mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999996425687032 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM910004)
known disease mutation: rs3589 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:76226985T>CN/A show variant in all transcripts IGV

HGNC symbol

ACADM

Ensembl transcript ID

ENST00000543667

Genbank transcript ID

N/A

UniProt peptide

P11310

alteration type

single base exchange

alteration region

CDS

DNA changes

c.557T>C
cDNA.875T>C
g.36950T>C

AA changes

I186T Score: 89 explain score(s)

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

186

frameshift

known variant

Reference ID: rs121434275
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs3589 (pathogenic for Medium-chain acyl-coenzyme A dehydrogenase deficiency) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910004)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910004)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910004)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.916	0.999
	4.377	1
(flanking)	-0.107	0.992

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	36947	wt: 0.8767 / mu: 0.8984 (marginal change - not scored)	wt: TGTGCAGATACTTGG mu: TGTGCAGACACTTGG	TGCA\|gata
Donor gained	36942	0.31	mu: GATGCTGTGCAGACA	TGCT\|gtgc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

186

mutated

not conserved

186

Ptroglodytes

all identical

ENSPTRG00000000871

375

Mmulatta

all identical

ENSMMUG00000007220

408

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000062908

375

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000007137

404

Drerio

all identical

ENSDARG00000038900

380

Dmelanogaster

all identical

FBgn0035811

371

Celegans

all identical

T08G2.3

365

Xtropicalis

all conserved

ENSXETG00000002983

380

protein features

start (aa)	end (aa)	feature	details
180	193	STRAND		lost
191	191	MUTAGEN	W->A: Loss of electron transfer to ETF.	might get lost (downstream of altered splice site)
191	191	MUTAGEN	W->F: Reduces rate of electron transfer to ETF about six-fold.	might get lost (downstream of altered splice site)
191	193	NP_BIND	FAD.	might get lost (downstream of altered splice site)
194	197	TURN		might get lost (downstream of altered splice site)
199	206	STRAND		might get lost (downstream of altered splice site)
212	212	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
215	217	HELIX		might get lost (downstream of altered splice site)
216	216	BINDING	Substrate.	might get lost (downstream of altered splice site)
219	225	STRAND		might get lost (downstream of altered splice site)
231	233	STRAND		might get lost (downstream of altered splice site)
237	237	MUTAGEN	E->A: Strongly reduced rate of electron transfer to ETF.	might get lost (downstream of altered splice site)
239	241	STRAND		might get lost (downstream of altered splice site)
247	258	STRAND		might get lost (downstream of altered splice site)
259	261	HELIX		might get lost (downstream of altered splice site)
262	265	STRAND		might get lost (downstream of altered splice site)
266	268	TURN		might get lost (downstream of altered splice site)
269	303	HELIX		might get lost (downstream of altered splice site)
278	281	REGION	Substrate binding.	might get lost (downstream of altered splice site)
279	279	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
301	301	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
306	308	NP_BIND	FAD.	might get lost (downstream of altered splice site)
309	312	STRAND		might get lost (downstream of altered splice site)
313	315	HELIX		might get lost (downstream of altered splice site)
316	317	NP_BIND	FAD.	might get lost (downstream of altered splice site)
317	345	HELIX		might get lost (downstream of altered splice site)
351	376	HELIX		might get lost (downstream of altered splice site)
356	356	CONFLICT	I -> T (in Ref. 3; AAF63626).	might get lost (downstream of altered splice site)
374	378	NP_BIND	FAD.	might get lost (downstream of altered splice site)
377	379	HELIX		might get lost (downstream of altered splice site)
384	384	MUTAGEN	E->A: Reduces rate of electron transfer to ETF three-fold.	might get lost (downstream of altered splice site)
384	384	MUTAGEN	E->Q: Reduces rate of electron transfer to ETF two-fold.	might get lost (downstream of altered splice site)
387	394	HELIX		might get lost (downstream of altered splice site)
395	398	HELIX		might get lost (downstream of altered splice site)
399	401	TURN		might get lost (downstream of altered splice site)
401	401	ACT_SITE	Proton acceptor.	might get lost (downstream of altered splice site)
402	402	BINDING	Substrate; via amide nitrogen.	might get lost (downstream of altered splice site)
403	405	NP_BIND	FAD.	might get lost (downstream of altered splice site)
404	417	HELIX		might get lost (downstream of altered splice site)
413	413	BINDING	Substrate.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

699 / 699

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

233 / 233

position of stopcodon in wt / mu cDNA

1017 / 1017

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

319 / 319

chromosome

strand

last intron/exon boundary

946

theoretical NMD boundary in CDS

577

length of CDS

699

coding sequence (CDS) position

557

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

875

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

36950

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

76226985

original gDNA sequence snippet

AGCTACTGATGCTGTGCAGATACTTGGAGGCAATGGATTTA

altered gDNA sequence snippet

AGCTACTGATGCTGTGCAGACACTTGGAGGCAATGGATTTA

original cDNA sequence snippet

AGCTACTGATGCTGTGCAGATACTTGGAGGCAATGGATTTA

altered cDNA sequence snippet

AGCTACTGATGCTGTGCAGACACTTGGAGGCAATGGATTTA

wildtype AA sequence

MWITNGGKAN WYFLLARSDP DPKAPANKAF TGFIVEADTP GIQIGRKELN MGQRCSDTRG
IVFEDVKVPK ENVLIGDGAG FKVAMGAFDK TRPVVAAGAV GLAQRALDEA TKYALERKTF
GKLLVEHQAI SFMLAEMAMK VELARMSYQR AAWEVDSGRR NTYYASIAKA FAGDIANQLA
TDAVQILGGN GFNTEYPVEK LMRDAKIYQI YEGTSQIQRL IVAREHIDKY KN*

mutated AA sequence

MWITNGGKAN WYFLLARSDP DPKAPANKAF TGFIVEADTP GIQIGRKELN MGQRCSDTRG
IVFEDVKVPK ENVLIGDGAG FKVAMGAFDK TRPVVAAGAV GLAQRALDEA TKYALERKTF
GKLLVEHQAI SFMLAEMAMK VELARMSYQR AAWEVDSGRR NTYYASIAKA FAGDIANQLA
TDAVQTLGGN GFNTEYPVEK LMRDAKIYQI YEGTSQIQRL IVAREHIDKY KN*

speed

1.25 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