Prediction |
polymorphism |
Model: simple_aae, prob: 1 (classification due to TGP/ExAC,
real probability is shown anyway)
(explain) |
| Summary |
- amino acid sequence changed
- homozygous in TGP or ExAC
- known disease mutation at this position (HGMD CM067657)
- protein features (might be) affected
- splice site changes
|
hyperlink |
| analysed issue |
analysis result |
| name of alteration | no title |
| alteration (phys. location) | chr1:158324425A>GN/A
show variant in all transcripts IGV
|
| HGNC symbol | CD1E |
| Ensembl transcript ID | ENST00000368165 |
| Genbank transcript ID | NM_001185107 |
| UniProt peptide | P15812 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.317A>G
cDNA.423A>G
g.1172A>G |
| AA changes | Q106R Score: 43 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 106 |
| frameshift | no |
| known variant | Reference ID: rs1065457
| database | homozygous (G/G) | heterozygous | allele carriers |
| 1000G | 1044 | 999 | 2043 |
| ExAC | 13486 | 5795 | 19281 |
known disease mutation at this position, please check HGMD for details (HGMD ID CM067657)
|
| regulatory features | N/A |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | -0.949 | 0 | | -1.691 | 0 | | (flanking) | -1.601 | 0 |
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 increased | 1163 | wt: 0.62 / mu: 0.69 | wt: GTTCCAGTTATACTTCCATAGTTTTATCCAGATAGTGCAAG
mu: GTTCCAGTTATACTTCCATAGTTTTATCCGGATAGTGCAAG | atag|TTTT | | Acc marginally increased | 1173 | wt: 0.6375 / mu: 0.6412 (marginal change - not scored) | wt: TACTTCCATAGTTTTATCCAGATAGTGCAAGCTTCTGCTGG
mu: TACTTCCATAGTTTTATCCGGATAGTGCAAGCTTCTGCTGG | ccag|ATAG | | Acc marginally increased | 1176 | wt: 0.4363 / mu: 0.4711 (marginal change - not scored) | wt: TTCCATAGTTTTATCCAGATAGTGCAAGCTTCTGCTGGTCA
mu: TTCCATAGTTTTATCCGGATAGTGCAAGCTTCTGCTGGTCA | gata|GTGC | | Acc marginally increased | 1171 | wt: 0.9201 / mu: 0.9705 (marginal change - not scored) | wt: TATACTTCCATAGTTTTATCCAGATAGTGCAAGCTTCTGCT
mu: TATACTTCCATAGTTTTATCCGGATAGTGCAAGCTTCTGCT | atcc|AGAT | | Donor increased | 1171 | wt: 0.67 / mu: 0.99 | wt: TTATCCAGATAGTGC
mu: TTATCCGGATAGTGC | ATCC|agat |
|
| distance from splice site | 39 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 106 | S | L | F | Q | L | Y | F | H | S | F | I | Q | I | V | Q | A | S | A | G | Q | F | Q | L | E |
| mutated | all conserved | | 106 | S | L | F | Q | L | Y | F | H | S | F | I | R | I | V | Q | A | S | A | G | Q | F | Q | L |
| Ptroglodytes | all conserved | ENSPTRG00000001501 | 106 | S | L | F | Q | L | Y | F | H | S | F | I | R | I | V | Q | A | S | A | G | Q | F | Q | L |
| Mmulatta | all conserved | ENSMMUG00000016784 | 106 | S | L | F | Q | L | Y | F | N | G | F | V | R | I | V | Q | A | S | A | G | Q | F | Q | L |
| Fcatus | no homologue | | | |
| Mmusculus | no homologue | | | |
| Ggallus | all conserved | ENSGALG00000012494 | 101 | S | S | I | K | S | Y | V | R | D | F | S | R | L | V | Q | | | | | | | | |
| Trubripes | no homologue | | | |
| Drerio | no homologue | | | |
| Dmelanogaster | no homologue | | | |
| Celegans | no homologue | | | |
