Prediction |
polymorphism |
Model: simple_aae, prob: 0.999999999999928 (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
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hyperlink |
analysed issue |
analysis result |
name of alteration | no title |
alteration (phys. location) | chr6:7310259A>GN/A
show variant in all transcripts IGV
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HGNC symbol | SSR1 |
Ensembl transcript ID | ENST00000489567 |
Genbank transcript ID | N/A |
UniProt peptide | P43307 |
alteration type | single base exchange |
alteration region | CDS |
DNA changes | c.83T>C cDNA.137T>C g.37421T>C |
AA changes | L28S Score: 145 explain score(s) |
position(s) of altered AA if AA alteration in CDS | 28 |
frameshift | no |
known variant | Reference ID: rs10004
database | homozygous (G/G) | heterozygous | allele carriers |
1000G | 279 | 916 | 1195 |
ExAC | 4436 | 22037 | 26473 |
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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 H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation |
phyloP / phastCons | | PhyloP | PhastCons |
(flanking) | -0.344 | 0.002 | | 0.828 | 0.013 | (flanking) | 0.493 | 0.017 | 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 | 37415 | wt: 0.43 / mu: 0.52 | wt: CTTTTTCTGTATTTTATCATTAGGCTTGTTAGCAGTGGCAC mu: CTTTTTCTGTATTTTATCATTAGGCTCGTTAGCAGTGGCAC | catt|AGGC | Acc marginally increased | 37421 | wt: 0.7394 / mu: 0.7579 (marginal change - not scored) | wt: CTGTATTTTATCATTAGGCTTGTTAGCAGTGGCACAAGATC mu: CTGTATTTTATCATTAGGCTCGTTAGCAGTGGCACAAGATC | gctt|GTTA | Acc marginally increased | 37416 | wt: 0.9741 / mu: 0.9779 (marginal change - not scored) | wt: TTTTTCTGTATTTTATCATTAGGCTTGTTAGCAGTGGCACA mu: TTTTTCTGTATTTTATCATTAGGCTCGTTAGCAGTGGCACA | atta|GGCT | Acc marginally increased | 37414 | wt: 0.8499 / mu: 0.8917 (marginal change - not scored) | wt: GCTTTTTCTGTATTTTATCATTAGGCTTGTTAGCAGTGGCA mu: GCTTTTTCTGTATTTTATCATTAGGCTCGTTAGCAGTGGCA | tcat|TAGG | Acc marginally increased | 37413 | wt: 0.9869 / mu: 0.9885 (marginal change - not scored) | wt: TGCTTTTTCTGTATTTTATCATTAGGCTTGTTAGCAGTGGC mu: TGCTTTTTCTGTATTTTATCATTAGGCTCGTTAGCAGTGGC | atca|TTAG | Acc marginally increased | 37417 | wt: 0.8103 / mu: 0.8221 (marginal change - not scored) | wt: TTTTCTGTATTTTATCATTAGGCTTGTTAGCAGTGGCACAA mu: TTTTCTGTATTTTATCATTAGGCTCGTTAGCAGTGGCACAA | ttag|GCTT | Donor increased | 37416 | wt: 0.65 / mu: 0.85 | wt: TCATTAGGCTTGTTA mu: TCATTAGGCTCGTTA | ATTA|ggct |
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distance from splice site | 4 |
Kozak consensus sequence altered? | N/A |
conservation protein level for non-synonymous changes | species | match | gene | aa | alignment | Human | | | 28 | A | T | V | L | F | R | G | G | P | R | G | L | L | A | V | A | Q | D | L | T | E | D | E | E |
mutated | not conserved | | 28 | A | T | V | L | F | R | G | G | P | R | G | S | L | A | V | A | Q | D | L | T | E | D | E |
Ptroglodytes | not conserved | ENSPTRG00000017698 | 28 | A | T | V | L | F | R | G | G | P | R | G | S | L | A | V | A | Q | D | L | T | EDEETVEDSIIEDEDDEAEVEE | D | E |
Mmulatta | not conserved | ENSMMUG00000002147 | 28 | A | T | V | L | F | R | G | G | P | R | G | S | L | A | V | A | Q | D | L | T | EDEETVEDSIIEDEDDEAEVEE | D | E |
Fcatus | no homologue | | | |
Mmusculus | not conserved | ENSMUSG00000021427 | 28 | A | A | V | L | L | R | G | G | P | G | G | S | L | A | L | A | Q | D | P | TEDEEIVEDSIIEDEDDEAEVE | E | D | E |
Ggallus | all identical | ENSGALG00000012798 | 28 | A | A | L | L | L | R | G | S | G | T | GSG | L | L | V | A | A | Q | D | A | T | E | D | E |
