UniProtKB/SwissProt variant VAR

Phosphoserine phosphatase
Gene: PSPH
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Variant information Variant position:

35 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 Alanine (A) to Threonine (T) at position 35 (A35T, p.Ala35Thr). 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 hydrophobic (A) to medium size and polar (T) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score:

0 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; decreased L-phosphoserine phosphatase activity. Any additional useful information about the variant.

Sequence information Variant position:

35 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:

DAVCFDVDSTVIREEGIDEL A KICGVEDAVSEMTRRAMGGA 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                         DA--------------------------------------------VCFDVDSTVIREEGIDELAKICGVEDAVSEMTRRAMGGA

Mouse                         DA---------------------------------------

Rat                           DA---------------------------------------

Bovine                        DA---------------------------------------

Drosophila                    NGTTGGAAKTT------------VASAITPPKQPQLAAKVI

Baker's yeast                 TDIFIEVAGSIVQKDLKNKLTNVIDSHNDVDVIVSVDNEYR

Fission yeast                 TLVSGQLKGTF--EDAKDA-CNRISATENVDCNCLSEATFS

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 – 225	Phosphoserine phosphatase
Active site	20 – 20	Nucleophile
Active site	22 – 22	Proton donor
Binding site	20 – 20
Binding site	22 – 22
Binding site	52 – 52
Binding site	53 – 53
Mutagenesis	23 – 23	S -> A. Reduces L-phosphoserine phosphatase activity by about 50%.
Mutagenesis	23 – 23	S -> T. Reduces L-phosphoserine phosphatase activity by about 80%.
Mutagenesis	29 – 29	E -> D. Reduces L-phosphoserine phosphatase activity by about 95%.
Mutagenesis	29 – 29	E -> Q. Loss of L-phosphoserine phosphatase activity.
Helix	30 – 37

Literature citations
Phosphoserine phosphatase (PSPH) gene mutation in an intellectual disability family from Pakistan.
Vincent J.B.; Jamil T.; Rafiq M.A.; Anwar Z.; Ayaz M.; Hameed A.; Nasr T.; Naeem F.; Khattak N.A.; Carter M.; Ahmed I.; John P.; Wiame E.; Andrade D.M.; Schaftingen E.V.; Mir A.; Ayub M.;
Clin. Genet. 87:296-298(2015)
Cited for: VARIANT PSPHD THR-35; CHARACTERIZATION OF VARIANT PSPHD THR-35; FUNCTION; CATALYTIC ACTIVITY; PATHWAY;

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.

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P78330: Variant p.Ala35Thr