mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999997343774726 (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

ENST00000541113

Genbank transcript ID

N/A

UniProt peptide

P11310

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1016T>C
cDNA.1069T>C
g.36950T>C

AA changes

I339T Score: 89 explain score(s)

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

339

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

339

mutated

not conserved

339

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
317	345	HELIX		lost
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

1158 / 1158

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

386 / 386

position of stopcodon in wt / mu cDNA

1211 / 1211

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

54 / 54

chromosome

strand

last intron/exon boundary

1140

theoretical NMD boundary in CDS

1036

length of CDS

1158

coding sequence (CDS) position

1016

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

1069

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

MLQEFTEQQK EFQATARKFA REEIIPVAAE YDKTGEYPVP LIRRAWELGL MNTHIPENCG
GLGLGTFDAC LISEELAYGC TGVQTAIEGN SLGQMPIIIA GNDQQKKKYL GRMTEEPLMC
AYCVTEPGAG SDVAGIKTKA EKKGDEYIIN GQKMWITNGG KANWYFLLAR SDPDPKAPAN
KAFTGFIVEA DTPGIQIGRK ELNMGQRCSD TRGIVFEDVK VPKENVLIGD GAGFKVAMGA
FDKTRPVVAA GAVGLAQRAL DEATKYALER KTFGKLLVEH QAISFMLAEM AMKVELARMS
YQRAAWEVDS GRRNTYYASI AKAFAGDIAN QLATDAVQIL GGNGFNTEYP VEKLMRDAKI
YQIYEGTSQI QRLIVAREHI DKYKN*

mutated AA sequence

MLQEFTEQQK EFQATARKFA REEIIPVAAE YDKTGEYPVP LIRRAWELGL MNTHIPENCG
GLGLGTFDAC LISEELAYGC TGVQTAIEGN SLGQMPIIIA GNDQQKKKYL GRMTEEPLMC
AYCVTEPGAG SDVAGIKTKA EKKGDEYIIN GQKMWITNGG KANWYFLLAR SDPDPKAPAN
KAFTGFIVEA DTPGIQIGRK ELNMGQRCSD TRGIVFEDVK VPKENVLIGD GAGFKVAMGA
FDKTRPVVAA GAVGLAQRAL DEATKYALER KTFGKLLVEH QAISFMLAEM AMKVELARMS
YQRAAWEVDS GRRNTYYASI AKAFAGDIAN QLATDAVQTL GGNGFNTEYP VEKLMRDAKI
YQIYEGTSQI QRLIVAREHI DKYKN*

speed

1.12 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