mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.000515108227700299 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:13980350G>AN/A show variant in all transcripts IGV

HGNC symbol

COX10

Ensembl transcript ID

ENST00000261643

Genbank transcript ID

NM_001303

UniProt peptide

Q12887

alteration type

single base exchange

alteration region

CDS

DNA changes

c.476G>A
cDNA.553G>A
g.7538G>A

AA changes

R159Q Score: 43 explain score(s)

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

159

frameshift

known variant

Reference ID: rs2072279

database	homozygous (A/A)	heterozygous	allele carriers
1000G	568	1187	1755
ExAC	14893	2981	17874

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.418	0.891
	3.914	0.89
(flanking)	-2.099	0.128

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 gained	7534	0.71	mu: TTTTGGCTCAACTAT	TTGG\|ctca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

159

mutated

all conserved

159

Ptroglodytes

all identical

ENSPTRG00000008790

159

Mmulatta

all identical

ENSMMUG00000016157

159

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000042148

158

Ggallus

all identical

ENSGALG00000001375

151

Trubripes

no homologue

Drerio

all identical

ENSDARG00000034309

165

Dmelanogaster

all conserved

FBgn0032222

LSQYK

Celegans

not conserved

Y46G5A.2

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
174	194	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
235	255	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
257	277	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
280	300	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
303	303	CONFLICT	A -> T (in Ref. 1; AAA21148).	might get lost (downstream of altered splice site)
309	329	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
364	384	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
394	394	CONFLICT	Y -> H (in Ref. 1; AAA21148).	might get lost (downstream of altered splice site)
411	431	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1332 / 1332

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

444 / 444

position of stopcodon in wt / mu cDNA

1409 / 1409

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

78 / 78

chromosome

strand

last intron/exon boundary

1006

theoretical NMD boundary in CDS

878

length of CDS

1332

coding sequence (CDS) position

476

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

553

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

7538

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

13980350

original gDNA sequence snippet

TTTGCCAGGAATTTTGGCTCGACTATCCAAAATCAAACTCA

altered gDNA sequence snippet

TTTGCCAGGAATTTTGGCTCAACTATCCAAAATCAAACTCA

original cDNA sequence snippet

TTTGCCAGGAATTTTGGCTCGACTATCCAAAATCAAACTCA

altered cDNA sequence snippet

TTTGCCAGGAATTTTGGCTCAACTATCCAAAATCAAACTCA

wildtype AA sequence

MAASPHTLSS RLLTGCVGGS VWYLERRTIQ DSPHKFLHLL RNVNKQWITF QHFSFLKRMY
VTQLNRSHNQ QVRPKPEPVA SPFLEKTSSG QAKAEIYEMR PLSPPSLSLS RKPNEKELIE
LEPDSVIEDS IDVGKETKEE KRWKEMKLQV YDLPGILARL SKIKLTALVV STTAAGFALA
PGPFDWPCFL LTSVGTGLAS CAANSINQFF EVPFDSNMNR TKNRPLVRGQ ISPLLAVSFA
TCCAVPGVAI LTLGVNPLTG ALGLFNIFLY TCCYTPLKRI SIANTWVGAV VGAIPPVMGW
TAATGSLDAG AFLLGGILYS WQFPHFNALS WGLREDYSRG GYCMMSVTHP GLCRRVALRH
CLALLVLSAA APVLDITTWT FPIMALPINA YISYLGFRFY VDADRRSSRR LFFCSLWHLP
LLLLLMLTCK RPSGGGDAGP PPS*

mutated AA sequence

MAASPHTLSS RLLTGCVGGS VWYLERRTIQ DSPHKFLHLL RNVNKQWITF QHFSFLKRMY
VTQLNRSHNQ QVRPKPEPVA SPFLEKTSSG QAKAEIYEMR PLSPPSLSLS RKPNEKELIE
LEPDSVIEDS IDVGKETKEE KRWKEMKLQV YDLPGILAQL SKIKLTALVV STTAAGFALA
PGPFDWPCFL LTSVGTGLAS CAANSINQFF EVPFDSNMNR TKNRPLVRGQ ISPLLAVSFA
TCCAVPGVAI LTLGVNPLTG ALGLFNIFLY TCCYTPLKRI SIANTWVGAV VGAIPPVMGW
TAATGSLDAG AFLLGGILYS WQFPHFNALS WGLREDYSRG GYCMMSVTHP GLCRRVALRH
CLALLVLSAA APVLDITTWT FPIMALPINA YISYLGFRFY VDADRRSSRR LFFCSLWHLP
LLLLLMLTCK RPSGGGDAGP PPS*

speed

0.65 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