Prediction |
disease causing |
Model: simple_aae, prob: 1
(explain) |
Summary |
- amino acid sequence changed
- known as potential disease variant: rs1977 (probable pathogenic)
- known disease mutation at this position (HGMD CM034198)
- known disease mutation at this position (HGMD CM962529)
- 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) | chr20:43255238C>AN/A
show variant in all transcripts IGV
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HGNC symbol | ADA |
Ensembl transcript ID | ENST00000372874 |
Genbank transcript ID | NM_000022 |
UniProt peptide | P00813 |
alteration type | single base exchange |
alteration region | CDS |
DNA changes | c.221G>T cDNA.356G>T g.25637G>T |
AA changes | G74V Score: 109 explain score(s) |
position(s) of altered AA if AA alteration in CDS | 74 |
frameshift | no |
known variant | Reference ID: rs199422328
database | homozygous (A/A) | heterozygous | allele carriers |
1000G | - | - | - |
ExAC | 0 | 1 | 1 |
known as potential disease variant: rs1977 (probable pathogenic for Severe combined immunodeficiency due to ADA deficiency) dbSNP
NCBI variation viewer known disease mutation at this position, please check HGMD for details (HGMD ID CM962529)
known disease mutation at this position, please check HGMD for details (HGMD ID CM962529) known disease mutation at this position, please check HGMD for details (HGMD ID CM034198)
known disease mutation at this position, please check HGMD for details (HGMD ID CM962529) known disease mutation at this position, please check HGMD for details (HGMD ID CM034198) known disease mutation at this position, please check HGMD for details (HGMD ID CM034198)
known disease mutation at this position, please check HGMD for details (HGMD ID CM962529) known disease mutation at this position, please check HGMD for details (HGMD ID CM034198) known disease mutation at this position, please check HGMD for details (HGMD ID CM034198) known disease mutation at this position, please check HGMD for details (HGMD ID CM962529)
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regulatory features | H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
phyloP / phastCons | | PhyloP | PhastCons |
(flanking) | 0.392 | 1 | | 5.458 | 1 | (flanking) | 5.458 | 1 | 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 | Acceptor lost | 25634.5 | sequence motif lost | - | wt: ccca|GGGG mu: ccca.GGGT | Acc marginally increased | 25627 | wt: 0.9656 / mu: 0.9666 (marginal change - not scored) | wt: GTTCCCAACCCCTTTCTTCCCTTCCCAGGGGCTGCCGGGAG mu: GTTCCCAACCCCTTTCTTCCCTTCCCAGGGTCTGCCGGGAG | tccc|TTCC | Acc marginally increased | 25635 | wt: 0.9672 / mu: 0.9825 (marginal change - not scored) | wt: CCCCTTTCTTCCCTTCCCAGGGGCTGCCGGGAGGCTATCAA mu: CCCCTTTCTTCCCTTCCCAGGGTCTGCCGGGAGGCTATCAA | cagg|GGCT | Acc marginally increased | 25628 | wt: 0.8912 / mu: 0.8984 (marginal change - not scored) | wt: TTCCCAACCCCTTTCTTCCCTTCCCAGGGGCTGCCGGGAGG mu: TTCCCAACCCCTTTCTTCCCTTCCCAGGGTCTGCCGGGAGG | ccct|TCCC | Acc marginally increased | 25633 | wt: 0.9939 / mu: 0.9941 (marginal change - not scored) | wt: AACCCCTTTCTTCCCTTCCCAGGGGCTGCCGGGAGGCTATC mu: AACCCCTTTCTTCCCTTCCCAGGGTCTGCCGGGAGGCTATC | ccca|GGGG | Acc marginally increased | 25634 | wt: 0.9630 / mu: 0.9655 (marginal change - not scored) | wt: ACCCCTTTCTTCCCTTCCCAGGGGCTGCCGGGAGGCTATCA mu: ACCCCTTTCTTCCCTTCCCAGGGTCTGCCGGGAGGCTATCA | ccag|GGGC | Donor increased | 25642 | wt: 0.44 / mu: 0.79 | wt: GCTGCCGGGAGGCTA mu: TCTGCCGGGAGGCTA | TGCC|ggga | Acc gained | 25643 | 0.31 | mu: TTCCCTTCCCAGGGTCTGCCGGGAGGCTATCAAAAGGATCG | gccg|GGAG | Acc gained | 25639 | 0.50 | mu: TTTCTTCCCTTCCCAGGGTCTGCCGGGAGGCTATCAAAAGG | gtct|GCCG |
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distance from splice site | 3 |
Kozak consensus sequence altered? | N/A |
conservation protein level for non-synonymous changes | |
