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
- protein features (might be) affected
- splice site changes
|
hyperlink |
| analysed issue |
analysis result |
| name of alteration | no title |
| alteration (phys. location) | chr1:153320372T>GN/A
show variant in all transcripts IGV
|
| HGNC symbol | PGLYRP4 |
| Ensembl transcript ID | ENST00000368739 |
| Genbank transcript ID | N/A |
| UniProt peptide | Q96LB8 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.37A>C
cDNA.396A>C
g.945A>C |
| AA changes | I13L Score: 5 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 13 |
| frameshift | no |
| known variant | Reference ID: rs3006458
| database | homozygous (G/G) | heterozygous | allele carriers |
| 1000G | 1599 | 779 | 2378 |
| ExAC | - | - | - |
|
| regulatory features | H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 1.859 | 0.013 | | -0.469 | 0.003 | | (flanking) | 1.859 | 0.006 |
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 marginally increased | 937 | wt: 0.9327 / mu: 0.9482 (marginal change - not scored) | wt: GTGGCTTCTTGTCTTCTCTGCTCTGGGTATCCAGGCCTGGG
mu: GTGGCTTCTTGTCTTCTCTGCTCTGGGTCTCCAGGCCTGGG | ctgc|TCTG | | Acc marginally increased | 941 | wt: 0.9794 / mu: 0.9799 (marginal change - not scored) | wt: CTTCTTGTCTTCTCTGCTCTGGGTATCCAGGCCTGGGGTAA
mu: CTTCTTGTCTTCTCTGCTCTGGGTCTCCAGGCCTGGGGTAA | tctg|GGTA | | Acc increased | 946 | wt: 0.24 / mu: 0.28 | wt: TGTCTTCTCTGCTCTGGGTATCCAGGCCTGGGGTAAGTTTT
mu: TGTCTTCTCTGCTCTGGGTCTCCAGGCCTGGGGTAAGTTTT | gtat|CCAG | | Acc increased | 950 | wt: 0.26 / mu: 0.71 | wt: TTCTCTGCTCTGGGTATCCAGGCCTGGGGTAAGTTTTCTTT
mu: TTCTCTGCTCTGGGTCTCCAGGCCTGGGGTAAGTTTTCTTT | ccag|GCCT | | Acc increased | 949 | wt: 0.75 / mu: 0.89 | wt: CTTCTCTGCTCTGGGTATCCAGGCCTGGGGTAAGTTTTCTT
mu: CTTCTCTGCTCTGGGTCTCCAGGCCTGGGGTAAGTTTTCTT | tcca|GGCC |
|
| distance from splice site | 13 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 13 | L | P | W | L | L | V | F | S | A | L | G | I | Q | A | W | G | D | S | S | W | N | K | T | Q |
| mutated | all conserved | | 13 | L | P | W | L | L | V | F | S | A | L | G | L | Q | A | W | G | D | S | S | W | N | K | T |
| Ptroglodytes | all conserved | ENSPTRG00000001344 | 13 | L | P | W | L | L | V | F | S | A | L | G | L | Q | A | W | G | D | S | S | W | N | K | T |
| Mmulatta | all conserved | ENSMMUG00000006865 | 13 | L | P | W | L | L | V | F | S | A | L | G | L | Q | A | W | D | D | S | S | W | N | K | T |
| Fcatus | no homologue | | | |
| Mmusculus | all conserved | ENSMUSG00000042250 | 13 | L | S | W | L | L | V | F | S | I | L | V | L | L | A | Q | G | V | S | S | W | E | N | P |
| Ggallus | no homologue | | | |
| Trubripes | no homologue | | | |
| Drerio | no alignment | ENSDARG00000068382 | n/a | |
| Dmelanogaster | no alignment | FBgn0043575 | n/a | |
| Celegans | no homologue | | | |
| Xtropicalis | no alignment | ENSXETG00000018262 | n/a | |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 1 | 17 | SIGNAL | Potential. | lost | | 22 | 22 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 39 | 39 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 109 | 109 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 145 | 145 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 167 | 167 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 210 | 210 | DISULFID | | might get lost (downstream of altered splice site) | | 212 | 214 | STRAND | | might get lost (downstream of altered splice site) | | 216 | 219 | HELIX | | might get lost (downstream of altered splice site) | | 226 | 226 | DISULFID | | might get lost (downstream of altered splice site) | | 231 | 240 | STRAND | | might get lost (downstream of altered splice site) | | 246 | 246 | DISULFID | | might get lost (downstream of