UniProtKB/SwissProt variant VAR

Variant information

Variant position:

646

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

Type of variant:

LB/B

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 Glutamate (E) to Aspartate (D) at position 646 (E646D, p.Glu646Asp).

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 acidic.

The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:

2

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

Other resources:

Links to websites of interest for the variant.

Variant rs35424709 [ dbSNP | Ensembl ]

Sequence information

Variant position:

646

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

Protein sequence length:

1196

The length of the canonical sequence.

Location on the sequence:

APERVASFCQPETVPTSFVS E LQIYTTQGFRVIALAYKKLE

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                         APERVASFCQPETVPTSFVSELQIYTTQGFRVIALAYKKLE

Mouse                         APERVASFCQPDTVPTSFISELQIYTTQGFRVIALAYKKLE

Chicken                       APEMVATLCRAETVPSNFESKLLFYTAQGFRVIGLAYKSLQ

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.

Type	Positions	Description
Chain	1 – 1196	Probable cation-transporting ATPase 13A4
Topological domain	458 – 900	Cytoplasmic
Alternative sequence	1 – 984	Missing. In isoform 4.
Alternative sequence	577 – 1196	Missing. In isoform 3.

Literature citations

Characterization of a novel cation transporter ATPase gene (ATP13A4) interrupted by 3q25-q29 inversion in an individual with language delay.
Kwasnicka-Crawford D.A.; Carson A.R.; Roberts W.; Summers A.M.; Rehnstrom K.; Jarvela I.; Scherer S.W.;
Genomics 86:182-194(2005)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); TISSUE SPECIFICITY; INDUCTION; CHROMOSOMAL REARRANGEMENT; VARIANTS MET-181; ALA-353 AND ASP-646;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q4VNC1: Variant p.Glu646Asp