glorious-saucy.yml

unique-id: glorious-saucy
phe-label: VUI202102/03
alternate-names:
- UK1188
belongs-to-lineage:
- PANGO: B.1.525
description: This variant is a cluster of E484K containing genomes
information-sources:
-
variants:
- codon-change: TTC-TTT
  gene: ORF1ab
  one-based-reference-position: 1498
  predicted-effect: synonymous
  protein: nsp2
  protein-codon-position: 231
  reference-base: C
  type: SNP
  variant-base: T
- codon-change: GGA-GGG
  gene: ORF1ab
  one-based-reference-position: 1807
  predicted-effect: synonymous
  protein: nsp2
  protein-codon-position: 334
  reference-base: A
  type: SNP
  variant-base: G
- codon-change: GTT-GTC
  gene: ORF1ab
  one-based-reference-position: 8593
  predicted-effect: synonymous
  protein: nsp4
  protein-codon-position: 13
  reference-base: T
  type: SNP
  variant-base: C
- codon-change: TTC-TTT
  gene: ORF1ab
  one-based-reference-position: 9565
  predicted-effect: synonymous
  protein: nsp4
  protein-codon-position: 337
  reference-base: C
  type: SNP
  variant-base: T
- amino-acid-change: P323F
  codon-change: CCT-TTT
  gene: ORF1ab
  one-based-reference-position: 14407
  predicted-effect: non-synonymous
  protein: nsp12
  protein-codon-position: 323
  reference-base: CCT
  type: MNP
  variant-base: TTT
- codon-change: GGC-GGT
  gene: ORF1ab
  one-based-reference-position: 18171
  predicted-effect: synonymous
  protein: nsp14
  protein-codon-position: 44
  reference-base: C
  type: SNP
  variant-base: T
- codon-change: TTA-TTG
  gene: ORF1ab
  one-based-reference-position: 20724
  predicted-effect: synonymous
  protein: nsp16
  protein-codon-position: 22
  reference-base: A
  type: SNP
  variant-base: G
- amino-acid-change: Q52R
  codon-change: CAG-CGG
  gene: S
  one-based-reference-position: 21717
  predicted-effect: non-synonymous
  protein: surface glycoprotein
  protein-codon-position: 52
  reference-base: A
  type: SNP
  variant-base: G
- amino-acid-change: E484K
  codon-change: GAA-AAA
  gene: S
  one-based-reference-position: 23012
  predicted-effect: non-synonymous
  protein: surface glycoprotein
  protein-codon-position: 484
  reference-base: G
  type: SNP
  variant-base: A
- amino-acid-change: Q677H
  codon-change: CAG-CAC
  gene: S
  one-based-reference-position: 23593
  predicted-effect: non-synonymous
  protein: surface glycoprotein
  protein-codon-position: 677
  reference-base: G
  type: SNP
  variant-base: C
- amino-acid-change: F888L
  codon-change: TTT-CTT
  gene: S
  one-based-reference-position: 24224
  predicted-effect: non-synonymous
  protein: surface glycoprotein
  protein-codon-position: 888
  reference-base: T
  type: SNP
  variant-base: C
- codon-change: TTC-TTT
  gene: S
  one-based-reference-position: 24748
  predicted-effect: synonymous
  protein: surface glycoprotein
  protein-codon-position: 1062
  reference-base: C
  type: SNP
  variant-base: T
- amino-acid-change: L21F
  codon-change: CTT-TTT
  gene: E
  one-based-reference-position: 26305
  predicted-effect: non-synonymous
  protein: envelope protein
  protein-codon-position: 21
  reference-base: C
  type: SNP
  variant-base: T
- amino-acid-change: I82T
  codon-change: ATC-ACC
  gene: M
  one-based-reference-position: 26767
  predicted-effect: non-synonymous
  protein: membrane glycoprotein
  protein-codon-position: 82
  reference-base: T
  type: SNP
  variant-base: C
- codon-change: CCA-CCG
  gene: N
  one-based-reference-position: 28699
  predicted-effect: synonymous
  protein: nucleocapsid phosphoprotein
  protein-codon-position: 142
  reference-base: A
  type: SNP
  variant-base: G
- gene: .
  one-based-reference-position: 29543
  protein: .
  reference-base: G
  type: SNP
  variant-base: T
  predicted-effect: no-effect
calling-definition:
  confirmed:
    mutations-required: 16
    indels-required: 0
    allowed-wildtype: 0
  probable:
    mutations-required: 5
    indels-required: 0
    allowed-wildtype: 0
  low-qc:
    mutations-required: 0
    indels-required: 0
    allowed-wildtype: 0
acknowledgements:
curators:
- Natalie Groves
- Ulf Schaefer
- Nick Loman