UniProtKB/Swiss-Prot Q969N2: Variant p.Arg507Trp

• Variant information
• Sequence information
• Literature citations
• All

Variant information

Variant position: 507 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: LP/P [Disclaimer: Variants classification is intended for research purposes only, not for clinical and diagnostic use. The label disease variant is assigned according to literature reports on probable disease-association that can be based on theoretical reasons. This label must not be considered as a definitive proof for the pathogenic role of a variant.] 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 Arginine (R) to Tryptophan (W) at position 507 (R507W, p.Arg507Trp). 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 basic (R) to large size and aromatic (W) 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 MCAHS3; decreased function in GPI-anchor attachment to protein; does not rescue GPI-anchored proteins surface expression as efficiently as the wild-type in PIGT-knockout cells. Any additional useful information about the variant.
Other resources: Links to websites of interest for the variant.

• Variant rs146484791 [ dbSNP | Ensembl ]

Sequence information

Variant position: 507 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: 578 The length of the canonical sequence.
Location on the sequence: EESPLFNSLFPVSDGSNYFV R LYTEPLLVNLPTPDFSMPYN 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.
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	22 – 578	GPI-anchor transamidase component PIGT
Topological domain	22 – 525	Lumenal
Binding site	521 – 521
Binding site	523 – 523
Binding site	527 – 527
Mutagenesis	521 – 521	D -> A. Decreases the GPI-anchor transamidase activity to 28.9%,.
Mutagenesis	521 – 521	D -> L. Decreases the GPI-anchor transamidase activity to 18.8%. Almost abolishes the GPI-anchor transamidase activity to 6.2%; when associated with F-523.
Mutagenesis	523 – 523	S -> F. Decreases the GPI-anchor transamidase activity to 76.5% Almost abolishes the GPI-anchor transamidase activity to 6.2%; when associated with L-521.
Mutagenesis	523 – 523	S -> W. Decreases the GPI-anchor transamidase activity to 76.8%.
Beta strand	503 – 509

Literature citations

Deep-Phenotyping the Less Severe Spectrum of PIGT Deficiency and Linking the Gene to Myoclonic Atonic Seizures.
Bayat A.; Pendziwiat M.; Obersztyn E.; Goldenberg P.; Zacher P.; Doering J.H.; Syrbe S.; Begtrup A.; Borovikov A.; Sharkov A.; Karasinska A.; Gizewska M.; Mitchell W.; Morava E.; Moeller R.S.; Rubboli G.;
Front. Genet. 12:663643-663643(2021)
Cited for: VARIANTS MCAHS3 330-ARG--LEU-578 DEL; PRO-376; TRP-448; GLN-507; TRP-507; SER-527 AND MET-528; Case report: Functional analysis of the p.Arg507Trp variant of the PIGT gene supporting the moderate epilepsy phenotype of mutations in the C-terminal region.
Ben Ayed I.; Jallouli O.; Murakami Y.; Souissi A.; Mallouli S.; Bouzid A.; Kamoun F.; Elloumi I.; Frikha F.; Tlili A.; Weckhuysen S.; Kinoshita T.; Triki C.C.; Masmoudi S.;
Front. Neurol. 14:1092887-1092887(2023)
Cited for: VARIANT MCAHS3 TRP-507; CHARACTERIZATION OF VARIANT MCAHS3 TRP-507; FUNCTION; PATHWAY;