Prediction |
polymorphism |
Model: simple_aae, prob: 0.999646926746738 (classification due to TGP/ExAC,
real probability is shown anyway)
(explain) |
Summary |
- amino acid sequence changed
- homozygous in TGP or ExAC
- known disease mutation at this position (HGMD CM102490)
- protein features (might be) affected
- splice site changes
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hyperlink |
analysed issue |
analysis result |
name of alteration | no title |
alteration (phys. location) | chr6:3010390C>TN/A
show variant in all transcripts IGV
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HGNC symbol | NQO2 |
Ensembl transcript ID | ENST00000338130 |
Genbank transcript ID | N/A |
UniProt peptide | P16083 |
alteration type | single base exchange |
alteration region | CDS |
DNA changes | c.139C>T cDNA.851C>T g.22170C>T |
AA changes | L47F Score: 22 explain score(s) |
position(s) of altered AA if AA alteration in CDS | 47 |
frameshift | no |
known variant | Reference ID: rs1143684
database | homozygous (T/T) | heterozygous | allele carriers |
1000G | 1621 | 752 | 2373 |
ExAC | - | - | - |
known disease mutation at this position, please check HGMD for details (HGMD ID CM102490)
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regulatory features | H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation |
phyloP / phastCons | | PhyloP | PhastCons |
(flanking) | 0.574 | 0.998 | | 2.538 | 1 | (flanking) | 3.98 | 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 | Acc increased | 22174 | wt: 0.32 / mu: 0.51 | wt: TTTGTATGCCATGAACCTTGAGCCGAGGGCCACAGACAAAG mu: TTTGTATGCCATGAACTTTGAGCCGAGGGCCACAGACAAAG | ttga|GCCG | Acc increased | 22160 | wt: 0.43 / mu: 0.55 | wt: GTCACAGTGTCTGATTTGTATGCCATGAACCTTGAGCCGAG mu: GTCACAGTGTCTGATTTGTATGCCATGAACTTTGAGCCGAG | gtat|GCCA |
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distance from splice site | 34 |
Kozak consensus sequence altered? | N/A |
conservation protein level for non-synonymous changes | species | match | gene | aa | alignment | Human | | | 47 | T | V | T | V | S | D | L | Y | A | M | N | L | E | P | R | A | T | D | K | D | I | T | G | T |
mutated | not conserved | | 47 | T | V | T | V | S | D | L | Y | A | M | N | F | E | P | R | A | T | D | K | D | I | T | G |
Ptroglodytes | not conserved | ENSPTRG00000017670 | 47 | T | V | T | V | S | D | L | Y | A | M | N | F | E | P | R | A | T | D | K | D | I | T | G |
Mmulatta | not conserved | ENSMMUG00000008487 | 47 | T | V | T | V | S | D | L | Y | A | M | N | F | E | P | R | A | T | R | K | D | I | T | A |
Fcatus | no alignment | ENSFCAG00000013029 | n/a | |
Mmusculus | not conserved | ENSMUSG00000046949 | 47 | T | V | T | V | S | D | L | Y | S | M | N | F | E | P | R | A | T | R | N | D | I | T | G |
Ggallus | not conserved | ENSGALG00000012828 | 47 | S | V | T | V | S | D | L | Y | A | M | Q | F | E | P | R | A | T | R | N | D | I | V | G |
Trubripes | no homologue | | | |
Drerio | no homologue | | | |
Dmelanogaster | no homologue | | | |
Celegans | no homologue | | | |
Xtropicalis | no homologue | | | |
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protein features | start (aa) | end (aa) | feature | details | | 42 | 46 | TURN | | might get lost (downstream of altered splice site) | 53 | 55 | HELIX | | might get lost (downstream of altered splice site) | 63 | 65 | STRAND | | might get lost (downstream of altered splice site) | 68 | 78 | HELIX | | might get lost (downstream of altered splice site) | 80 | 80 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | 83 | 94 | HELIX | | might get lost (downstream of altered splice site) | 96 | 103 | STRAND | | might get lost (downstream of altered splice site) | 104 | 107 | NP_BIND | FAD. | might get lost (downstream of altered splice site) | 105 | 108 | STRAND | | might get lost (downstream of altered splice site) | 111 | 