UniProtKB/SwissProt variant VAR

Variant information

Variant position:

1018

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 Tyrosine (Y) to Serine (S) at position 1018 (Y1018S, p.Tyr1018Ser).

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:

Change from large size and aromatic (Y) to small size and polar (S)

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

Variant description:

Likely benign variant; no effect on inositol phosphate phosphatase activity.

Any additional useful information about the variant.

Sequence information

Variant position:

1018

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

Protein sequence length:

1573

The length of the canonical sequence.

Location on the sequence:

LLGEDAEVAADFDMEGDVDD Y SAEVEELLPQHLQPSSSSGL

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                         LLGEDAEVAADFDMEGDVDDYSAEVEELLPQHLQPSSSSGL

Mouse                         LLGEDAEVAADFDMEGDVDDYSAEVEELLPQHLQPSSSSGL

Rat                           LLGEDAEVSADFDMEGDVDDYSAEVEELLPQHLQPSSSSGL

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 – 1573	Synaptojanin-1
Alternative sequence	525 – 1573	Missing. In isoform 4.

Literature citations

Loss of SYNJ1 dual phosphatase activity leads to early onset refractory seizures and progressive neurological decline.
Hardies K.; Cai Y.; Jardel C.; Jansen A.C.; Cao M.; May P.; Djemie T.; Hachon Le Camus C.; Keymolen K.; Deconinck T.; Bhambhani V.; Long C.; Sajan S.A.; Helbig K.L.; Suls A.; Balling R.; Helbig I.; De Jonghe P.; Depienne C.; De Camilli P.; Weckhuysen S.;
Brain 139:2420-2430(2016)
Cited for: FUNCTION; INVOLVEMENT IN DEE53; VARIANT DEE53 CYS-849; CHARACTERIZATION OF VARIANT DEE53 CYS-849; VARIANTS ILE-981 AND SER-1018; CHARACTERIZATION OF VARIANTS ILE-981 AND SER-1018;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot O43426: Variant p.Tyr1018Ser