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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q92643: Variant p.Ser53Phe

GPI-anchor transamidase
Gene: PIGK
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Variant information Variant position: help 53 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: help LP/P [Disclaimer] 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: help From Serine (S) to Phenylalanine (F) at position 53 (S53F, p.Ser53Phe). 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: help Change from small size and polar (S) to large size and aromatic (F) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help -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: help In NEDHCAS. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 53 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 395 The length of the canonical sequence.
Location on the sequence: help QAEQFFRSGHTNNWAVLVCT S RFWFNYRHVANTLSVYRSVK 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: help The multiple alignment of the region surrounding the variant against various orthologous sequences. 
Human                         QAEQFF----RSGHTNNWAVLVCTSRFWFNYRHVANTLSVYRSVK

Mouse                         QAEQFF----RSGHTNNWAVLVCTSRFWFNYRHVANTLSVY

Pig                           QAEQFF----RSGHTNNWAVLVCTSRFWFNYRHVANTLSVY

Bovine                        QAEQFF----RSGHTNNWAVLVCTSRFWFNYRHVANTLSVY

Caenorhabditis elegans        KIDELFD---TPGHTNNWAVLVCTSKFWFNYRHVSNVLALY

Drosophila                    LPEGFVDAAQRSTHTNNWAVLVDASRFWFNYRHVANVLSIY

Baker's yeast                 AAHEVI-----ATNTNNWAVLVSTSRFWFNYRHMANVLSMY

Fission yeast                 -----------SSHTNNWAVLISTSRFWFNYRHTANVLGIY
Sequence annotation in neighborhood: help 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.
TypePositionsDescription
Chain 28 – 395 GPI-anchor transamidase
Topological domain 28 – 368 Lumenal
Alternative sequence 50 – 125 Missing. In isoform 2.
Mutagenesis 54 – 54 R -> A. No effect on function in GPI-anchor attachment to protein.
Mutagenesis 58 – 58 N -> A. Decreased function in GPI-anchor attachment to protein. Substantially decreases GPI-anchor transamidase activity.
Mutagenesis 60 – 60 R -> A. Decreased function in GPI-anchor attachment to protein. Reduces by 25% the GPI-anchor transamidase activity.
Mutagenesis 60 – 60 R -> E. Reduces by 90% the GPI-anchor transamidase activity.
Mutagenesis 60 – 60 R -> K. Reduces by 60% the GPI-anchor transamidase activity.
Mutagenesis 60 – 60 R -> L. Reduces by 40% the GPI-anchor transamidase activity.
Mutagenesis 61 – 61 H -> A. Decreased function in GPI-anchor attachment to protein.



Literature citations
Bi-allelic variants in the GPI transamidase subunit PIGK cause a neurodevelopmental syndrome with hypotonia, cerebellar atrophy, and epilepsy.
Nguyen T.T.M.; Murakami Y.; Mobilio S.; Niceta M.; Zampino G.; Philippe C.; Moutton S.; Zaki M.S.; James K.N.; Musaev D.; Mu W.; Baranano K.; Nance J.R.; Rosenfeld J.A.; Braverman N.; Ciolfi A.; Millan F.; Person R.E.; Bruel A.L.; Thauvin-Robinet C.; Ververi A.; DeVile C.; Male A.; Efthymiou S.; Maroofian R.; Houlden H.; Maqbool S.; Rahman F.; Baratang N.V.; Rousseau J.; St-Denis A.; Elrick M.J.; Anselm I.; Rodan L.H.; Tartaglia M.; Gleeson J.; Kinoshita T.; Campeau P.M.;
Am. J. Hum. Genet. 106:484-495(2020)
Cited for: INVOLVEMENT IN NEDHCAS; VARIANTS NEDHCAS 33-GLN--PHE-395 DEL; PHE-53; PRO-86; VAL-87; ASN-88; SER-160; VAL-184; LYS-246 AND ARG-275;
Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. They are not in any way intended to be used as a substitute for professional medical advice, diagnostic, treatment or care.