Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999999379938 (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 CM056992)
- protein features (might be) affected
- splice site changes
|
hyperlink |
| analysed issue |
analysis result |
| name of alteration | no title |
| alteration (phys. location) | chr6:33272855G>CN/A
show variant in all transcripts IGV
|
| HGNC symbol | TAPBP |
| Ensembl transcript ID | ENST00000489157 |
| Genbank transcript ID | NM_172209 |
| UniProt peptide | O15533 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.518C>G
cDNA.731C>G
g.9310C>G |
| AA changes | T173R Score: 71 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 173 |
| frameshift | no |
| known variant | Reference ID: rs2071888
| database | homozygous (C/C) | heterozygous | allele carriers |
| 1000G | 917 | 1127 | 2044 |
| ExAC | 20032 | -7297 | 12735 |
known disease mutation at this position, please check HGMD for details (HGMD ID CM056992)
|
| regulatory features | H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | -0.372 | 0.356 | | 0.821 | 0.372 | | (flanking) | 0.324 | 0.372 |
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 gained | 9309 | 0.33 | mu: ATGGGACCTTCTGGCTGCCTAGAGTTCAACCCTTTCAGGAG | ccta|GAGT | | Donor gained | 9304 | 0.63 | mu: CTGGCTGCCTAGAGT | GGCT|gcct | | Donor gained | 9306 | 0.89 | mu: GGCTGCCTAGAGTTC | CTGC|ctag |
|
| distance from splice site | 90 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 173 | P | W | T | G | N | G | T | F | W | L | P | T | V | Q | P | F | Q | E | G | T | Y | L | A | T |
| mutated | not conserved | | 173 | P | W | T | G | N | G | T | F | W | L | P | R | V | Q | P | F | Q | E | G | | | | |
| Ptroglodytes | not conserved | ENSPTRG00000018043 | 260 | P | W | T | G | N | G | T | F | W | L | P | R | V | Q | P | F | Q | E | G | T | Y | L | A |
| Mmulatta | not conserved | ENSMMUG00000003875 | 260 | P | W | T | G | N | G | T | F | W | L | P | R | V | Q | P | F | Q | E | G | T | Y | L | A |
| Fcatus | no homologue | | | |
| Mmusculus | not conserved | ENSMUSG00000024308 | 263 | P | W | T | G | N | G | T | F | W | L | P | A | V | K | P | S | Q | E | G | V | Y | L | A |
| Ggallus | not conserved | ENSGALG00000008022 | 251 | D | G | V | T | A | V | T | L | R | L | A | Q | P | S | P | G | D | E | G | T | Y | I | C |
| Trubripes | not conserved | ENSTRUG00000003327 | 261 | - | - | R | G | N | A | S | L | I | L | Q | K | A | E | V | H | H | S | G | | | | |
| Drerio | not conserved | ENSDARG00000079402 | 264 | Y | Q | T | G | N | V | S | L | I | L | E | E | S | Q | V | R | H | S | G | T | Y | I | C |
| Dmelanogaster | no homologue | | | |
| Celegans | no homologue | | | |
| Xtropicalis | no homologue | | | |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 21 | 414 | TOPO_DOM | Lumenal (Potential). | lost | | 169 | 171 | STRAND | | might get lost (downstream of altered splice site) | | 176 | 178 | STRAND | | might get lost (downstream of altered splice site) | | 181 | 184 | STRAND | | might get lost (downstream of altered splice site) | | 203 | 210 | STRAND | | might get lost (downstream of altered splice site) | | 213 | 220 | STRAND | | might get lost (downstream of altered splice site) | | 236 | 242 | STRAND | | might get lost (downstream of altered splice site) | | 250 | 258 | STRAND | | might get lost (downstream of altered splice site) | | 253 | 253 | CARBOHYD | N-linked (GlcNAc...). | might get lost (downstream of altered splice