mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999997895639 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM025383)
known disease mutation: rs1499 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:73949644T>CN/A show variant in all transcripts IGV

HGNC symbol

ACOX1

Ensembl transcript ID

ENST00000301608

Genbank transcript ID

NM_007292

UniProt peptide

Q15067

alteration type

single base exchange

alteration region

CDS

DNA changes

c.832A>G
cDNA.893A>G
g.25872A>G

AA changes

M278V Score: 21 explain score(s)

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

278

frameshift

known variant

Reference ID: rs118204090
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs1499 (pathogenic for Peroxisomal acyl-CoA oxidase deficiency) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM025383)

known disease mutation at this position, please check HGMD for details (HGMD ID CM025383)
known disease mutation at this position, please check HGMD for details (HGMD ID CM025383)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.969	1
	4.969	1
(flanking)	3.278	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 gained	25871	0.85	mu: GGGACCGTGGTGTTT	GACC\|gtgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

278

mutated

all conserved

278

Ptroglodytes

all identical

ENSPTRG00000009665

278

Mmulatta

all identical

ENSMMUG00000014172

278

Fcatus

all identical

ENSFCAG00000005765

279

Mmusculus

all identical

ENSMUSG00000020777

278

Ggallus

all identical

ENSGALG00000002159

279

Trubripes

no homologue

Drerio

all identical

ENSDARG00000014727

278

Dmelanogaster

all identical

FBgn0027572

291

Celegans

all identical

F59F4.1

288

Xtropicalis

all identical

ENSXETG00000012601

291

protein features

start (aa)	end (aa)	feature	details
310	310	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
332	332	CONFLICT	F -> L (in Ref. 2; AAA18595).	might get lost (downstream of altered splice site)
421	421	ACT_SITE	Proton acceptor (By similarity).	might get lost (downstream of altered splice site)
437	437	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
449	449	CONFLICT	C -> R (in Ref. 2; AAA18595).	might get lost (downstream of altered splice site)
490	490	CONFLICT	R -> L (in Ref. 5; BAF85654).	might get lost (downstream of altered splice site)
500	500	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
504	504	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
531	531	CONFLICT	C -> L (in Ref. 1; AAA19113/AAA19114 and 2; AAA18595).	might get lost (downstream of altered splice site)
534	535	CONFLICT	VV -> GL (in Ref. 1; AAA19113/AAA19114 and 2; AAA18595).	might get lost (downstream of altered splice site)
615	615	CONFLICT	V -> A (in Ref. 3; CAA50574).	might get lost (downstream of altered splice site)
643	643	MOD_RES	N6-acetyllysine (By similarity).	might get lost (downstream of altered splice site)
649	649	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
650	650	CONFLICT	Y -> YH (in Ref. 4; AAB30019).	might get lost (downstream of altered splice site)
651	651	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
658	660	MOTIF	Microbody targeting signal.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1983 / 1983

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

661 / 661

position of stopcodon in wt / mu cDNA

2044 / 2044

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

62 / 62

chromosome

strand

-1

last intron/exon boundary

1997

theoretical NMD boundary in CDS

1885

length of CDS

1983

coding sequence (CDS) position

832

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

893

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

25872

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

73949644

original gDNA sequence snippet

ACAAGCTGACTTACGGGACCATGGTGTTTGTCAGGTCCTTC

altered gDNA sequence snippet

ACAAGCTGACTTACGGGACCGTGGTGTTTGTCAGGTCCTTC

original cDNA sequence snippet

ACAAGCTGACTTACGGGACCATGGTGTTTGTCAGGTCCTTC

altered cDNA sequence snippet

ACAAGCTGACTTACGGGACCGTGGTGTTTGTCAGGTCCTTC

wildtype AA sequence

MNPDLRRERD SASFNPELLT HILDGSPEKT RRRREIENMI LNDPDFQHED LNFLTRSQRY
EVAVRKSAIM VKKMREFGIA DPDEIMWFKK LHLVNFVEPV GLNYSMFIPT LLNQGTTAQK
EKWLLSSKGL QIIGTYAQTE MGHGTHLRGL ETTATYDPET QEFILNSPTV TSIKWWPGGL
GKTSNHAIVL AQLITKGKCY GLHAFIVPIR EIGTHKPLPG ITVGDIGPKF GYDEIDNGYL
KMDNHRIPRE NMLMKYAQVK PDGTYVKPLS NKLTYGTMVF VRSFLVGEAA RALSKACTIA
IRYSAVRHQS EIKPGEPEPQ ILDFQTQQYK LFPLLATAYA FQFVGAYMKE TYHRINEGIG
QGDLSELPEL HALTAGLKAF TSWTANTGIE ACRMACGGHG YSHCSGLPNI YVNFTPSCTF
EGENTVMMLQ TARFLMKSYD QVHSGKLVCG MVSYLNDLPS QRIQPQQVAV WPTMVDINSP
ESLTEAYKLR AARLVEIAAK NLQKEVIHRK SKEVAWNLTS VDLVRASEAH CHYVVVKLFS
EKLLKIQDKA IQAVLRSLCL LYSLYGISQN AGDFLQGSIM TEPQITQVNQ RVKELLTLIR
SDAVALVDAF DFQDVTLGSV LGRYDGNVYE NLFEWAKNSP LNKAEVHESY KHLKSLQSKL
*

mutated AA sequence

MNPDLRRERD SASFNPELLT HILDGSPEKT RRRREIENMI LNDPDFQHED LNFLTRSQRY
EVAVRKSAIM VKKMREFGIA DPDEIMWFKK LHLVNFVEPV GLNYSMFIPT LLNQGTTAQK
EKWLLSSKGL QIIGTYAQTE MGHGTHLRGL ETTATYDPET QEFILNSPTV TSIKWWPGGL
GKTSNHAIVL AQLITKGKCY GLHAFIVPIR EIGTHKPLPG ITVGDIGPKF GYDEIDNGYL
KMDNHRIPRE NMLMKYAQVK PDGTYVKPLS NKLTYGTVVF VRSFLVGEAA RALSKACTIA
IRYSAVRHQS EIKPGEPEPQ ILDFQTQQYK LFPLLATAYA FQFVGAYMKE TYHRINEGIG
QGDLSELPEL HALTAGLKAF TSWTANTGIE ACRMACGGHG YSHCSGLPNI YVNFTPSCTF
EGENTVMMLQ TARFLMKSYD QVHSGKLVCG MVSYLNDLPS QRIQPQQVAV WPTMVDINSP
ESLTEAYKLR AARLVEIAAK NLQKEVIHRK SKEVAWNLTS VDLVRASEAH CHYVVVKLFS
EKLLKIQDKA IQAVLRSLCL LYSLYGISQN AGDFLQGSIM TEPQITQVNQ RVKELLTLIR
SDAVALVDAF DFQDVTLGSV LGRYDGNVYE NLFEWAKNSP LNKAEVHESY KHLKSLQSKL
*

speed

1.33 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