|atga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000008872

386

Mmulatta

all identical

ENSMMUG00000014130

386

Fcatus

all identical

ENSFCAG00000005180

335

Mmusculus

all identical

ENSMUSG00000010025

386

Ggallus

all identical

ENSGALG00000004763

389

Trubripes

all identical

ENSTRUG00000006126

389

Drerio

all identical

ENSDARG00000029381

389

Dmelanogaster

all identical

FBgn0010548

455

Celegans

all identical

T05H4.13

389

Xtropicalis

all identical

ENSXETG00000013484

386

protein features

start (aa)	end (aa)	feature	details
1	463	TOPO_DOM	Cytoplasmic.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

294 / 294

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

98 / 98

position of stopcodon in wt / mu cDNA

294 / 294

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

1 / 1

chromosome

strand

last intron/exon boundary

227

theoretical NMD boundary in CDS

176

length of CDS

294

coding sequence (CDS) position

176

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

176

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

16862

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

19568310

original gDNA sequence snippet

CAGTGGAGGTGTCACAGGCAATGACGTCATTATGCACTTCA

altered gDNA sequence snippet

CAGTGGAGGTGTCACAGGCAGTGACGTCATTATGCACTTCA

original cDNA sequence snippet

CAGTGGAGGTGTCACAGGCAATGACGTCATTATGCACTTCA

altered cDNA sequence snippet

CAGTGGAGGTGTCACAGGCAGTGACGTCATTATGCACTTCA

wildtype AA sequence

MQEEIFGPIL PIVPVKNVDE AINFINEREK PLALYVFSHN HKLIKRMIDE TSSGGVTGND
VIMHFTLNSF PFGGVGRILL KNDPVQPPSA STELFLF*

mutated AA sequence

MQEEIFGPIL PIVPVKNVDE AINFINEREK PLALYVFSHN HKLIKRMIDE TSSGGVTGSD
VIMHFTLNSF PFGGVGRILL KNDPVQPPSA STELFLF*

speed

0.56 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