mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999999999958 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM002057)
known disease mutation: rs6617 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:74531952C>TN/A show variant in all transcripts IGV

HGNC symbol

ALDH6A1

Ensembl transcript ID

ENST00000555126

Genbank transcript ID

N/A

UniProt peptide

Q02252

alteration type

single base exchange

alteration region

CDS

DNA changes

c.487G>A
cDNA.883G>A
g.19245G>A

AA changes

G163R Score: 125 explain score(s)

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

163

frameshift

known variant

Reference ID: rs72552258
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs6617 (pathogenic for Methylmalonate semialdehyde dehydrogenase deficiency) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002057)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002057)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002057)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	6.289	1
	6.289	1
(flanking)	0.713	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 marginally increased	19250	wt: 0.3247 / mu: 0.3554 (marginal change - not scored)	wt: GGAACTGCCATCTTC mu: AGAACTGCCATCTTC	AACT\|gcca
Donor increased	19237	wt: 0.43 / mu: 0.63	wt: CCCATATGGAAATGG mu: CCCATATGGAAATAG	CATA\|tgga
Donor increased	19243	wt: 0.49 / mu: 0.74	wt: TGGAAATGGAACTGC mu: TGGAAATAGAACTGC	GAAA\|tgga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

163

mutated

not conserved

163

Ptroglodytes

all identical

ENSPTRG00000006531

405

Mmulatta

all identical

ENSMMUG00000012684

450

Fcatus

all identical

ENSFCAG00000006202

447

Mmusculus

all identical

ENSMUSG00000021238

446

Ggallus

all identical

ENSGALG00000010211

449

Trubripes

all identical

ENSTRUG00000018226

436

Drerio

all identical

ENSDARG00000053485

436

Dmelanogaster

all identical

FBgn0023537

432

Celegans

all identical

F13D12.4

436

Xtropicalis

all identical

ENSXETG00000013304

434

protein features

start (aa)	end (aa)	feature	details
209	213	NP_BIND	NAD (Potential).	might get lost (downstream of altered splice site)
261	266	NP_BIND	NAD (Potential).	might get lost (downstream of altered splice site)
317	317	ACT_SITE	Nucleophile (By similarity).	might get lost (downstream of altered splice site)
331	331	MOD_RES	N6-acetyllysine (By similarity).	might get lost (downstream of altered splice site)
417	417	BINDING	NAD (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

759 / 759

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

253 / 253

position of stopcodon in wt / mu cDNA

1155 / 1155

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

397 / 397

chromosome

strand

-1

last intron/exon boundary

1051

theoretical NMD boundary in CDS

604

length of CDS

759

coding sequence (CDS) position

487

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

883

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

19245

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

74531952

original gDNA sequence snippet

ATAACAACCCATATGGAAATGGAACTGCCATCTTCACCACC

altered gDNA sequence snippet

ATAACAACCCATATGGAAATAGAACTGCCATCTTCACCACC

original cDNA sequence snippet

ATAACAACCCATATGGAAATGGAACTGCCATCTTCACCACC

altered cDNA sequence snippet

ATAACAACCCATATGGAAATAGAACTGCCATCTTCACCACC

wildtype AA sequence

MGAKNHGVVM PDANKENTLN QLVGAAFGAA GQRCMALSTA VLVGEAKKWL PELVEHAKNL
RVNAGDQPGA DLGPLITPQA KERVCNLIDS GTKEGASILL DGRKIKVKGY ENGNFVGPTI
ISNVKPNMTC YKEEIFGPVL VVLETETLDE AIQIVNNNPY GNGTAIFTTN GATARKYAHL
VDVGQVGVNV PIPVPLPMFS FTGSRSSFRG DTNFYGKQGI QFYTQLKTIT SQWKEEDATL
SSPAVVMPTM GR*

mutated AA sequence

MGAKNHGVVM PDANKENTLN QLVGAAFGAA GQRCMALSTA VLVGEAKKWL PELVEHAKNL
RVNAGDQPGA DLGPLITPQA KERVCNLIDS GTKEGASILL DGRKIKVKGY ENGNFVGPTI
ISNVKPNMTC YKEEIFGPVL VVLETETLDE AIQIVNNNPY GNRTAIFTTN GATARKYAHL
VDVGQVGVNV PIPVPLPMFS FTGSRSSFRG DTNFYGKQGI QFYTQLKTIT SQWKEEDATL
SSPAVVMPTM GR*

speed

1.06 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