UniProtKB/Swiss-Prot Q969N2: Variant p.Thr183Pro

• Variant information
• Sequence information
• Literature citations
• All

Variant information

Variant position: 183 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 Threonine (T) to Proline (P) at position 183 (T183P, p.Thr183Pro). 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 medium size and polar (T) to medium size and hydrophobic (P) 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
Variant description: In MCAHS3; decreased function in GPI-anchor attachment to protein; flow cytometric analysis of patient granulocytes and monocytes show decreased amounts of GPI-anchored proteins CD16B and CD59 compared to controls. Any additional useful information about the variant.
Other resources: Links to websites of interest for the variant.

• Variant rs587777027 [ dbSNP | Ensembl ]

Sequence information

Variant position: 183 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: ANDTDHYFLRYAVLPREVVC T ENLTPWKKLLPCSSKAGLSV 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 transamidase component PIG-T
Topological domain	22 – 527	Lumenal
Glycosylation	164 – 164	N-linked (GlcNAc...) asparagine
Disulfide bond	182 – 182	Interchain (with C-92 in PIGK/GPI8)
Alternative sequence	63 – 256	Missing. In isoform 2.
Mutagenesis	164 – 164	N -> Q. No effect on function in GPI-anchor attachment to protein.
Mutagenesis	182 – 182	C -> S. Decreased function in GPI-anchor attachment to protein.
Mutagenesis	184 – 184	E -> A. No effect on function in GPI-anchor attachment to protein.
Helix	183 – 191

Literature citations

A novel intellectual disability syndrome caused by GPI anchor deficiency due to homozygous mutations in PIGT.
Kvarnung M.; Nilsson D.; Lindstrand A.; Korenke G.C.; Chiang S.C.; Blennow E.; Bergmann M.; Stodberg T.; Makitie O.; Anderlid B.M.; Bryceson Y.T.; Nordenskjold M.; Nordgren A.;
J. Med. Genet. 50:521-528(2013)
Cited for: VARIANT MCAHS3 PRO-183; INVOLVEMENT IN MCAHS3; Case report of a child bearing a novel deleterious splicing variant in PIGT.
Mason S.; Castilla-Vallmanya L.; James C.; Andrews P.I.; Balcells S.; Grinberg D.; Kirk E.P.; Urreizti R.;
Medicine (Baltimore) 98:e14524-e14524(2019)
Cited for: VARIANT MCAHS3 PRO-183;