protein features | start (aa) | end (aa) | feature | details | | 76 | 91 | HELIX | | might get lost (downstream of altered splice site) | 92 | 94 | TURN | | might get lost (downstream of altered splice site) | 95 | 102 | STRAND | | might get lost (downstream of altered splice site) | 104 | 107 | HELIX | | might get lost (downstream of altered splice site) | 109 | 111 | STRAND | | might get lost (downstream of altered splice site) | 116 | 118 | HELIX | | might get lost (downstream of altered splice site) | 126 | 144 | HELIX | | might get lost (downstream of altered splice site) | 147 | 155 | STRAND | | might get lost (downstream of altered splice site) | 159 | 161 | HELIX | | might get lost (downstream of altered splice site) | 162 | 171 | HELIX | | might get lost (downstream of altered splice site) | 172 | 176 | TURN | | might get lost (downstream of altered splice site) | 177 | 184 | STRAND | | might get lost (downstream of altered splice site) | 184 | 184 | BINDING | Substrate; via amide nitrogen. | might get lost (downstream of altered splice site) | 191 | 193 | HELIX | | might get lost (downstream of altered splice site) | 195 | 207 | HELIX | | might get lost (downstream of altered splice site) | 210 | 219 | STRAND | | might get lost (downstream of altered splice site) | 214 | 214 | METAL | Zinc; catalytic. | might get lost (downstream of altered splice site) | 217 | 217 | ACT_SITE | Proton donor (Probable). | might get lost (downstream of altered splice site) | 221 | 229 | HELIX | | might get lost (downstream of altered splice site) | 232 | 232 | MOD_RES | N6-acetyllysine. | might get lost (downstream of altered splice site) | 234 | 238 | STRAND | | might get lost (downstream of altered splice site) | 238 | 238 | SITE | Important for catalytic activity (By similarity). | might get lost (downstream of altered splice site) | 240 | 244 | HELIX | | might get lost (downstream of altered splice site) | 246 | 254 | HELIX | | might get lost (downstream of altered splice site) | 258 | 261 | STRAND | | might get lost (downstream of altered splice site) | 263 | 268 | HELIX | | might get lost (downstream of altered splice site) | 270 | 272 | STRAND | | might get lost (downstream of altered splice site) | 279 | 285 | HELIX | | might get lost (downstream of altered splice site) | 290 | 292 | STRAND | | might get lost (downstream of altered splice site) | 295 | 295 | METAL | Zinc; catalytic. | might get lost (downstream of altered splice site) | 296 | 296 | BINDING | Substrate. | might get lost (downstream of altered splice site) | 297 | 300 | HELIX | | might get lost (downstream of altered splice site) | 304 | 315 | HELIX | | might get lost (downstream of altered splice site) | 319 | 331 | HELIX | | might get lost (downstream of altered splice site) | 333 | 335 | STRAND | | might get lost (downstream of altered splice site) | 337 | 351 | HELIX | | might get lost (downstream of altered splice site) | 340 | 340 | CONFLICT | K -> R (in Ref. 5; BAD97117). | might get lost (downstream of altered splice site) | 355 | 362 | HELIX | | 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 | 1092 / 1092 |
position (AA) of stopcodon in wt / mu AA sequence | 364 / 364 |
position of stopcodon in wt / mu cDNA | 1227 / 1227 |
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 | 136 / 136 |
chromosome | 20 |
strand | -1 |
last intron/exon boundary | 1214 |
theoretical NMD boundary in CDS | 1028 |
length of CDS | 1092 |
coding sequence (CDS) position | 221 |
cDNA position (for ins/del: last normal base / first normal base) | 356 |
gDNA position (for ins/del: last normal base / first normal base) | 25637 |
chromosomal position (for ins/del: last normal base / first normal base) | 43255238 |
original gDNA sequence snippet | CCTTTCTTCCCTTCCCAGGGGCTGCCGGGAGGCTATCAAAA |
altered gDNA sequence snippet | CCTTTCTTCCCTTCCCAGGGTCTGCCGGGAGGCTATCAAAA |
original cDNA sequence snippet | CTACATGCCTGCTATCGCGGGCTGCCGGGAGGCTATCAAAA |
altered cDNA sequence snippet | CTACATGCCTGCTATCGCGGTCTGCCGGGAGGCTATCAAAA |
wildtype AA sequence | MAQTPAFDKP KVELHVHLDG SIKPETILYY GRRRGIALPA NTAEGLLNVI GMDKPLTLPD FLAKFDYYMP AIAGCREAIK RIAYEFVEMK AKEGVVYVEV RYSPHLLANS KVEPIPWNQA EGDLTPDEVV ALVGQGLQEG ERDFGVKARS ILCCMRHQPN WSPKVVELCK KYQQQTVVAI DLAGDETIPG SSLLPGHVQA YQEAVKSGIH RTVHAGEVGS AEVVKEAVDI LKTERLGHGY HTLEDQALYN RLRQENMHFE ICPWSSYLTG AWKPDTEHAV IRLKNDQANY SLNTDDPLIF KSTLDTDYQM TKRDMGFTEE EFKRLNINAA KSSFLPEDEK RELLDLLYKA YGMPPSASAG QNL* |
mutated AA sequence | MAQTPAFDKP KVELHVHLDG SIKPETILYY GRRRGIALPA NTAEGLLNVI GMDKPLTLPD FLAKFDYYMP AIAVCREAIK RIAYEFVEMK AKEGVVYVEV RYSPHLLANS KVEPIPWNQA EGDLTPDEVV ALVGQGLQEG ERDFGVKARS ILCCMRHQPN WSPKVVELCK KYQQQTVVAI DLAGDETIPG SSLLPGHVQA YQEAVKSGIH RTVHAGEVGS AEVVKEAVDI LKTERLGHGY HTLEDQALYN RLRQENMHFE ICPWSSYLTG AWKPDTEHAV IRLKNDQANY SLNTDDPLIF KSTLDTDYQM TKRDMGFTEE EFKRLNINAA KSSFLPEDEK RELLDLLYKA YGMPPSASAG QNL* |
speed | 0.99 s |
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