mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM910001)
known disease mutation: rs3591 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:76200535G>AN/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

intron

DNA changes

g.10500G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121434277
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs3591 (pathogenic for Medium-chain acyl-coenzyme A dehydrogenase deficiency|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910001)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910001)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910001)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.006	1
	6.064	1
(flanking)	2.468	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

splice site change before start ATG (at aa -32) |

effect	gDNA position	score	detection sequence	exon-intron border
Donor marginally increased	10503	wt: 0.9901 / mu: 0.9948 (marginal change - not scored)	wt: ATGACTGAGGAGCCA mu: ATAACTGAGGAGCCA	GACT\|gagg
Donor increased	10492	wt: 0.45 / mu: 0.69	wt: ATTTGGGGAGAATGA mu: ATTTGGGGAGAATAA	TTGG\|ggag
Donor increased	10501	wt: 0.62 / mu: 0.85	wt: GAATGACTGAGGAGC mu: GAATAACTGAGGAGC	ATGA\|ctga
Donor increased	10500	wt: 0.29 / mu: 0.67	wt: AGAATGACTGAGGAG mu: AGAATAACTGAGGAG	AATG\|actg

distance from splice site

1928

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	25	TRANSIT	Mitochondrion.	might get lost (downstream of altered splice site)
36	38	STRAND		might get lost (downstream of altered splice site)
43	59	HELIX		might get lost (downstream of altered splice site)
61	70	HELIX		might get lost (downstream of altered splice site)
75	84	HELIX		might get lost (downstream of altered splice site)
86	86	MUTAGEN	L->M: Strongly reduced rate of electron transfer to ETF.	might get lost (downstream of altered splice site)
93	95	HELIX		might get lost (downstream of altered splice site)
98	98	MUTAGEN	L->W: Strongly reduced rate of electron transfer to ETF.	might get lost (downstream of altered splice site)
100	100	MUTAGEN	L->Y: Strongly reduced rate of electron transfer to ETF.	might get lost (downstream of altered splice site)
102	115	HELIX		might get lost (downstream of altered splice site)
108	108	MUTAGEN	I->M: Strongly reduced rate of electron transfer to ETF.	might get lost (downstream of altered splice site)
117	129	HELIX		might get lost (downstream of altered splice site)
131	136	HELIX		might get lost (downstream of altered splice site)
139	151	HELIX		might get lost (downstream of altered splice site)
156	159	STRAND		might get lost (downstream of altered splice site)
158	167	NP_BIND	FAD.	might get lost (downstream of altered splice site)
165	168	STRAND		might get lost (downstream of altered splice site)
167	167	BINDING	Substrate; via carbonyl oxygen.	might get lost (downstream of altered splice site)
169	171	HELIX		might get lost (downstream of altered splice site)
175	178	STRAND		might get lost (downstream of altered splice site)
180	193	STRAND		might get lost (downstream of altered splice site)
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->Q: Reduces rate of electron transfer to ETF two-fold.	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)
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

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

N/A

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

N/A

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

10500

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

76200535

original gDNA sequence snippet

AAGAAGTATTTGGGGAGAATGACTGAGGAGCCATTGATGTG

altered gDNA sequence snippet

AAGAAGTATTTGGGGAGAATAACTGAGGAGCCATTGATGTG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

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

N/A

speed

0.35 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