Prediction |
disease causing |
Model: simple_aae, prob: 1 (classification due to ClinVar,
real probability is shown anyway)
(explain) |
| Summary |
- amino acid sequence changed
- known disease mutation at this position (HGMD CM970534)
- known disease mutation: rs3982 (pathogenic)
- protein features (might be) affected
- splice site changes
|
hyperlink |
| analysed issue |
analysis result |
| name of alteration | no title |
| alteration (phys. location) | chr9:71679858G>TN/A
show variant in all transcripts IGV
|
| HGNC symbol | FXN |
| Ensembl transcript ID | ENST00000498653 |
| Genbank transcript ID | N/A |
| UniProt peptide | Q16595 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.164G>T
cDNA.269G>T
g.29684G>T |
| AA changes | G55V Score: 109 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 55 |
| frameshift | no |
| known variant | Reference ID: rs104894107
| database | homozygous (T/T) | heterozygous | allele carriers |
| 1000G | - | - | - |
| ExAC | 0 | 6 | 6 |
known disease mutation: rs3982 (pathogenic for Friedreich's ataxia|not provided) dbSNP
NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970534)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970534)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970534)
|
| regulatory features | H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 5.706 | 1 | | 5.706 | 1 | | (flanking) | -0.458 | 0.964 |
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 | 29674 | wt: 0.5958 / mu: 0.6065 (marginal change - not scored) | wt: TGCTTTTTTTCCACCTAATCCCCTAGAGTGGTGTCTTAACT
mu: TGCTTTTTTTCCACCTAATCCCCTAGAGTGTTGTCTTAACT | atcc|CCTA | | Acc decreased | 29679 | wt: 0.30 / mu: 0.21 | wt: TTTTTCCACCTAATCCCCTAGAGTGGTGTCTTAACTGTCAA
mu: TTTTTCCACCTAATCCCCTAGAGTGTTGTCTTAACTGTCAA | ctag|AGTG | | Acc marginally increased | 29675 | wt: 0.2590 / mu: 0.2848 (marginal change - not scored) | wt: GCTTTTTTTCCACCTAATCCCCTAGAGTGGTGTCTTAACTG
mu: GCTTTTTTTCCACCTAATCCCCTAGAGTGTTGTCTTAACTG | tccc|CTAG | | Donor increased | 29675 | wt: 0.85 / mu: 0.97 | wt: AATCCCCTAGAGTGG
mu: AATCCCCTAGAGTGT | TCCC|ctag | | Acc gained | 29694 | 0.51 | mu: CCCTAGAGTGTTGTCTTAACTGTCAAACTGGGTGGAGATCT | aact|GTCA |
|
| distance from splice site | 5 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 55 | T | F | E | D | Y | D | V | S | F | G | S | G | V | L | T | V | K | L | G | G | D | L | G | T |
| mutated | not conserved | | 55 | T | F | E | D | Y | D | V | S | F | G | S | V | V | L | T | V | K | | | | | | |
| Ptroglodytes | no homologue | | | |
| Mmulatta | all identical | ENSMMUG00000000357 | 130 | T | F | E | D | Y | D | V | S | F | G | S | G | V | L | T | V | K | | | | | | |
| Fcatus | all identical | ENSFCAG00000008813 | 128 | T | L | K | D | Y | D | V | S | F | G | S | G | V | L | T | V | K | | | | | | |
| Mmusculus | all identical | ENSMUSG00000059363 | 127 | T | L | E | D | Y | D | V | S | F | G | D | G | V | L | T | I | K | | | | | | |
| Ggallus | no homologue | | | |
| Trubripes | no homologue | | | |
| Drerio | all identical | ENSDARG00000074356 | 124 | T | G | L | D | Y | D | V | V | F | S | N | G | V | L | T | V | K | V | G | S | D | H | G |
| Dmelanogaster | all identical | FBgn0030092 | 108 | E | L | Q | G | T | D | V | A | Y | S | D | G | V | L | T | V | N | L | G | G | Q | H | G |
