Prediction |
disease causing |
Model: simple_aae, prob: 0.999999822325716 (classification due to ClinVar,
real probability is shown anyway)
(explain) |
| Summary |
- amino acid sequence changed
- known disease mutation at this position (HGMD CM900082)
- known disease mutation: rs234 (pathogenic)
- protein features (might be) affected
- splice site changes
|
hyperlink |
| analysed issue |
analysis result |
| name of alteration | no title |
| alteration (phys. location) | chr22:43024239A>GN/A
show variant in all transcripts IGV
|
| HGNC symbol | CYB5R3 |
| Ensembl transcript ID | ENST00000402438 |
| Genbank transcript ID | N/A |
| UniProt peptide | P00387 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.313T>C
cDNA.497T>C
g.21336T>C |
| AA changes | S105P Score: 74 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 105 |
| frameshift | no |
| known variant | Reference ID: rs121965006
| database | homozygous (G/G) | heterozygous | allele carriers |
| 1000G | - | - | - |
| ExAC | 0 | 1 | 1 |
known disease mutation: rs234 (pathogenic for Methemoglobinemia type 2) dbSNP
NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM900082)
known disease mutation at this position, please check HGMD for details (HGMD ID CM900082)
known disease mutation at this position, please check HGMD for details (HGMD ID CM900082)
|
| regulatory features | H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 1.745 | 1 | | 1.763 | 1 | | (flanking) | 3.578 | 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 | | Donor marginally increased | 21327 | wt: 0.3044 / mu: 0.3192 (marginal change - not scored) | wt: CTGGAGGGAAGATGT
mu: CTGGAGGGAAGATGC | GGAG|ggaa | | Donor gained | 21331 | 0.38 | mu: AGGGAAGATGCCTCA | GGAA|gatg | | Donor gained | 21335 | 0.53 | mu: AAGATGCCTCAGTAC | GATG|cctc |
|
| distance from splice site | 49 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 105 | T | H | P | K | F | P | A | G | G | K | M | S | Q | Y | L | E | S | M | Q | I | G | D | T | I |
| mutated | not conserved | | 105 | T | H | P | K | F | P | A | G | G | K | M | P | Q | Y | L | E | S | M | Q | I | G | D | T |
| Ptroglodytes | all identical | ENSPTRG00000014461 | 128 | T | H | P | K | F | P | A | G | G | K | M | S | Q | Y | L | E | S | M | Q | I | G | D | T |
| Mmulatta | all identical | ENSMMUG00000010198 | 128 | T | H | P | K | F | P | A | G | G | K | M | S | Q | Y | L | E | S | M | Q | I | G | D | T |
| Fcatus | no homologue | | | |
| Mmusculus | all identical | ENSMUSG00000018042 | 105 | T | H | P | K | F | P | A | G | G | K | M | S | Q | Y | L | E | N | M | K | I | G | D | T |
| Ggallus | all identical | ENSGALG00000014122 | 128 | V | H | P | K | F | P | D | G | G | K | M | S | Q | Y | L | D | N | L | K | I | G | D | T |
| Trubripes | all identical | ENSTRUG00000013823 | 126 | V | H | P | K | F | P | E | G | G | K | M | S | Q | Y | L | E | S | L | K | I | G | D | F |
| Drerio | all identical | ENSDARG00000005891 | 125 | I | H | P | K | F | P | D | G | G | K | M | S | Q | Y | L | E | S | L | R | I | G | D | T |
| Dmelanogaster | all conserved | FBgn0036211 | 142 | S | H | P | K | F | P | A | G | G | K | M | T | Q | H | L | E | Q | L | E | L | G | D | K |
| Celegans | all identical | T05H4.5 | 136 | T | N | E | K | F | P | E | G | G | K | M | S | Q | H | L | E | S | L | K | I | G | D | T |
| Xtropicalis | all identical | ENSXETG00000016513 | 130 | I | H | P | K | F | P | E | G | G | K | M | S | Q | Y | L | D | S | L | R | I | D | E | T |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 40 | 152 | DOMAIN | FAD-binding FR-type. | lost | | 104 | 111 | STRAND | | lost | | 115 | 118 | STRAND | | might get lost (downstream of altered splice site) | | 120 | 120 | MOD_RES | N6-acetyllysine (By similarity). | might get lost (downstream of altered splice site) | | 126 | 133 | HELIX | | might get lost (downstream of altered splice site) | | 130 | 130 | MOD_RES | Phosphotyrosine (By similarity). | might get lost (downstream of altered splice site) | | 132 | 147 | NP_BIND | FAD (By similarity). | might get lost (downstream of altered splice site) | | 139 | 146 | STRAND | | might get lost (downstream of altered splice site) | | 148 | 153 | STRAND | | might get lost (downstream of altered splice site) | | 156 | 159 | STRAND | | might get lost (downstream of altered splice site) | | 168 | 171 | STRAND | | might get lost (downstream of altered splice site) | | 171 | 206 | NP_BIND | FAD (By similarity). | might get lost (downstream of altered splice site) | | 173 | 180 | STRAND | | might get lost (downstream of altered splice site) | | 181 | 183 | HELIX | | might get lost (downstream of altered splice site) | | 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 | 1021 / 1021 |
| 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 | 185 / 185 |
| chromosome | 22 |
| strand | -1 |
| last intron/exon boundary | 849 |
| theoretical NMD boundary in CDS | 614 |
| length of CDS | 837 |
| coding sequence (CDS) position | 313 |
cDNA position
(for ins/del: last normal base / first normal base) | 497 |
gDNA position
(for ins/del: last normal base / first normal base) | 21336 |
chromosomal position
(for ins/del: last normal base / first normal base) | 43024239 |
| original gDNA sequence snippet | TTCCCGCTGGAGGGAAGATGTCTCAGTACCTGGAGAGCATG |
| altered gDNA sequence snippet | TTCCCGCTGGAGGGAAGATGCCTCAGTACCTGGAGAGCATG |
| original cDNA sequence snippet | TTCCCGCTGGAGGGAAGATGTCTCAGTACCTGGAGAGCATG |
| altered cDNA sequence snippet | TTCCCGCTGGAGGGAAGATGCCTCAGTACCTGGAGAGCATG |
| 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 GGKMPQYLES MQIGDTIEFR
GPSGLLVYQG KGKFAIRPDK KSNPIIRTVK SVGMIAGGTG ITPMLQVIRA IMKDPDDHTV
CHLLFANQTE KDILLRPELE ELRNKHSARF KLWYTLDRAP EAWDYGQGFV NEEMIRDHLP
PPEEEPLVLM CGPPPMIQYA CLPNLDHVGH PTERCFVF* |
| speed | 0.98 s |
|
|
