mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999998930620806 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM042965)
known disease mutation: rs65639 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:68552419A>CN/A show variant in all transcripts IGV

HGNC symbol

CPT1A

Ensembl transcript ID

ENST00000540367

Genbank transcript ID

N/A

UniProt peptide

P50416

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1027T>G
cDNA.1056T>G
g.59460T>G

AA changes

F343V Score: 50 explain score(s)

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

343

frameshift

known variant

Reference ID: rs80356783
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs65639 (pathogenic for Carnitine palmitoyltransferase 1A deficiency) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM042965)

known disease mutation at this position, please check HGMD for details (HGMD ID CM042965)
known disease mutation at this position, please check HGMD for details (HGMD ID CM042965)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.457	1
	4.809	1
(flanking)	0.937	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 increased	59460	wt: 0.65 / mu: 0.80	wt: GCTACTTCAAGGTCT mu: GCTACGTCAAGGTCT	TACT\|tcaa
Donor marginally increased	59459	wt: 0.9503 / mu: 0.9985 (marginal change - not scored)	wt: CGCTACTTCAAGGTC mu: CGCTACGTCAAGGTC	CTAC\|ttca
Donor increased	59454	wt: 0.56 / mu: 0.99	wt: GAGGACGCTACTTCA mu: GAGGACGCTACGTCA	GGAC\|gcta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

343

mutated

not conserved

343

Ptroglodytes

all identical

ENSPTRG00000003987

343

Mmulatta

all identical

ENSMMUG00000001780

343

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000024900

343

Ggallus

all identical

ENSGALG00000007077

343

Trubripes

all identical

ENSTRUG00000009681

344

Drerio

all conserved

ENSDARG00000062054

343

Dmelanogaster

all conserved

FBgn0261862

343

Celegans

all identical

Y46G5A.17

344

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
123	773	TOPO_DOM	Cytoplasmic (Potential).	lost
473	473	ACT_SITE	Proton acceptor (By similarity).	might get lost (downstream of altered splice site)
479	479	CONFLICT	P -> Q (in Ref. 1; AAC41748).	might get lost (downstream of altered splice site)
555	567	REGION	Coenzyme A binding (By similarity).	might get lost (downstream of altered splice site)
568	568	CONFLICT	A -> T (in Ref. 1; AAC41748).	might get lost (downstream of altered splice site)
588	588	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
589	589	BINDING	Carnitine (By similarity).	might get lost (downstream of altered splice site)
602	602	BINDING	Carnitine (By similarity).	might get lost (downstream of altered splice site)
604	604	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
741	741	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)
747	747	MOD_RES	Phosphoserine (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2271 / 2271

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

757 / 757

position of stopcodon in wt / mu cDNA

2300 / 2300

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

30 / 30

chromosome

strand

-1

last intron/exon boundary

2265

theoretical NMD boundary in CDS

2185

length of CDS

2271

coding sequence (CDS) position

1027

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

1056

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

59460

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

68552419

original gDNA sequence snippet

TGTACCATCGAGGACGCTACTTCAAGGTCTGGCTCTACCAT

altered gDNA sequence snippet

TGTACCATCGAGGACGCTACGTCAAGGTCTGGCTCTACCAT

original cDNA sequence snippet

TGTACCATCGAGGACGCTACTTCAAGGTCTGGCTCTACCAT

altered cDNA sequence snippet

TGTACCATCGAGGACGCTACGTCAAGGTCTGGCTCTACCAT

wildtype AA sequence

MAEAHQAVAF QFTVTPDGID LRLSHEALRQ IYLSGLHSWK KKFIRFKNGI ITGVYPASPS
SWLIVVVGVM TTMYAKIDPS LGIIAKINRT LETANCMSSQ TKNVVSGVLF GTGLWVALIV
TMRYSLKVLL SYHGWMFTEH GKMSRATKIW MGMVKIFSGR KPMLYSFQTS LPRLPVPAVK
DTVNRYLQSV RPLMKEEDFK RMTALAQDFA VGLGPRLQWY LKLKSWWATN YVSDWWEEYI
YLRGRGPLMV NSNYYAMDLL YILPTHIQAA RAGNAIHAIL LYRRKLDREE IKPIRLLGST
IPLCSAQWER MFNTSRIPGE ETDTIQHMRD SKHIVVYHRG RYFKVWLYHD GRLLKPREME
QQMQRILDNT SEPQPGEARL AALTAGDRVP WARCRQAYFG RGKNKQSLDA VEKAAFFVTL
DETEEGYRSE DPDTSMDSYA KSLLHGRCYD RWFDKSFTFV VFKNGKMGLN AEHSWADAPI
VAHLWEYVMS IDSLQLGYAE DGHCKGDINP NIPYPTRLQW DIPGECQEVI ETSLNTANLL
ANDVDFHSFP FVAFGKGIIK KCRTSPDAFV QLALQLAHYK DMGKFCLTYE ASMTRLFREG
RTETVRSCTT ESCDFVRAMV DPAQTVEQRL KLFKLASEKH QHMYRLAMTG SGIDRHLFCL
YVVSKYLAVE SPFLKEVLSE PWRLSTSQTP QQQVELFDLE NNPEYVSSGG GFGPVADDGY
GVSYILVGEN LINFHISSKF SCPETGIISQ GPSSDT*

mutated AA sequence

MAEAHQAVAF QFTVTPDGID LRLSHEALRQ IYLSGLHSWK KKFIRFKNGI ITGVYPASPS
SWLIVVVGVM TTMYAKIDPS LGIIAKINRT LETANCMSSQ TKNVVSGVLF GTGLWVALIV
TMRYSLKVLL SYHGWMFTEH GKMSRATKIW MGMVKIFSGR KPMLYSFQTS LPRLPVPAVK
DTVNRYLQSV RPLMKEEDFK RMTALAQDFA VGLGPRLQWY LKLKSWWATN YVSDWWEEYI
YLRGRGPLMV NSNYYAMDLL YILPTHIQAA RAGNAIHAIL LYRRKLDREE IKPIRLLGST
IPLCSAQWER MFNTSRIPGE ETDTIQHMRD SKHIVVYHRG RYVKVWLYHD GRLLKPREME
QQMQRILDNT SEPQPGEARL AALTAGDRVP WARCRQAYFG RGKNKQSLDA VEKAAFFVTL
DETEEGYRSE DPDTSMDSYA KSLLHGRCYD RWFDKSFTFV VFKNGKMGLN AEHSWADAPI
VAHLWEYVMS IDSLQLGYAE DGHCKGDINP NIPYPTRLQW DIPGECQEVI ETSLNTANLL
ANDVDFHSFP FVAFGKGIIK KCRTSPDAFV QLALQLAHYK DMGKFCLTYE ASMTRLFREG
RTETVRSCTT ESCDFVRAMV DPAQTVEQRL KLFKLASEKH QHMYRLAMTG SGIDRHLFCL
YVVSKYLAVE SPFLKEVLSE PWRLSTSQTP QQQVELFDLE NNPEYVSSGG GFGPVADDGY
GVSYILVGEN LINFHISSKF SCPETGIISQ GPSSDT*

speed

0.62 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