site) | | 263 | 265 | HELIX | | might get lost (downstream of altered splice site) | | 267 | 275 | STRAND | | might get lost (downstream of altered splice site) | | 274 | 274 | CONFLICT | H -> Y (in Ref. 10; AAH80574). | might get lost (downstream of altered splice site) | | 278 | 290 | STRAND | | might get lost (downstream of altered splice site) | | 292 | 399 | DOMAIN | Ig-like C1-type. | might get lost (downstream of altered splice site) | | 293 | 300 | STRAND | | might get lost (downstream of altered splice site) | | 313 | 323 | STRAND | | might get lost (downstream of altered splice site) | | 315 | 315 | DISULFID | | might get lost (downstream of altered splice site) | | 327 | 337 | STRAND | | might get lost (downstream of altered splice site) | | 345 | 349 | STRAND | | might get lost (downstream of altered splice site) | | 360 | 367 | STRAND | | might get lost (downstream of altered splice site) | | 373 | 375 | HELIX | | might get lost (downstream of altered splice site) | | 379 | 385 | STRAND | | might get lost (downstream of altered splice site) | | 382 | 382 | DISULFID | | might get lost (downstream of altered splice site) | | 394 | 399 | STRAND | | might get lost (downstream of altered splice site) | | 412 | 412 | CONFLICT | D -> N (in Ref. 7; AAD32924). | might get lost (downstream of altered splice site) | | 415 | 435 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) | | 428 | 428 | SITE | May be involved in interaction with TAP. | might get lost (downstream of altered splice site) | | 436 | 448 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 1086 / 1086 |
| position (AA) of stopcodon in wt / mu AA sequence | 362 / 362 |
| position of stopcodon in wt / mu cDNA | 1299 / 1299 |
| 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 | 214 / 214 |
| chromosome | 6 |
| strand | -1 |
| last intron/exon boundary | 1288 |
| theoretical NMD boundary in CDS | 1024 |
| length of CDS | 1086 |
| coding sequence (CDS) position | 518 |
cDNA position
(for ins/del: last normal base / first normal base) | 731 |
gDNA position
(for ins/del: last normal base / first normal base) | 9310 |
chromosomal position
(for ins/del: last normal base / first normal base) | 33272855 |
| original gDNA sequence snippet | TGGGACCTTCTGGCTGCCTACAGTTCAACCCTTTCAGGAGG |
| altered gDNA sequence snippet | TGGGACCTTCTGGCTGCCTAGAGTTCAACCCTTTCAGGAGG |
| original cDNA sequence snippet | TGGGACCTTCTGGCTGCCTACAGTTCAACCCTTTCAGGAGG |
| altered cDNA sequence snippet | TGGGACCTTCTGGCTGCCTAGAGTTCAACCCTTTCAGGAGG |
| wildtype AA sequence | MKSLSLLLAV ALGLATAVSA GPAVIECWFV EDASGKGLAK RPGALLLRQG PGEPPPRPDL
DPELYLSVHV VLTVLTHTPA PRVRLGQDAL LDLSFAYMPP TSEAASSLAP GPPPFGLEWR
RQHLGKGHLL LAATPGLNGQ MPAAQEGAVA FAAWDDDEPW GPWTGNGTFW LPTVQPFQEG
TYLATIHLPY LQGQVTLELA VYKPPKVSLM PATLARAAPG EAPPELLCLV SHFYPSGGLE
VEWELRGGPG GRSQKAEGQR WLSALRHHSD GSVSLSGHLQ PPPVTTEQHG ARYACRIHHP
SLPASGRSAE VTLEVAGLSG PSLEDSVGLF LSAFLLLGLF KALGWAAVYL STCKDSKKKA
E* |
| mutated AA sequence | MKSLSLLLAV ALGLATAVSA GPAVIECWFV EDASGKGLAK RPGALLLRQG PGEPPPRPDL
DPELYLSVHV VLTVLTHTPA PRVRLGQDAL LDLSFAYMPP TSEAASSLAP GPPPFGLEWR
RQHLGKGHLL LAATPGLNGQ MPAAQEGAVA FAAWDDDEPW GPWTGNGTFW LPRVQPFQEG
TYLATIHLPY LQGQVTLELA VYKPPKVSLM PATLARAAPG EAPPELLCLV SHFYPSGGLE
VEWELRGGPG GRSQKAEGQR WLSALRHHSD GSVSLSGHLQ PPPVTTEQHG ARYACRIHHP
SLPASGRSAE VTLEVAGLSG PSLEDSVGLF LSAFLLLGLF KALGWAAVYL STCKDSKKKA
E* |
| speed | 1.23 s |
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