mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 2.97068054545935e-13 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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)

chr15:91452595A>GN/A show variant in all transcripts IGV

HGNC symbol

MAN2A2

Ensembl transcript ID

ENST00000431652

Genbank transcript ID

N/A

UniProt peptide

P49641

alteration type

single base exchange

alteration region

5'UTR

DNA changes

cDNA.147A>G
g.7148A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs2106673

database	homozygous (G/G)	heterozygous	allele carriers
1000G	816	930	1746
ExAC	12566	7635	20201

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.769	1
	0.96	1
(flanking)	2.769	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 -14) |

effect	gDNA position	score	detection sequence	exon-intron border
Donor gained	7142	0.36	mu: GAAGAAGTCCCGGCT	AGAA\|gtcc

distance from splice site

Kozak consensus sequence altered?

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	5	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
6	26	TRANSMEM	Helical; Signal-anchor for type II membrane protein; (Potential).	might get lost (downstream of altered splice site)
27	796	TOPO_DOM	Lumenal (Potential).	might get lost (downstream of altered splice site)
95	95	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
175	175	METAL	Zinc (By similarity).	might get lost (downstream of altered splice site)
177	177	METAL	Zinc (By similarity).	might get lost (downstream of altered splice site)
289	289	METAL	Zinc (By similarity).	might get lost (downstream of altered splice site)
289	289	ACT_SITE	Nucleophile (By similarity).	might get lost (downstream of altered splice site)
305	305	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
569	569	METAL	Zinc (By similarity).	might get lost (downstream of altered splice site)
1093	1093	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1131	1131	CARBOHYD	N-linked (GlcNAc...) (Potential).	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

186 / 186

chromosome

strand

last intron/exon boundary

2010

theoretical NMD boundary in CDS

1774

length of CDS

1977

coding sequence (CDS) position

N/A

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

147

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

7148

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

91452595

original gDNA sequence snippet

CCAATACCGGAAGAAGTCCCAGCTGTTCCGAAGCAACGTCC

altered gDNA sequence snippet

CCAATACCGGAAGAAGTCCCGGCTGTTCCGAAGCAACGTCC

original cDNA sequence snippet

CCAATACCGGAAGAAGTCCCAGCTGTTCCGAAGCAACGTCC

altered cDNA sequence snippet

CCAATACCGGAAGAAGTCCCGGCTGTTCCGAAGCAACGTCC

wildtype AA sequence

MTSDMTSPRS GMPSSSTTNG SLTSSTAGLT SMCRGAEVLY SLAAAHARRS GLAGRYPLSD
FTLLTEARRT LGLFQHHDAI TGTAKEAVVV DYGVRLLRSL VNLKQVIIHA AHYLVLGDKE
TYHFDPEAPF LQVDDTRLSH DALPERTVIQ LDSSPRFVVL FNPLEQERFS MVSLLVNSPR
VRVLSEEGQP LAVQISAHWS SATEAVPDVY QVSVPVRLPA LGLGVLQLQL GLDGHRTLPS
SVRIYLHGRQ LSVSRHEAFP LRVIDSGTSD FALSNRYMQV WFSGLTGLLK SIRRVDEEHE
QQVDMQVLVY GTRTSKDKSG AYLFLPDGEA KPYVPKEPPV LRVTEGPFFS EVVAYYEHIH
QAVRLYNLPG VEGLSLDISS LVDIRDYVNK ELALHIHTDI DSQGIFFTDL NGFQVQPRRY
LKKLPLQANF YPMPVMAYIQ DAQKRLTLHT AQALGVSSLK DGQLEVILDR RLMQDDNRGL
GQGLKDNKRT CNRFRLLLER RTVGSEVQDS HSTSYPSLLS HLTSMYLNAP ALALPVARMQ
LPGPGLRSFH PLASSLPCDF HLLNLRTLQA EEDTLPSAET ALILHRKGFD CGLEAKNLGF
NCTTSQGKVA LGSLFHGLDV VFLQPTSLTL LYPLASPSNS TDVYLEPMEI ATFRLRLG*

mutated AA sequence

N/A

speed

0.91 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