Trubripes | not conserved | ENSTRUG00000002722 | 28 | A | S | L | L | I | K | A | G | P | E | - | - | - | V | S | A | Q | D | L | TEDEEAEAVDEDIVEDVTAEDE | D | D | E |
Drerio | not conserved | ENSDARG00000040518 | 28 | A | T | L | M | L | K | G | P | - | - | - | - | V | V | S | A | Q | D | A | T | E | E | E |
Dmelanogaster | not conserved | FBgn0028327 | 25 | I | V | I | C | T | F | S | A | P | N | K | F | G | A | Y | A | A | - | - | - | - | - | - |
Celegans | no alignment | Y71F9AM.6 | n/a | |
Xtropicalis | not conserved | ENSXETG00000020431 | 35 | V | T | L | I | - | - | G | N | S | K | G | P | L | V | A | A | Q | D | A | T | E | D | E |
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protein features | start (aa) | end (aa) | feature | details | | 19 | 207 | TOPO_DOM | Lumenal (Potential). | lost | 37 | 37 | CONFLICT | E -> A (in Ref. 6; BAD96529). | might get lost (downstream of altered splice site) | 130 | 130 | CONFLICT | Y -> H (in Ref. 1; CAA78290). | might get lost (downstream of altered splice site) | 136 | 136 | CARBOHYD | N-linked (GlcNAc...). | might get lost (downstream of altered splice site) | 190 | 190 | CONFLICT | F -> Y (in Ref. 4; BAF84239). | might get lost (downstream of altered splice site) | 191 | 191 | CARBOHYD | N-linked (GlcNAc...). | might get lost (downstream of altered splice site) | 208 | 228 | TRANSMEM | Helical; (Potential). | might get lost (downstream of altered splice site) | 220 | 220 | CONFLICT | L -> P (in Ref. 6; BAD96529). | might get lost (downstream of altered splice site) | 229 | 286 | TOPO_DOM | Cytoplasmic (Potential). | might get lost (downstream of altered splice site) | 247 | 247 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | 260 | 260 | MOD_RES | Phosphothreonine. | might get lost (downstream of altered splice site) | 263 | 263 | CONFLICT | Q -> R (in Ref. 4; BAF84239). | might get lost (downstream of altered splice site) | 268 | 268 | MOD_RES | Phosphoserine. | might get lost (downstream of altered splice site) | 286 | 286 | CONFLICT | E -> D (in Ref. 5; CAG33242). | 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 | 657 / 657 |
position (AA) of stopcodon in wt / mu AA sequence | 219 / 219 |
position of stopcodon in wt / mu cDNA | 711 / 711 |
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 | 55 / 55 |
chromosome | 6 |
strand | -1 |
last intron/exon boundary | 644 |
theoretical NMD boundary in CDS | 539 |
length of CDS | 657 |
coding sequence (CDS) position | 83 |
cDNA position (for ins/del: last normal base / first normal base) | 137 |
gDNA position (for ins/del: last normal base / first normal base) | 37421 |
chromosomal position (for ins/del: last normal base / first normal base) | 7310259 |
original gDNA sequence snippet | CTGTATTTTATCATTAGGCTTGTTAGCAGTGGCACAAGATC |
altered gDNA sequence snippet | CTGTATTTTATCATTAGGCTCGTTAGCAGTGGCACAAGATC |
original cDNA sequence snippet | CCGAGGCGGCCCCAGAGGCTTGTTAGCAGTGGCACAAGATC |
altered cDNA sequence snippet | CCGAGGCGGCCCCAGAGGCTCGTTAGCAGTGGCACAAGATC |
wildtype AA sequence | MRLLPRLLLL LLLVFPATVL FRGGPRGLLA VAQDLTEDEE TVEDSIIEDE DDEAEVEEDE PTDLVEDKEE EDVSGEPEAS PSADTTILFV KGEEPMGGRP FGLVINLNYK DLNGNVFQDA VFNQTVTVIE REDGLDGETI FMYMFLAGLG LLVIVGLHQL LESRKRKRPI QKVEMGTSSQ NDVDMSWIPQ ETLNQINKAS PRRLPRKRAQ KRSVGSDE* |
mutated AA sequence | MRLLPRLLLL LLLVFPATVL FRGGPRGSLA VAQDLTEDEE TVEDSIIEDE DDEAEVEEDE PTDLVEDKEE EDVSGEPEAS PSADTTILFV KGEEPMGGRP FGLVINLNYK DLNGNVFQDA VFNQTVTVIE REDGLDGETI FMYMFLAGLG LLVIVGLHQL LESRKRKRPI QKVEMGTSSQ NDVDMSWIPQ ETLNQINKAS PRRLPRKRAQ KRSVGSDE* |
speed | 1.09 s |
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