120 | HELIX | | might get lost (downstream of altered splice site) | 123 | 125 | TURN | | might get lost (downstream of altered splice site) | 127 | 129 | REGION | Substrate binding. | might get lost (downstream of altered splice site) | 129 | 132 | STRAND | | might get lost (downstream of altered splice site) | 133 | 135 | HELIX | | might get lost (downstream of altered splice site) | 137 | 140 | TURN | | might get lost (downstream of altered splice site) | 140 | 140 | CONFLICT | G -> C (in Ref. 2; AAB60642). | might get lost (downstream of altered splice site) | 142 | 148 | STRAND | | might get lost (downstream of altered splice site) | 148 | 151 | NP_BIND | FAD. | might get lost (downstream of altered splice site) | 153 | 156 | TURN | | might get lost (downstream of altered splice site) | 156 | 156 | BINDING | FAD. | might get lost (downstream of altered splice site) | 160 | 162 | STRAND | | might get lost (downstream of altered splice site) | 162 | 162 | MUTAGEN | N->H: Loss of activity toward CB1954, no effect toward menadione. | might get lost (downstream of altered splice site) | 165 | 173 | HELIX | | might get lost (downstream of altered splice site) | 174 | 174 | METAL | Zinc. | might get lost (downstream of altered splice site) | 174 | 178 | HELIX | | might get lost (downstream of altered splice site) | 178 | 178 | METAL | Zinc. | might get lost (downstream of altered splice site) | 179 | 181 | TURN | | might get lost (downstream of altered splice site) | 188 | 190 | STRAND | | might get lost (downstream of altered splice site) | 193 | 195 | TURN | | might get lost (downstream of altered splice site) | 194 | 194 | BINDING | FAD. | might get lost (downstream of altered splice site) | 197 | 197 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | 198 | 213 | HELIX | | might get lost (downstream of altered splice site) | 201 | 201 | BINDING | FAD. | might get lost (downstream of altered splice site) | 214 | 217 | HELIX | | might get lost (downstream of altered splice site) | 223 | 223 | METAL | Zinc. | might get lost (downstream of altered splice site) | 225 | 229 | HELIX | | might get lost (downstream of altered splice site) |
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length of protein | normal |
AA sequence altered | yes |
position of stopcodon in wt / mu CDS | 696 / 696 |
position (AA) of stopcodon in wt / mu AA sequence | 232 / 232 |
position of stopcodon in wt / mu cDNA | 1408 / 1408 |
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 | 713 / 713 |
chromosome | 6 |
strand | 1 |
last intron/exon boundary | 1232 |
theoretical NMD boundary in CDS | 469 |
length of CDS | 696 |
coding sequence (CDS) position | 139 |
cDNA position (for ins/del: last normal base / first normal base) | 851 |
gDNA position (for ins/del: last normal base / first normal base) | 22170 |
chromosomal position (for ins/del: last normal base / first normal base) | 3010390 |
original gDNA sequence snippet | CTGATTTGTATGCCATGAACCTTGAGCCGAGGGCCACAGAC |
altered gDNA sequence snippet | CTGATTTGTATGCCATGAACTTTGAGCCGAGGGCCACAGAC |
original cDNA sequence snippet | CTGATTTGTATGCCATGAACCTTGAGCCGAGGGCCACAGAC |
altered cDNA sequence snippet | CTGATTTGTATGCCATGAACTTTGAGCCGAGGGCCACAGAC |
wildtype AA sequence | MAGKKVLIVY AHQEPKSFNG SLKNVAVDEL SRQGCTVTVS DLYAMNLEPR ATDKDITGTL SNPEVFNYGV ETHEAYKQRS LASDITDEQK KVREADLVIF QFPLYWFSVP AILKGWMDRV LCQGFAFDIP GFYDSGLLQG KLALLSVTTG GTAEMYTKTG VNGDSRYFLW PLQHGTLHFC GFKVLAPQIS FAPEIASEEE RKGMVAAWSQ RLQTIWKEEP IPCTAHWHFG Q* |
mutated AA sequence | MAGKKVLIVY AHQEPKSFNG SLKNVAVDEL SRQGCTVTVS DLYAMNFEPR ATDKDITGTL SNPEVFNYGV ETHEAYKQRS LASDITDEQK KVREADLVIF QFPLYWFSVP AILKGWMDRV LCQGFAFDIP GFYDSGLLQG KLALLSVTTG GTAEMYTKTG VNGDSRYFLW PLQHGTLHFC GFKVLAPQIS FAPEIASEEE RKGMVAAWSQ RLQTIWKEEP IPCTAHWHFG Q* |
speed | 0.76 s |
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