UniProtKB/SwissProt variant VAR

Variant information

Variant position:

12

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 Serine (S) to Cysteine (C) at position 12 (S12C, p.Ser12Cys).

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 small size and polar (S) to medium size and polar (C)

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

BLOSUM score:

-1

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 rs121918345 [ dbSNP | Ensembl ]

Sequence information

Variant position:

12

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

Protein sequence length:

594

The length of the canonical sequence.

Location on the sequence:

MASSTPSSSAT S SNAGADPNTTNLRPTTYDTW

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                         MASSTPSSSATSSNAGADPNTTNLRPTTYDTW

                              MASSTPSSSATSSNAGADPNTANLRPTTYDTW

Chimpanzee                    MASSTPSSSATSSNAGADPNTTNLRPTTYDTW

Mouse                         MASSTP-SPATSSNAGADPNTTNLRPTTYDTW

Rat                           MASSTP-SPATSSNAGADPNTTNLRPTTYDTW

Pig                           MASSTPSSSATSSNAGPDPNTTNLRPTTYDTW

Bovine                        MASSTPSSSATSSNAGADPNTTNLRPTTYDTW

Cat                           MASSTPSSSATSSNAGADPNTTNLRPTTYDTW

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 – 594	Glutamate decarboxylase 1
Region	1 – 23	Disordered

Literature citations

Homozygosity for a missense mutation in the 67 kDa isoform of glutamate decarboxylase in a family with autosomal recessive spastic cerebral palsy: parallels with Stiff-Person Syndrome and other movement disorders.
Lynex C.N.; Carr I.M.; Leek J.P.; Achuthan R.; Mitchell S.; Maher E.R.; Woods C.G.; Bonthon D.T.; Markham A.F.;
BMC Neurol. 4:20-20(2004)
Cited for: VARIANT CYS-12;

Evidence that autosomal recessive spastic cerebral palsy-1 (CPSQ1) is caused by a missense variant in HPDL.
Morgan N.V.; Yngvadottir B.; O'Driscoll M.; Clark G.R.; Walsh D.; Martin E.; Tee L.; Reid E.; Titheradge H.L.; Maher E.R.;
Brain Commun. 3:fcab002-fcab002(2021)
Cited for: VARIANT CYS-12;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q99259: Variant p.Ser12Cys