Prediction |
disease causing |
Model: simple_aae, prob: 0.999999998623678 (classification due to ClinVar,
real probability is shown anyway)
(explain) |
Summary |
- amino acid sequence changed
- known disease mutation at this position (HGMD CM910019)
- known disease mutation: rs16862 (pathogenic)
- 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) | chr9:116153078C>TN/A
show variant in all transcripts IGV
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HGNC symbol | ALAD |
Ensembl transcript ID | ENST00000277315 |
Genbank transcript ID | N/A |
UniProt peptide | P13716 |
alteration type | single base exchange |
alteration region | CDS |
DNA changes | c.346G>A cDNA.608G>A g.10536G>A |
AA changes | G116R Score: 125 explain score(s) |
position(s) of altered AA if AA alteration in CDS | 116 |
frameshift | no |
known variant | Reference ID: rs121912980
database | homozygous (T/T) | heterozygous | allele carriers |
1000G | - | - | - |
ExAC | 0 | 2 | 2 |
known disease mutation: rs16862 (pathogenic for Porphobilinogen synthase deficiency) dbSNP
NCBI variation viewer known disease mutation at this position, please check HGMD for details (HGMD ID CM910019)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910019) known disease mutation at this position, please check HGMD for details (HGMD ID CM910019)
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regulatory features | H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
phyloP / phastCons | | PhyloP | PhastCons |
(flanking) | 5.433 | 1 | | 2.76 | 0.996 | (flanking) | -0.895 | 0.627 | explain score(s) and/or inspect your position(s) in in UCSC Genome Browser |
splice sites | alteration within used splice site, likely to disturb normal splicing effect | gDNA position | score | detection sequence | exon-intron border | Donor lost | 10536 | sequence motif lost | - | wt: TGCG|gtga mu: TGCA.gtga | Acc marginally increased | 10526 | wt: 0.8708 / mu: 0.8879 (marginal change - not scored) | wt: CTGTGTCCCTACACCTCCCATGGTCACTGCGGTGAGTTCCC mu: CTGTGTCCCTACACCTCCCATGGTCACTGCAGTGAGTTCCC | ccat|GGTC | Acc marginally increased | 10537 | wt: 0.2161 / mu: 0.2371 (marginal change - not scored) | wt: CACCTCCCATGGTCACTGCGGTGAGTTCCCTCCCTCCCACC mu: CACCTCCCATGGTCACTGCAGTGAGTTCCCTCCCTCCCACC | gcgg|TGAG | Donor increased | 10533 | wt: 0.45 / mu: 0.49 | wt: GTCACTGCGGTGAGT mu: GTCACTGCAGTGAGT | CACT|gcgg | Donor gained | 10531 | 0.79 | mu: TGGTCACTGCAGTGA | GTCA|ctgc |
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distance from splice site | 2 |
Kozak consensus sequence altered? | N/A |
conservation protein level for non-synonymous changes | species | match | gene | aa | alignment | Human | | | 116 | C | L | C | P | Y | T | S | H | G | H | C | G | L | L | S | E | N | G | A | F | R | A | E | E |
mutated | not conserved | | 116 | C | L | C | P | Y | T | S | H | G | H | C | R | L | L | S | E | | | | | | | |
Ptroglodytes | no homologue | | | |
Mmulatta | all identical | ENSMMUG00000031965 | 162 | C | L | C | P | Y | T | S | H | G | H | C | G | L | L | S | E | N | G | A | F | R | A | E |
Fcatus | all identical | ENSFCAG00000009244 | 149 | C | L | C | P | Y | T | S | H | G | H | C | G | L | L | G | K | N | G | T | F | Q | A | E |
Mmusculus | all identical | ENSMUSG00000028393 | 133 | C | L | C | P | Y | T | S | H | G | H | C | G | L | L | S | E | N | G | A | F | L | A | E |
Ggallus | all identical | ENSGALG00000008869 | 140 | C | L | C | P | Y | T | S | H | G | H | C | G | I | L | R | E | D | G | T | I | Q | N | E |
Trubripes | all identical | ENSTRUG00000010590 | 142 | | L | C | P | Y | T | S | H | G | H | C | G | I | L | N | D | D | G | T | L | N | N | D |
Drerio | all identical | ENSDARG00000052815 | 135 | | | C | P | Y | T | S | H | G | H | C | G | I | L | R | E | D | G | S | L | D | N | A |
Dmelanogaster | all identical | FBgn0036271 | 131 | | | | | | S | S | H | G | H | C | G | L | L | G | E | T | G | L | E | N | G | P |
Celegans | no homologue | | | |
Xtropicalis | all identical | ENSXETG00000023474 | 79 | C | L | C | P | Y | T | S | H | G | H | C | G | I | L | R | E | D | G | S | L | Q | N | E |
