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UniProtKB/Swiss-Prot Q9NY47: Variant p.Leu1053Pro

Voltage-dependent calcium channel subunit alpha-2/delta-2
Gene: CACNA2D2
Variant information

Variant position:  1053
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  US
The variants are classified into three categories: LP/P, LB/B and US.
  • LP/P: likely pathogenic or pathogenic.
  • LB/B: likely benign or benign.
  • US: uncertain significance

Residue change:  From Leucine (L) to Proline (P) at position 1053 (L1053P, p.Leu1053Pro).
Indicates the amino acid change of the variant. The one-letter and three-letter codes for amino acids used in UniProtKB/Swiss-Prot are those adopted by the commission on Biochemical Nomenclature of the IUPAC-IUB.

Physico-chemical properties:  Similar physico-chemical property. Both residues are medium size and hydrophobic.
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  -3
The score within a Blosum matrix for the corresponding wild-type to variant amino acid change. The log-odds score measures the logarithm for the ratio of the likelihood of two amino acids appearing by chance. The Blosum62 substitution matrix is used. This substitution matrix contains scores for all possible exchanges of one amino acid with another:
  • Lowest score: -4 (low probability of substitution).
  • Highest score: 11 (high probability of substitution).
More information can be found on the following page

Variant description:  In CASVDD; unknown pathological significance.
Any additional useful information about the variant.

Other resources:  
Links to websites of interest for the variant.



Sequence information

Variant position:  1053
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  1150
The length of the canonical sequence.

Location on the sequence:   IDCGNCSRLFHAQRLTNTNL  L FVVAEKPLCSQCEAGRLLQK
The residue change on the sequence. Unless the variant is located at the beginning or at the end of the protein sequence, both residues upstream (20) and downstream (20) of the variant will be shown.

Residue conservation: 
The multiple alignment of the region surrounding the variant against various orthologous sequences.

Human                         IDCGNCSRLFHAQRLTNTNLLFVVAEKPLCSQCEAGRLLQK

Mouse                         IDCGNCSRLFHAQRLTNTNLLFVVAEKPLCSQCEAGRLLQK

Rat                           IDCGNCSRLFHAQRLTNTNLLFVVAEKPLCSQCEVGRLLQK

Sequence annotation in neighborhood:  
The regions or sites of interest surrounding the variant. In general the features listed are posttranslational modifications, binding sites, enzyme active sites, local secondary structure or other characteristics reported in the cited references. The "Sequence annotation in neighborhood" lines have a fixed format:
  • Type: the type of sequence feature.
  • Positions: endpoints of the sequence feature.
  • Description: contains additional information about the feature.

TypePositionsDescription
Chain 19 – 1150 Voltage-dependent calcium channel subunit alpha-2/delta-2
Chain 1002 – 1150 Voltage-dependent calcium channel subunit delta-2
Topological domain 19 – 1113 Extracellular
Disulfide bond 443 – 1098 Interchain (between alpha-2-2 and delta-2 chains)


Literature citations

Epileptic encephalopathy and cerebellar atrophy resulting from compound heterozygous CACNA2D2 variants.
Butler K.M.; Holt P.J.; Milla S.S.; da Silva C.; Alexander J.J.; Escayg A.;
Case Rep. Genet. 2018:6308283-6308283(2018)
Cited for: INVOLVEMENT IN CASVDD; VARIANTS CASVDD LEU-261 AND PRO-1053;

Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. They are not in any way intended to be used as a substitute for professional medical advice, diagnostic, treatment or care.