Prediction |
disease causing |
Model: simple_aae, prob: 0.999999999703457
(explain) |
| Summary |
- amino acid sequence changed
- known as potential disease variant: rs3595 (probable pathogenic)
- known disease mutation at this position (HGMD CM970026)
- protein features (might be) affected
- splice site changes
|
hyperlink |
| analysed issue |
analysis result |
| name of alteration | no title |
| alteration (phys. location) | chr1:76205773A>GN/A
show variant in all transcripts IGV
|
| HGNC symbol | ACADM |
| Ensembl transcript ID | ENST00000420607 |
| Genbank transcript ID | NM_001127328 |
| UniProt peptide | P11310 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.589A>G
cDNA.597A>G
g.15738A>G |
| AA changes | T197A Score: 58 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 197 |
| frameshift | no |
| known variant | Reference ID: rs121434279
Allele 'G' was neither found in ExAC nor 1000G.
known as potential disease variant: rs3595 (probable pathogenic for Medium-chain acyl-coenzyme A dehydrogenase deficiency) dbSNP
NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970026)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970026)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970026)
|
| regulatory features | H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 1.368 | 1 | | 4.94 | 1 | | (flanking) | 5.984 | 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 | 15741 | wt: 0.8986 / mu: 0.9181 (marginal change - not scored) | wt: TAACCAACGGAGGAA
mu: TAGCCAACGGAGGAA | ACCA|acgg | | Donor gained | 15737 | 0.70 | mu: TGGATAGCCAACGGA | GATA|gcca | | Donor gained | 15732 | 0.40 | mu: AGATGTGGATAGCCA | ATGT|ggat |
|
| distance from splice site | 23 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 197 | E | Y | I | I | N | G | Q | K | M | W | I | T | N | G | G | K | A | N | W | Y | F | L | L | A |
| mutated | not conserved | | 197 | E | Y | I | I | N | G | Q | K | M | W | I | A | N | G | G | K | A | N | W | Y | F | L | L |
| Ptroglodytes | all identical | ENSPTRG00000000871 | 193 | E | Y | I | I | N | G | Q | K | M | W | I | T | N | G | G | K | A | N | W | Y | F | L | L |
| Mmulatta | all identical | ENSMMUG00000007220 | 226 | E | Y | I | I | N | G | Q | K | M | W | I | T | N | G | G | K | A | S | W | Y | F | L | |
| Fcatus | no homologue | | | |
| Mmusculus | all identical | ENSMUSG00000062908 | 193 | E | Y | V | I | N | G | Q | K | M | W | I | T | N | G | G | K | A | N | W | Y | F | L | L |
| Ggallus | no homologue | | | |
| Trubripes | all identical | ENSTRUG00000007137 | 222 | E | Y | V | V | N | G | Q | K | M | W | I | T | N | G | G | K | A | N | W | Y | F | L | L |
| Drerio | all identical | ENSDARG00000038900 | 198 | D | Y | V | I | N | G | Q | K | M | W | I | T | N | G | G | K | A | N | W | Y | F | L | L |
| Dmelanogaster | all identical | FBgn0035811 | 189 | | | | | | | Q | K | M | W | I | T | N | G | G | V | A | N | W | Y | F | V | L |
| Celegans | all identical | T08G2.3 | 183 | E | Y | I | I | N | G | S | K | A | W | I | T | G | G | G | H | A | K | W | F | F | V | L |
| Xtropicalis | all identical | ENSXETG00000002983 | 198 | | Y | I | I | N | G | Q | K | M | W | I | T | N | G | G | K | A | N | W | Y | F | L | L |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 194 | 197 | TURN | | lost | | 199 | 206 | STRAND | | might get lost (downstream of altered splice site) | | 212 | 212 | MOD_RES | N6-acetyllysine. | might get lost (downstream of altered splice site) | | 215 | 217 | HELIX | | might get lost (downstream of altered splice site) | | 216 | 216 | BINDING | Substrate. | might get lost (downstream of altered splice site) | | 219 | 225 | STRAND | | might get lost (downstream of altered splice site) | | 231 | 233 | STRAND | | might get lost (downstream of altered splice site) | | 237 | 237 | MUTAGEN | E->A: Strongly reduced rate of electron transfer to ETF. | might get lost (downstream of altered splice site) | | 239 | 241 | STRAND | | might get lost (downstream of altered splice site) | | 247 | 258 | STRAND | | might get lost (downstream of altered splice site) | | 259 | 261 | HELIX | | might get lost (downstream of altered splice site) | | 262 | 265 | STRAND | | might get