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UniProtKB/Swiss-Prot P78330: Variant p.Asp32Asn

Phosphoserine phosphatase
Gene: PSPH
Variant information

Variant position:  32
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  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:  From Aspartate (D) to Asparagine (N) at position 32 (D32N, p.Asp32Asn).
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 acidic (D) to medium size and polar (N)
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 PSPHD.
Any additional useful information about the variant.

Other resources:  
Links to websites of interest for the variant.



Sequence information

Variant position:  32
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  225
The length of the canonical sequence.

Location on the sequence:   YSADAVCFDVDSTVIREEGI  D ELAKICGVEDAVSEMTRRAM
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                         YSADAV--------------------------------------------CFDVDSTVIREEGIDELAKICGVEDAVSEMTRRAM

Mouse                         CSADAV-----------------------------------

Rat                           CSADAV-----------------------------------

Bovine                        CSADAV-----------------------------------

Drosophila                    CNGNGTTGGAAKTT------------VASAITPPKQPQLAA

Baker's yeast                 ARATDIFIEVAGSIVQKDLKNKLTNVIDSHNDVDVIVSVDN

Fission yeast                 EQWTLVSGQLKGTF--EDAKDA-CNRISATENVDCNCLSEA

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.

TypePositionsDescription
Chain 1 – 225 Phosphoserine phosphatase
Active site 20 – 20 Nucleophile
Active site 22 – 22 Proton donor
Metal binding 20 – 20 Magnesium
Metal binding 22 – 22 Magnesium; via carbonyl oxygen
Binding site 29 – 29 Substrate
Mutagenesis 23 – 23 S -> A. Reduces activity by about 50%.
Mutagenesis 23 – 23 S -> T. Reduces activity by about 80%.
Mutagenesis 29 – 29 E -> D. Reduces activity by about 95%.
Mutagenesis 29 – 29 E -> Q. Loss of activity.
Helix 30 – 37


Literature citations

Mutations responsible for 3-phosphoserine phosphatase deficiency.
Veiga-da-Cunha M.; Collet J.F.; Prieur B.; Jaeken J.; Peeraer Y.; Rabbijns A.; Van Schaftingen E.;
Eur. J. Hum. Genet. 12:163-166(2004)
Cited for: VARIANTS PSPHD ASN-32 AND THR-52;

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.