mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999999996764 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM950336)
known disease mutation: rs241 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr22:43023333A>GN/A show variant in all transcripts IGV

HGNC symbol

CYB5R3

Ensembl transcript ID

ENST00000396303

Genbank transcript ID

NM_001129819

UniProt peptide

P00387

alteration type

single base exchange

alteration region

CDS

DNA changes

c.541T>C
cDNA.693T>C
g.22242T>C

AA changes

C181R Score: 180 explain score(s)

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

181

frameshift

known variant

Reference ID: rs121965011

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation: rs241 (pathogenic for Methemoglobinemia type 2) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950336)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950336)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950336)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.598	1
	1.867	0.973
(flanking)	-0.037	0.451

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
Acc marginally increased	22249	wt: 0.2613 / mu: 0.2875 (marginal change - not scored)	wt: TGACCACACTGTGTGCCACCTGCTCTTTGCCAACCAGGTCA mu: TGACCACACTGTGCGCCACCTGCTCTTTGCCAACCAGGTCA	acct\|GCTC
Donor increased	22242	wt: 0.32 / mu: 0.68	wt: CTGTGTGCCACCTGC mu: CTGTGCGCCACCTGC	GTGT\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

181

mutated

not conserved

181

Ptroglodytes

all identical

ENSPTRG00000014461

204

Mmulatta

all identical

ENSMMUG00000010198

204

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000018042

181

Ggallus

all identical

ENSGALG00000014122

204

Trubripes

all identical

ENSTRUG00000013823

202

Drerio

all identical

ENSDARG00000005891

201

Dmelanogaster

not conserved

FBgn0036211

218

Celegans

not conserved

T05H4.5

212

Xtropicalis

all identical

ENSXETG00000016513

206

protein features

start (aa)	end (aa)	feature	details
171	206	NP_BIND	FAD (By similarity).	lost
181	183	HELIX		lost
184	195	HELIX		might get lost (downstream of altered splice site)
187	188	CONFLICT	ML -> IV (in Ref. 4; CAA09006/CAA09007).	might get lost (downstream of altered splice site)
191	192	CONFLICT	IR -> MS (in Ref. 4; CAA09006/CAA09007).	might get lost (downstream of altered splice site)
192	192	CONFLICT	R -> G (in Ref. 11; AAA52306).	might get lost (downstream of altered splice site)
203	212	STRAND		might get lost (downstream of altered splice site)
213	215	HELIX		might get lost (downstream of altered splice site)
219	228	HELIX		might get lost (downstream of altered splice site)
230	232	TURN		might get lost (downstream of altered splice site)
233	234	CONFLICT	FK -> CN (in Ref. 4; CAA09006/CAA09007).	might get lost (downstream of altered splice site)
233	241	STRAND		might get lost (downstream of altered splice site)
247	252	STRAND		might get lost (downstream of altered splice site)
255	261	HELIX		might get lost (downstream of altered splice site)
265	267	HELIX		might get lost (downstream of altered splice site)
270	275	STRAND		might get lost (downstream of altered splice site)
277	282	HELIX		might get lost (downstream of altered splice site)
280	280	CONFLICT	I -> N (in Ref. 3; AAL87744).	might get lost (downstream of altered splice site)
285	291	HELIX		might get lost (downstream of altered splice site)
295	297	HELIX		might get lost (downstream of altered splice site)
298	300	STRAND		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

837 / 837

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

279 / 279

position of stopcodon in wt / mu cDNA

989 / 989

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

153 / 153

chromosome

strand

-1

last intron/exon boundary

817

theoretical NMD boundary in CDS

614

length of CDS

837

coding sequence (CDS) position

541

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

693

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

22242

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

43023333

original gDNA sequence snippet

ACCCTGATGACCACACTGTGTGCCACCTGCTCTTTGCCAAC

altered gDNA sequence snippet

ACCCTGATGACCACACTGTGCGCCACCTGCTCTTTGCCAAC

original cDNA sequence snippet

ACCCTGATGACCACACTGTGTGCCACCTGCTCTTTGCCAAC

altered cDNA sequence snippet

ACCCTGATGACCACACTGTGCGCCACCTGCTCTTTGCCAAC

wildtype AA sequence

MKLFQRSTPA ITLESPDIKY PLRLIDREII SHDTRRFRFA LPSPQHILGL PVGQHIYLSA
RIDGNLVVRP YTPISSDDDK GFVDLVIKVY FKDTHPKFPA GGKMSQYLES MQIGDTIEFR
GPSGLLVYQG KGKFAIRPDK KSNPIIRTVK SVGMIAGGTG ITPMLQVIRA IMKDPDDHTV
CHLLFANQTE KDILLRPELE ELRNKHSARF KLWYTLDRAP EAWDYGQGFV NEEMIRDHLP
PPEEEPLVLM CGPPPMIQYA CLPNLDHVGH PTERCFVF*

mutated AA sequence

MKLFQRSTPA ITLESPDIKY PLRLIDREII SHDTRRFRFA LPSPQHILGL PVGQHIYLSA
RIDGNLVVRP YTPISSDDDK GFVDLVIKVY FKDTHPKFPA GGKMSQYLES MQIGDTIEFR
GPSGLLVYQG KGKFAIRPDK KSNPIIRTVK SVGMIAGGTG ITPMLQVIRA IMKDPDDHTV
RHLLFANQTE KDILLRPELE ELRNKHSARF KLWYTLDRAP EAWDYGQGFV NEEMIRDHLP
PPEEEPLVLM CGPPPMIQYA CLPNLDHVGH PTERCFVF*

speed

0.76 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