lost (downstream of altered splice site) | | 266 | 268 | TURN | | might get lost (downstream of altered splice site) | | 269 | 303 | HELIX | | might get lost (downstream of altered splice site) | | 278 | 281 | REGION | Substrate binding. | might get lost (downstream of altered splice site) | | 279 | 279 | MOD_RES | N6-acetyllysine. | might get lost (downstream of altered splice site) | | 301 | 301 | MOD_RES | N6-acetyllysine. | might get lost (downstream of altered splice site) | | 306 | 308 | NP_BIND | FAD. | might get lost (downstream of altered splice site) | | 309 | 312 | STRAND | | might get lost (downstream of altered splice site) | | 313 | 315 | HELIX | | might get lost (downstream of altered splice site) | | 316 | 317 | NP_BIND | FAD. | might get lost (downstream of altered splice site) | | 317 | 345 | HELIX | | might get lost (downstream of altered splice site) | | 351 | 376 | HELIX | | might get lost (downstream of altered splice site) | | 356 | 356 | CONFLICT | I -> T (in Ref. 3; AAF63626). | might get lost (downstream of altered splice site) | | 374 | 378 | NP_BIND | FAD. | might get lost (downstream of altered splice site) | | 377 | 379 | HELIX | | might get lost (downstream of altered splice site) | | 384 | 384 | MUTAGEN | E->A: Reduces rate of electron transfer to ETF three-fold. | might get lost (downstream of altered splice site) | | 384 | 384 | MUTAGEN | E->Q: Reduces rate of electron transfer to ETF two-fold. | might get lost (downstream of altered splice site) | | 387 | 394 | HELIX | | might get lost (downstream of altered splice site) | | 395 | 398 | HELIX | | might get lost (downstream of altered splice site) | | 399 | 401 | TURN | | might get lost (downstream of altered splice site) | | 401 | 401 | ACT_SITE | Proton acceptor. | might get lost (downstream of altered splice site) | | 402 | 402 | BINDING | Substrate; via amide nitrogen. | might get lost (downstream of altered splice site) | | 403 | 405 | NP_BIND | FAD. | might get lost (downstream of altered splice site) | | 404 | 417 | HELIX | | might get lost (downstream of altered splice site) | | 413 | 413 | BINDING | Substrate. | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 1278 / 1278 |
| position (AA) of stopcodon in wt / mu AA sequence | 426 / 426 |
| position of stopcodon in wt / mu cDNA | 1286 / 1286 |
| 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 | 9 / 9 |
| chromosome | 1 |
| strand | 1 |
| last intron/exon boundary | 1215 |
| theoretical NMD boundary in CDS | 1156 |
| length of CDS | 1278 |
| coding sequence (CDS) position | 589 |
cDNA position
(for ins/del: last normal base / first normal base) | 597 |
gDNA position
(for ins/del: last normal base / first normal base) | 15738 |
chromosomal position
(for ins/del: last normal base / first normal base) | 76205773 |
| original gDNA sequence snippet | ATGGTCAGAAGATGTGGATAACCAACGGAGGAAAAGCTAAT |
| altered gDNA sequence snippet | ATGGTCAGAAGATGTGGATAGCCAACGGAGGAAAAGCTAAT |
| original cDNA sequence snippet | ATGGTCAGAAGATGTGGATAACCAACGGAGGAAAAGCTAAT |
| altered cDNA sequence snippet | ATGGTCAGAAGATGTGGATAGCCAACGGAGGAAAAGCTAAT |
| wildtype AA sequence | MAAGFGRCCR CSLQVLRSIS RFHWRSQHTK ANRQREPGLG FSFEFTEQQK EFQATARKFA
REEIIPVAAE YDKTGEYPVP LIRRAWELGL MNTHIPENCG GLGLGTFDAC LISEELAYGC
TGVQTAIEGN SLGQMPIIIA GNDQQKKKYL GRMTEEPLMC AYCVTEPGAG SDVAGIKTKA
EKKGDEYIIN GQKMWITNGG KANWYFLLAR SDPDPKAPAN KAFTGFIVEA DTPGIQIGRK
ELNMGQRCSD TRGIVFEDVK VPKENVLIGD GAGFKVAMGA FDKTRPVVAA GAVGLAQRAL
DEATKYALER KTFGKLLVEH QAISFMLAEM AMKVELARMS YQRAAWEVDS GRRNTYYASI
AKAFAGDIAN QLATDAVQIL GGNGFNTEYP VEKLMRDAKI YQIYEGTSQI QRLIVAREHI
DKYKN* |
| mutated AA sequence | MAAGFGRCCR CSLQVLRSIS RFHWRSQHTK ANRQREPGLG FSFEFTEQQK EFQATARKFA
REEIIPVAAE YDKTGEYPVP LIRRAWELGL MNTHIPENCG GLGLGTFDAC LISEELAYGC
TGVQTAIEGN SLGQMPIIIA GNDQQKKKYL GRMTEEPLMC AYCVTEPGAG SDVAGIKTKA
EKKGDEYIIN GQKMWIANGG KANWYFLLAR SDPDPKAPAN KAFTGFIVEA DTPGIQIGRK
ELNMGQRCSD TRGIVFEDVK VPKENVLIGD GAGFKVAMGA FDKTRPVVAA GAVGLAQRAL
DEATKYALER KTFGKLLVEH QAISFMLAEM AMKVELARMS YQRAAWEVDS GRRNTYYASI
AKAFAGDIAN QLATDAVQIL GGNGFNTEYP VEKLMRDAKI YQIYEGTSQI QRLIVAREHI
DKYKN* |
| speed | 0.95 s |
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