mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999997355949 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CI991949)
known disease mutation at this position (HGMD CM960002)
known disease mutation: rs21024 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:7125522C>TN/A show variant in all transcripts IGV

HGNC symbol

ACADVL

Ensembl transcript ID

ENST00000356839

Genbank transcript ID

NM_000018

UniProt peptide

P49748

alteration type

single base exchange

alteration region

CDS

DNA changes

c.779C>T
cDNA.958C>T
g.5079C>T

AA changes

T260M Score: 81 explain score(s)

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

260

frameshift

known variant

Reference ID: rs113994168

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

known disease mutation: rs21024 (pathogenic for Very long chain acyl-CoA dehydrogenase deficiency|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960002)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960002)
known disease mutation at this position, please check HGMD for details (HGMD ID CI991949)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960002)
known disease mutation at this position, please check HGMD for details (HGMD ID CI991949)
known disease mutation at this position, please check HGMD for details (HGMD ID CI991949)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960002)
known disease mutation at this position, please check HGMD for details (HGMD ID CI991949)
known disease mutation at this position, please check HGMD for details (HGMD ID CI991949)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960002)

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.469	1
	3.817	0.999
(flanking)	-1.109	0.529

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 increased	5090	wt: 0.60 / mu: 0.74	wt: ACATCTTCACGGTCTTTGCCAAGACACCAGTTACAGATCCA mu: ACATCTTCATGGTCTTTGCCAAGACACCAGTTACAGATCCA	gcca\|AGAC
Acc increased	5088	wt: 0.43 / mu: 0.52	wt: AGACATCTTCACGGTCTTTGCCAAGACACCAGTTACAGATC mu: AGACATCTTCATGGTCTTTGCCAAGACACCAGTTACAGATC	ttgc\|CAAG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

260

mutated

not conserved

260

Ptroglodytes

all identical

ENSPTRG00000008664

283

Mmulatta

all identical

ENSMMUG00000010538

260

IRQSASHFSPYPPPNSRPRCS

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000018574

261

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000013710

262

Drerio

all identical

ENSDARG00000016687

265

Dmelanogaster

all identical

FBgn0034432

233

Celegans

all identical

E04F6.5

229

Xtropicalis

all identical

ENSXETG00000031271

protein features

start (aa)	end (aa)	feature	details
41	482	REGION	Catalytic.	lost
257	268	STRAND		lost
270	272	TURN		might get lost (downstream of altered splice site)
275	285	STRAND		might get lost (downstream of altered splice site)
276	276	MOD_RES	N6-acetyllysine (By similarity).	might get lost (downstream of altered splice site)
286	288	HELIX		might get lost (downstream of altered splice site)
289	293	STRAND		might get lost (downstream of altered splice site)
307	318	STRAND		might get lost (downstream of altered splice site)
319	321	HELIX		might get lost (downstream of altered splice site)
322	325	STRAND		might get lost (downstream of altered splice site)
329	365	HELIX		might get lost (downstream of altered splice site)
331	331	CROSSLNK	Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) (By similarity).	might get lost (downstream of altered splice site)
331	331	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
338	341	REGION	Substrate binding (By similarity).	might get lost (downstream of altered splice site)
366	366	BINDING	FAD (By similarity).	might get lost (downstream of altered splice site)
373	375	HELIX		might get lost (downstream of altered splice site)
377	405	HELIX		might get lost (downstream of altered splice site)
412	437	HELIX		might get lost (downstream of altered splice site)
435	439	NP_BIND	FAD (By similarity).	might get lost (downstream of altered splice site)
439	442	HELIX		might get lost (downstream of altered splice site)
448	455	HELIX		might get lost (downstream of altered splice site)
456	459	HELIX		might get lost (downstream of altered splice site)
461	463	STRAND		might get lost (downstream of altered splice site)
462	462	ACT_SITE	Proton acceptor.	might get lost (downstream of altered splice site)
462	463	REGION	Substrate binding.	might get lost (downstream of altered splice site)
463	463	BINDING	Substrate; via amide nitrogen (By similarity).	might get lost (downstream of altered splice site)
464	466	NP_BIND	FAD.	might get lost (downstream of altered splice site)
465	485	HELIX		might get lost (downstream of altered splice site)
483	516	REGION	Membrane-anchoring (Probable).	might get lost (downstream of altered splice site)
486	488	HELIX		might get lost (downstream of altered splice site)
522	524	TURN		might get lost (downstream of altered splice site)
527	529	HELIX		might get lost (downstream of altered splice site)
530	554	HELIX		might get lost (downstream of altered splice site)
555	560	HELIX		might get lost (downstream of altered splice site)
562	591	HELIX		might get lost (downstream of altered splice site)
596	622	HELIX		might get lost (downstream of altered splice site)
627	644	HELIX		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1968 / 1968