altered splice site) | | 247 | 247 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 249 | 265 | HELIX | | might get lost (downstream of altered splice site) | | 252 | 252 | DISULFID | | might get lost (downstream of altered splice site) | | 263 | 263 | BINDING | Murein. | might get lost (downstream of altered splice site) | | 270 | 270 | DISULFID | | might get lost (downstream of altered splice site) | | 274 | 274 | BINDING | Murein. | might get lost (downstream of altered splice site) | | 275 | 278 | STRAND | | might get lost (downstream of altered splice site) | | 284 | 288 | STRAND | | might get lost (downstream of altered splice site) | | 290 | 292 | STRAND | | might get lost (downstream of altered splice site) | | 293 | 302 | REGION | Interaction with murein. | might get lost (downstream of altered splice site) | | 298 | 300 | TURN | | might get lost (downstream of altered splice site) | | 301 | 303 | HELIX | | might get lost (downstream of altered splice site) | | 304 | 311 | STRAND | | might get lost (downstream of altered splice site) | | 314 | 316 | STRAND | | might get lost (downstream of altered splice site) | | 320 | 335 | HELIX | | might get lost (downstream of altered splice site) | | 332 | 332 | DISULFID | | might get lost (downstream of altered splice site) | | 338 | 347 | STRAND | | might get lost (downstream of altered splice site) | | 348 | 351 | HELIX | | might get lost (downstream of altered splice site) | | 352 | 354 | STRAND | | might get lost (downstream of altered splice site) | | 353 | 354 | REGION | Interaction with murein. | might get lost (downstream of altered splice site) | | 359 | 365 | HELIX | | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 1110 / 1110 |
| position (AA) of stopcodon in wt / mu AA sequence | 370 / 370 |
| position of stopcodon in wt / mu cDNA | 1469 / 1469 |
| 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 | 360 / 360 |
| chromosome | 1 |
| strand | -1 |
| last intron/exon boundary | 1291 |
| theoretical NMD boundary in CDS | 881 |
| length of CDS | 1110 |
| coding sequence (CDS) position | 37 |
cDNA position
(for ins/del: last normal base / first normal base) | 396 |
gDNA position
(for ins/del: last normal base / first normal base) | 945 |
chromosomal position
(for ins/del: last normal base / first normal base) | 153320372 |
| original gDNA sequence snippet | TTGTCTTCTCTGCTCTGGGTATCCAGGCCTGGGGTAAGTTT |
| altered gDNA sequence snippet | TTGTCTTCTCTGCTCTGGGTCTCCAGGCCTGGGGTAAGTTT |
| original cDNA sequence snippet | TTGTCTTCTCTGCTCTGGGTATCCAGGCCTGGGGTGATTCC |
| altered cDNA sequence snippet | TTGTCTTCTCTGCTCTGGGTCTCCAGGCCTGGGGTGATTCC |
| wildtype AA sequence | MLPWLLVFSA LGIQAWGDSS WNKTQAKQVS EGLQYLFENI SQLTEKDVST TVSRKAWGAE
AVGCSIQLTT PVNVLVIHHV PGLECHDQTV CSQRLRELQA HHVHNNSGCD VAYNFLVGDD
GRVYEGVGWN IQGVHTQGYN NISLGFAFFG TKKGHSPSPA ALSAMENLIT YAVQKGHLSS
SYVQPLLGKG ENCLAPRQKT SLKKACPGVV PRSVWGARET HCPRMTLPAK YGIIIHTAGR
TCNISDECRL LVRDIQSFYI DRLKSCDIGY NFLVGQDGAI YEGVGWNVQG SSTPGYDDIA
LGITFMGTFT GIPPNAAALE AAQDLIQCAM VKGYLTPNYL LVGHSDVART LSPGQALYNI
ISTWPHFKH* |
| mutated AA sequence | MLPWLLVFSA LGLQAWGDSS WNKTQAKQVS EGLQYLFENI SQLTEKDVST TVSRKAWGAE
AVGCSIQLTT PVNVLVIHHV PGLECHDQTV CSQRLRELQA HHVHNNSGCD VAYNFLVGDD
GRVYEGVGWN IQGVHTQGYN NISLGFAFFG TKKGHSPSPA ALSAMENLIT YAVQKGHLSS
SYVQPLLGKG ENCLAPRQKT SLKKACPGVV PRSVWGARET HCPRMTLPAK YGIIIHTAGR
TCNISDECRL LVRDIQSFYI DRLKSCDIGY NFLVGQDGAI YEGVGWNVQG SSTPGYDDIA
LGITFMGTFT GIPPNAAALE AAQDLIQCAM VKGYLTPNYL LVGHSDVART LSPGQALYNI
ISTWPHFKH* |
| speed | 1.27 s |
|
|
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
- protein features (might be) affected
- splice site changes
|
hyperlink |
| analysed issue |
analysis result |
| name of alteration | no title |