| Xtropicalis | no homologue | | | |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 87 | 111 | HELIX | | lost | | 112 | 116 | TURN | | might get lost (downstream of altered splice site) | | 119 | 129 | STRAND | | might get lost (downstream of altered splice site) | | 132 | 134 | STRAND | | might get lost (downstream of altered splice site) | | 136 | 139 | STRAND | | might get lost (downstream of altered splice site) | | 142 | 145 | STRAND | | might get lost (downstream of altered splice site) | | 159 | 161 | TURN | | might get lost (downstream of altered splice site) | | 163 | 174 | HELIX | | might get lost (downstream of altered splice site) | | 176 | 201 | HELIX | | might get lost (downstream of altered splice site) | | 191 | 301 | DOMAIN | Ig-like. | might get lost (downstream of altered splice site) | | 202 | 205 | TURN | | might get lost (downstream of altered splice site) | | 209 | 209 | CONFLICT | V -> A (in Ref. 3; BAG64215). | might get lost (downstream of altered splice site) | | 222 | 224 | STRAND | | might get lost (downstream of altered splice site) | | 228 | 230 | STRAND | | might get lost (downstream of altered splice site) | | 230 | 230 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 232 | 234 | STRAND | | might get lost (downstream of altered splice site) | | 236 | 238 | STRAND | | might get lost (downstream of altered splice site) | | 241 | 244 | STRAND | | might get lost (downstream of altered splice site) | | 248 | 248 | CONFLICT | E -> G (in Ref. 3; BAG64215). | might get lost (downstream of altered splice site) | | 260 | 262 | STRAND | | might get lost (downstream of altered splice site) | | 263 | 265 | TURN | | might get lost (downstream of altered splice site) | | 266 | 269 | STRAND | | might get lost (downstream of altered splice site) | | 271 | 273 | STRAND | | might get lost (downstream of altered splice site) | | 277 | 280 | HELIX | | might get lost (downstream of altered splice site) | | 285 | 285 | DISULFID | By similarity. | might get lost (downstream of altered splice site) | | 285 | 288 | STRAND | | might get lost (downstream of altered splice site) | | 290 | 292 | TURN | | might get lost (downstream of altered splice site) | | 300 | 302 | STRAND | | might get lost (downstream of altered splice site) | | 305 | 325 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 897 / 897 |
| position (AA) of stopcodon in wt / mu AA sequence | 299 / 299 |
| position of stopcodon in wt / mu cDNA | 1003 / 1003 |
| 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 | 107 / 107 |
| chromosome | 1 |
| strand | 1 |
| last intron/exon boundary | 835 |
| theoretical NMD boundary in CDS | 678 |
| length of CDS | 897 |
| coding sequence (CDS) position | 317 |
cDNA position
(for ins/del: last normal base / first normal base) | 423 |
gDNA position
(for ins/del: last normal base / first normal base) | 1172 |
chromosomal position
(for ins/del: last normal base / first normal base) | 158324425 |
| original gDNA sequence snippet | ATACTTCCATAGTTTTATCCAGATAGTGCAAGCTTCTGCTG |
| altered gDNA sequence snippet | ATACTTCCATAGTTTTATCCGGATAGTGCAAGCTTCTGCTG |
| original cDNA sequence snippet | ATACTTCCATAGTTTTATCCAGATAGTGCAAGCTTCTGCTG |
| altered cDNA sequence snippet | ATACTTCCATAGTTTTATCCGGATAGTGCAAGCTTCTGCTG |
| wildtype AA sequence | MLLLFLLFEG LCCPGENTAA PQALQSYHLA AEEQLSFRML QTSSFANHSW AHSEGSGWLG
DLQTHGWDTV LGTIRFLKPW SHGNFSKQEL KNLQSLFQLY FHSFIQIVQA SAGQFQLELK
PEAWLSCGPS PGPGRLQLVC HVSGFYPKPV WVMWMRGEQE QRGTQRGDVL PNADETWYLR
ATLDVAAGEA AGLSCRVKHS SLGGHDLIIH WGGYSIFLIL ICLTVIVTLV ILVVVDSRLK
KQSSNKNILS PHTPSPVFLM GANTQDTKNS RHQFCLAQVS WIKNRVLKKW KTRLNQLW* |
| mutated AA sequence | MLLLFLLFEG LCCPGENTAA PQALQSYHLA AEEQLSFRML QTSSFANHSW AHSEGSGWLG
DLQTHGWDTV LGTIRFLKPW SHGNFSKQEL KNLQSLFQLY FHSFIRIVQA SAGQFQLELK
PEAWLSCGPS PGPGRLQLVC HVSGFYPKPV WVMWMRGEQE QRGTQRGDVL PNADETWYLR
ATLDVAAGEA AGLSCRVKHS SLGGHDLIIH WGGYSIFLIL ICLTVIVTLV ILVVVDSRLK
KQSSNKNILS PHTPSPVFLM GANTQDTKNS RHQFCLAQVS WIKNRVLKKW KTRLNQLW* |
| speed | 1.31 s |
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