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

656 / 656

position of stopcodon in wt / mu cDNA

2147 / 2147

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

180 / 180

chromosome

strand

last intron/exon boundary

2007

theoretical NMD boundary in CDS

1777

length of CDS

1968

coding sequence (CDS) position

779

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

958

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

5079

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

7125522

original gDNA sequence snippet

GGGCCTAGCAGACATCTTCACGGTCTTTGCCAAGACACCAG

altered gDNA sequence snippet

GGGCCTAGCAGACATCTTCATGGTCTTTGCCAAGACACCAG

original cDNA sequence snippet

GGGCCTAGCAGACATCTTCACGGTCTTTGCCAAGACACCAG

altered cDNA sequence snippet

GGGCCTAGCAGACATCTTCATGGTCTTTGCCAAGACACCAG

wildtype AA sequence

MQAARMAASL GRQLLRLGGG SSRLTALLGQ PRPGPARRPY AGGAAQLALD KSDSHPSDAL
TRKKPAKAES KSFAVGMFKG QLTTDQVFPY PSVLNEEQTQ FLKELVEPVS RFFEEVNDPA
KNDALEMVEE TTWQGLKELG AFGLQVPSEL GGVGLCNTQY ARLVEIVGMH DLGVGITLGA
HQSIGFKGIL LFGTKAQKEK YLPKLASGET VAAFCLTEPS SGSDAASIRT SAVPSPCGKY
YTLNGSKLWI SNGGLADIFT VFAKTPVTDP ATGAVKEKIT AFVVERGFGG ITHGPPEKKM
GIKASNTAEV FFDGVRVPSE NVLGEVGSGF KVAMHILNNG RFGMAAALAG TMRGIIAKAV
DHATNRTQFG EKIHNFGLIQ EKLARMVMLQ YVTESMAYMV SANMDQGATD FQIEAAISKI
FGSEAAWKVT DECIQIMGGM GFMKEPGVER VLRDLRIFRI FEGTNDILRL FVALQGCMDK
GKELSGLGSA LKNPFGNAGL LLGEAGKQLR RRAGLGSGLS LSGLVHPELS RSGELAVRAL
EQFATVVEAK LIKHKKGIVN EQFLLQRLAD GAIDLYAMVV VLSRASRSLS EGHPTAQHEK
MLCDTWCIEA AARIREGMAA LQSDPWQQEL YRNFKSISKA LVERGGVVTS NPLGF*

mutated AA sequence

MQAARMAASL GRQLLRLGGG SSRLTALLGQ PRPGPARRPY AGGAAQLALD KSDSHPSDAL
TRKKPAKAES KSFAVGMFKG QLTTDQVFPY PSVLNEEQTQ FLKELVEPVS RFFEEVNDPA
KNDALEMVEE TTWQGLKELG AFGLQVPSEL GGVGLCNTQY ARLVEIVGMH DLGVGITLGA
HQSIGFKGIL LFGTKAQKEK YLPKLASGET VAAFCLTEPS SGSDAASIRT SAVPSPCGKY
YTLNGSKLWI SNGGLADIFM VFAKTPVTDP ATGAVKEKIT AFVVERGFGG ITHGPPEKKM
GIKASNTAEV FFDGVRVPSE NVLGEVGSGF KVAMHILNNG RFGMAAALAG TMRGIIAKAV
DHATNRTQFG EKIHNFGLIQ EKLARMVMLQ YVTESMAYMV SANMDQGATD FQIEAAISKI
FGSEAAWKVT DECIQIMGGM GFMKEPGVER VLRDLRIFRI FEGTNDILRL FVALQGCMDK
GKELSGLGSA LKNPFGNAGL LLGEAGKQLR RRAGLGSGLS LSGLVHPELS RSGELAVRAL
EQFATVVEAK LIKHKKGIVN EQFLLQRLAD GAIDLYAMVV VLSRASRSLS EGHPTAQHEK
MLCDTWCIEA AARIREGMAA LQSDPWQQEL YRNFKSISKA LVERGGVVTS NPLGF*

speed

0.71 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