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protein features | start (aa) | end (aa) | feature | details | | 115 | 121 | STRAND | | lost | 122 | 122 | MUTAGEN | C->A: Reduces enzyme activity about 1000000-fold; when associated with A-124 and A-132. | might get lost (downstream of altered splice site) | 122 | 122 | METAL | Zinc 1; catalytic. | might get lost (downstream of altered splice site) | 123 | 126 | STRAND | | might get lost (downstream of altered splice site) | 124 | 124 | MUTAGEN | C->A: Reduces enzyme activity about 1000000-fold; when associated with A-122 and A-132. | might get lost (downstream of altered splice site) | 124 | 124 | METAL | Zinc 1; catalytic. | might get lost (downstream of altered splice site) | 131 | 131 | METAL | Zinc 2. | might get lost (downstream of altered splice site) | 131 | 131 | MUTAGEN | H->A: No effect on catalytic activity; when associated with A-223. | might get lost (downstream of altered splice site) | 132 | 132 | METAL | Zinc 1; catalytic. | might get lost (downstream of altered splice site) | 132 | 132 | MUTAGEN | C->A: Reduces enzyme activity about 1000000-fold; when associated with A-122 and A-124. | might get lost (downstream of altered splice site) | 141 | 160 | HELIX | | might get lost (downstream of altered splice site) | 163 | 167 | STRAND | | might get lost (downstream of altered splice site) | 174 | 184 | HELIX | | might get lost (downstream of altered splice site) | 188 | 190 | TURN | | might get lost (downstream of altered splice site) | 192 | 194 | STRAND | | might get lost (downstream of altered splice site) | 198 | 200 | STRAND | | might get lost (downstream of altered splice site) | 199 | 199 | ACT_SITE | Schiff-base intermediate with substrate. | might get lost (downstream of altered splice site) | 203 | 205 | HELIX | | might get lost (downstream of altered splice site) | 206 | 210 | HELIX | | might get lost (downstream of altered splice site) | 209 | 209 | BINDING | Substrate 1. | might get lost (downstream of altered splice site) | 221 | 221 | BINDING | Substrate 1. | might get lost (downstream of altered splice site) | 221 | 223 | HELIX | | might get lost (downstream of altered splice site) | 223 | 223 | METAL | Zinc 2. | might get lost (downstream of altered splice site) | 223 | 223 | MUTAGEN | C->A: No effect on catalytic activity; when associated with A-131. | might get lost (downstream of altered splice site) | 231 | 243 | HELIX | | might get lost (downstream of altered splice site) | 247 | 253 | STRAND | | might get lost (downstream of altered splice site) | 252 | 252 | ACT_SITE | Schiff-base intermediate with substrate. | might get lost (downstream of altered splice site) | 255 | 257 | HELIX | | might get lost (downstream of altered splice site) | 258 | 267 | HELIX | | might get lost (downstream of altered splice site) | 273 | 277 | STRAND | | might get lost (downstream of altered splice site) | 279 | 279 | BINDING | Substrate 2. | might get lost (downstream of altered splice site) | 279 | 290 | HELIX | | might get lost (downstream of altered splice site) | 296 | 310 | HELIX | | might get lost (downstream of altered splice site) | 313 | 317 | STRAND | | might get lost (downstream of altered splice site) | 318 | 318 | BINDING | Substrate 2. | might get lost (downstream of altered splice site) | 320 | 326 | HELIX | | might get lost (downstream of altered splice site) | 327 | 329 | TURN | | 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 | 942 / 942 |
position (AA) of stopcodon in wt / mu AA sequence | 314 / 314 |
position of stopcodon in wt / mu cDNA | 1204 / 1204 |
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 | 263 / 263 |
chromosome | 9 |
strand | -1 |
last intron/exon boundary | 1143 |
theoretical NMD boundary in CDS | 830 |
length of CDS | 942 |
coding sequence (CDS) position | 346 |
cDNA position (for ins/del: last normal base / first normal base) | 608 |
gDNA position (for ins/del: last normal base / first normal base) | 10536 |
chromosomal position (for ins/del: last normal base / first normal base) | 116153078 |
original gDNA sequence snippet | ACACCTCCCATGGTCACTGCGGTGAGTTCCCTCCCTCCCAC |
altered gDNA sequence snippet | ACACCTCCCATGGTCACTGCAGTGAGTTCCCTCCCTCCCAC |
original cDNA sequence snippet | ACACCTCCCATGGTCACTGCGGGCTCCTGAGTGAAAACGGA |
altered cDNA sequence snippet | ACACCTCCCATGGTCACTGCAGGCTCCTGAGTGAAAACGGA |
wildtype AA sequence | MQPQSVLHSG YFHPLLRAWQ TATTTLNASN LIYPIFVTYG VKRLEEMLRP LVEEGLRCVL IFGVPSRVPK DERGSAADSE ESPAIEAIHL LRKTFPNLLV ACDVCLCPYT SHGHCGLLSE NGAFRAEESR QRLAEVALAY AKAGCQVVAP SDMMDGRVEA IKEALMAHGL GNRVSVMSYS AKFASCFYGP FRDAAKSSPA FGDRRCYQLP PGARGLALRA VDRDVREGAD MLMVKPGMPY LDIVREVKDK HPDLPLAVYH VSGEFAMLWH GAQAGAFDLK AAVLEAMTAF RRAGADIIIT YYTPQLLQWL KEE* |
mutated AA sequence | MQPQSVLHSG YFHPLLRAWQ TATTTLNASN LIYPIFVTYG VKRLEEMLRP LVEEGLRCVL IFGVPSRVPK DERGSAADSE ESPAIEAIHL LRKTFPNLLV ACDVCLCPYT SHGHCRLLSE NGAFRAEESR QRLAEVALAY AKAGCQVVAP SDMMDGRVEA IKEALMAHGL GNRVSVMSYS AKFASCFYGP FRDAAKSSPA FGDRRCYQLP PGARGLALRA VDRDVREGAD MLMVKPGMPY LDIVREVKDK HPDLPLAVYH VSGEFAMLWH GAQAGAFDLK AAVLEAMTAF RRAGADIIIT YYTPQLLQWL KEE* |
speed | 1.10 s |
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