| alteration (phys. location) | chr1:153320372T>GN/A
show variant in all transcripts IGV
|
| HGNC symbol | PGLYRP4 |
| Ensembl transcript ID | ENST00000359650 |
| Genbank transcript ID | NM_020393 |
| UniProt peptide | Q96LB8 |
| alteration type | single base exchange |
| alteration region | CDS |
| DNA changes | c.37A>C
cDNA.102A>C
g.945A>C |
| AA changes | I13L Score: 5 explain score(s) |
position(s) of altered AA
if AA alteration in CDS | 13 |
| frameshift | no |
| known variant | Reference ID: rs3006458
| database | homozygous (G/G) | heterozygous | allele carriers |
| 1000G | 1599 | 779 | 2378 |
| ExAC | - | - | - |
|
| regulatory features | H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation |
| phyloP / phastCons | | PhyloP | PhastCons |
| (flanking) | 1.859 | 0.013 | | -0.469 | 0.003 | | (flanking) | 1.859 | 0.006 |
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 marginally increased | 937 | wt: 0.9327 / mu: 0.9482 (marginal change - not scored) | wt: GTGGCTTCTTGTCTTCTCTGCTCTGGGTATCCAGGCCTGGG
mu: GTGGCTTCTTGTCTTCTCTGCTCTGGGTCTCCAGGCCTGGG | ctgc|TCTG | | Acc marginally increased | 941 | wt: 0.9794 / mu: 0.9799 (marginal change - not scored) | wt: CTTCTTGTCTTCTCTGCTCTGGGTATCCAGGCCTGGGGTAA
mu: CTTCTTGTCTTCTCTGCTCTGGGTCTCCAGGCCTGGGGTAA | tctg|GGTA | | Acc increased | 946 | wt: 0.24 / mu: 0.28 | wt: TGTCTTCTCTGCTCTGGGTATCCAGGCCTGGGGTAAGTTTT
mu: TGTCTTCTCTGCTCTGGGTCTCCAGGCCTGGGGTAAGTTTT | gtat|CCAG | | Acc increased | 950 | wt: 0.26 / mu: 0.71 | wt: TTCTCTGCTCTGGGTATCCAGGCCTGGGGTAAGTTTTCTTT
mu: TTCTCTGCTCTGGGTCTCCAGGCCTGGGGTAAGTTTTCTTT | ccag|GCCT | | Acc increased | 949 | wt: 0.75 / mu: 0.89 | wt: CTTCTCTGCTCTGGGTATCCAGGCCTGGGGTAAGTTTTCTT
mu: CTTCTCTGCTCTGGGTCTCCAGGCCTGGGGTAAGTTTTCTT | tcca|GGCC |
|
| distance from splice site | 13 |
| Kozak consensus sequence altered? | N/A |
conservation
protein level for non-synonymous changes | | species | match | gene | aa | alignment | | Human | | | 13 | L | P | W | L | L | V | F | S | A | L | G | I | Q | A | W | G | D | S | S | W | N | K | T | Q |
| mutated | all conserved | | 13 | L | P | W | L | L | V | F | S | A | L | G | L | Q | A | W | G | D | S | S | W | N | K | T |
| Ptroglodytes | all conserved | ENSPTRG00000001344 | 13 | L | P | W | L | L | V | F | S | A | L | G | L | Q | A | W | G | D | S | S | W | N | K | T |
| Mmulatta | all conserved | ENSMMUG00000006865 | 13 | L | P | W | L | L | V | F | S | A | L | G | L | Q | A | W | D | D | S | S | W | N | K | T |
| Fcatus | no homologue | | | |
| Mmusculus | all conserved | ENSMUSG00000042250 | 13 | L | S | W | L | L | V | F | S | I | L | V | L | L | A | Q | G | V | S | S | W | E | N | P |
| Ggallus | no homologue | | | |
| Trubripes | no homologue | | | |
| Drerio | no alignment | ENSDARG00000068382 | n/a | |
| Dmelanogaster | no alignment | FBgn0043575 | n/a | |
| Celegans | no homologue | | | |
| Xtropicalis | no alignment | ENSXETG00000018262 | n/a | |
|
| protein features | | start (aa) | end (aa) | feature | details | | | 1 | 17 | SIGNAL | Potential. | lost | | 22 | 22 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 39 | 39 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 109 | 109 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 145 | 145 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 167 | 167 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | | 210 | 210 | DISULFID | | might get lost (downstream of altered splice site) | | 212 | 214 | STRAND | | might get lost (downstream of altered splice site) | | 216 | 219 | HELIX | | might get lost (downstream of altered splice site) | | 226 | 226 | DISULFID | | might get lost (downstream of altered splice site) | | 231 | 240 | STRAND | | might get lost (downstream of altered splice site) | | 246 | 246 | DISULFID | | might get lost (downstream of altered splice site) | | 247 | 247 | CARBOHYD | N-linked (GlcNAc...) (Potential). | might get lost (downstream of altered splice site) | | 249 | 265 | HELIX | | might get lost (downstream of altered splice site) | | 252 | 252 | DISULFID | | might get lost (downstream of altered splice site) | | 263 | 263 | BINDING | Murein. | might get lost (downstream of altered splice site) | | 270 | 270 | DISULFID | | might get lost (downstream of altered splice site) | | 274 | 274 | BINDING | Murein. | might get lost (downstream of altered splice site) | | 275 | 278 | STRAND | | might get lost (downstream of altered splice site) | | 284 | 288 | STRAND | | might get lost (downstream of altered splice site) | | 290 | 292 | STRAND | | might get lost (downstream of altered splice site) | | 293 | 302 | REGION | Interaction with murein. | might get lost (downstream of altered splice site) | | 298 | 300 | TURN | | might get lost (downstream of altered splice site) | | 301 | 303 | HELIX | | might get lost (downstream of altered splice site) | | 304 | 311 | STRAND | | might get lost (downstream of altered splice site) | | 314 | 316 | STRAND | | might get lost (downstream of altered splice site) | | 320 | 335 | HELIX | | might get lost (downstream of altered splice site) | | 332 | 332 | DISULFID | | might get lost (downstream of altered splice site) | | 338 | 347 | STRAND | | might get lost (downstream of altered splice site) | | 348 | 351 | HELIX | | might get lost (downstream of altered splice site) | | 352 | 354 | STRAND | | might get lost (downstream of altered splice site) | | 353 | 354 | REGION | Interaction with murein. | might get lost (downstream of altered splice site) | | 359 | 365 | HELIX | | might get lost (downstream of altered splice site) |
|
| length of protein | normal |
| AA sequence altered | yes |
| position of stopcodon in wt / mu CDS | 1122 / 1122 |
| position (AA) of stopcodon in wt / mu AA sequence | 374 / 374 |
| position of stopcodon in wt / mu cDNA | 1187 / 1187 |
| 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 | 66 / 66 |
| chromosome | 1 |
| strand | -1 |
| last intron/exon boundary | 1009 |
| theoretical NMD boundary in CDS | 893 |
| length of CDS | 1122 |
| coding sequence (CDS) position | 37 |
cDNA position
(for ins/del: last normal base / first normal base) | 102 |
gDNA position
(for ins/del: last normal base / first normal base) | 945 |
chromosomal position
(for ins/del: last normal base / first normal base) | 153320372 |
| original gDNA sequence snippet | TTGTCTTCTCTGCTCTGGGTATCCAGGCCTGGGGTAAGTTT |
| altered gDNA sequence snippet | TTGTCTTCTCTGCTCTGGGTCTCCAGGCCTGGGGTAAGTTT |
| original cDNA sequence snippet | TTGTCTTCTCTGCTCTGGGTATCCAGGCCTGGGGTGATTCC |
| altered cDNA sequence snippet | TTGTCTTCTCTGCTCTGGGTCTCCAGGCCTGGGGTGATTCC |
| wildtype AA sequence | MLPWLLVFSA LGIQAWGDSS WNKTQAKQVS EGLQYLFENI SQLTEKGLPT DVSTTVSRKA
WGAEAVGCSI QLTTPVNVLV IHHVPGLECH DQTVCSQRLR ELQAHHVHNN SGCDVAYNFL
VGDDGRVYEG VGWNIQGVHT QGYNNISLGF AFFGTKKGHS PSPAALSAME NLITYAVQKG
HLSSSYVQPL LGKGENCLAP RQKTSLKKAC PGVVPRSVWG ARETHCPRMT LPAKYGIIIH
TAGRTCNISD ECRLLVRDIQ SFYIDRLKSC DIGYNFLVGQ DGAIYEGVGW NVQGSSTPGY
DDIALGITFM GTFTGIPPNA AALEAAQDLI QCAMVKGYLT PNYLLVGHSD VARTLSPGQA
LYNIISTWPH FKH* |
| mutated AA sequence | MLPWLLVFSA LGLQAWGDSS WNKTQAKQVS EGLQYLFENI SQLTEKGLPT DVSTTVSRKA
WGAEAVGCSI QLTTPVNVLV IHHVPGLECH DQTVCSQRLR ELQAHHVHNN SGCDVAYNFL
VGDDGRVYEG VGWNIQGVHT QGYNNISLGF AFFGTKKGHS PSPAALSAME NLITYAVQKG
HLSSSYVQPL LGKGENCLAP RQKTSLKKAC PGVVPRSVWG ARETHCPRMT LPAKYGIIIH
TAGRTCNISD ECRLLVRDIQ SFYIDRLKSC DIGYNFLVGQ DGAIYEGVGW NVQGSSTPGY
DDIALGITFM GTFTGIPPNA AALEAAQDLI QCAMVKGYLT PNYLLVGHSD VARTLSPGQA
LYNIISTWPH FKH* |
| speed | 0.89 s |
|
|
