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
|
hyperlink |
| analysed issue |
analysis result |
| name of alteration | no title |
| alteration (phys. location) | chr6:3010390C>TN/A
show variant in all transcripts IGV
|
| HGNC symbol | NQO2 |
| Ensembl transcript ID | ENST00000380430 |
| Genbank transcript ID | N/A |
| UniProt peptide | P16083 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.139C>T
cDNA.434C>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)
|
| 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 |
|
| 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 | | | |
|
| 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) |
|
| 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 | 991 / 991 |
| 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 | 296 / 296 |
| chromosome | 6 |
| strand | 1 |
| last intron/exon boundary | 815 |
| 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) | 434 |
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 | 1.22 s |
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