| Celegans | all identical | F59G1.7 | 60 | V | S | E | Q | F | D | V | S | H | A | M | G | V | L | T | V | N | V | S | K | S | V | G |
| Xtropicalis | no homologue | | | |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 53 | 54 | MUTAGEN | RR->GG: No effect on processing of wild- type FXN. | might get lost (downstream of altered splice site) | | 78 | 79 | MUTAGEN | LR->GG: Abolishes cleavage to yield frataxin mature form and allows accumulation of frataxin(56-210) and frataxin(78-210). | might get lost (downstream of altered splice site) | | 79 | 80 | MUTAGEN | RK->GG: Abolishes cleavage to yield frataxin mature form and allows the accumulation of frataxin(56-210). | might get lost (downstream of altered splice site) | | 92 | 114 | HELIX | | might get lost (downstream of altered splice site) | | 124 | 128 | STRAND | | might get lost (downstream of altered splice site) | | 131 | 135 | STRAND | | might get lost (downstream of altered splice site) | | 138 | 140 | TURN | | might get lost (downstream of altered splice site) | | 142 | 148 | STRAND | | might get lost (downstream of altered splice site) | | 149 | 152 | TURN | | might get lost (downstream of altered splice site) | | 153 | 157 | STRAND | | might get lost (downstream of altered splice site) | | 159 | 161 | STRAND | | might get lost (downstream of altered splice site) | | 164 | 168 | STRAND | | might get lost (downstream of altered splice site) | | 170 | 175 | STRAND | | might get lost (downstream of altered splice site) | | 175 | 175 | CONFLICT | Y -> F (in Ref. 1; AAA98508/AAA98510). | might get lost (downstream of altered splice site) | | 176 | 178 | TURN | | might get lost (downstream of altered splice site) | | 182 | 194 | HELIX | | might get lost (downstream of altered splice site) | | 202 | 202 | CONFLICT | S -> W (in Ref. 1; AAA98508/AAA98510). | might get lost (downstream of altered splice site) | | 206 | 208 | STRAND | | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 408 / 408 |
| position (AA) of stopcodon in wt / mu AA sequence | 136 / 136 |
| position of stopcodon in wt / mu cDNA | 513 / 513 |
| 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 | 106 / 106 |
| chromosome | 9 |
| strand | 1 |
| last intron/exon boundary | 363 |
| theoretical NMD boundary in CDS | 207 |
| length of CDS | 408 |
| coding sequence (CDS) position | 164 |
cDNA position
(for ins/del: last normal base / first normal base) | 269 |
gDNA position
(for ins/del: last normal base / first normal base) | 29684 |
chromosomal position
(for ins/del: last normal base / first normal base) | 71679858 |
| original gDNA sequence snippet | CCACCTAATCCCCTAGAGTGGTGTCTTAACTGTCAAACTGG |
| altered gDNA sequence snippet | CCACCTAATCCCCTAGAGTGTTGTCTTAACTGTCAAACTGG |
| original cDNA sequence snippet | TGATGTCTCCTTTGGGAGTGGTGTCTTAACTGTCAAACTGG |
| altered cDNA sequence snippet | TGATGTCTCCTTTGGGAGTGTTGTCTTAACTGTCAAACTGG |
| wildtype AA sequence | MNLRKSGTLG HPGSLDETTY ERLAEETLDS LAEFFEDLAD KPYTFEDYDV SFGSGVLTVK
LGGDLGTYVI NKQTPNKQIW LSSPSSGPKR YDWTGKNWVY SHDGVSLHEL LAAELTKALK
TKLDLSSLAY SGKDA* |
| mutated AA sequence | MNLRKSGTLG HPGSLDETTY ERLAEETLDS LAEFFEDLAD KPYTFEDYDV SFGSVVLTVK
LGGDLGTYVI NKQTPNKQIW LSSPSSGPKR YDWTGKNWVY SHDGVSLHEL LAAELTKALK
TKLDLSSLAY SGKDA* |
| speed | 1.02 s |
|
|
