UniProtKB/SwissProt variant VAR

Variant information

Variant position:

502

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

Type of variant:

Disease [Disclaimer]

The variants are classified into three categories: Disease, Polymorphism and Unclassified.

Disease: Variants implicated in disease according to literature reports.
Polymorphism: Variants not reported to be implicated in disease.
Unclassified: Variants with uncertain implication in disease according to literature reports. Evidence against or in favor of a pathogenic role is limited and/or conflicting.

Residue change:

From Aspartate (D) to Tyrosine (Y) at position 502 (D502Y, p.Asp502Tyr).

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 large size and aromatic (Y)

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

Involvement in disease:

Immunodeficiency 23 (IMD23) [MIM:615816]: A primary immunodeficiency syndrome characterized by recurrent respiratory and skin infections beginning in early childhood, severe atopy, increased serum IgE, and developmental delay or cognitive impairment of varying severity. {ECO:0000269|PubMed:24589341, ECO:0000269|PubMed:24698316, ECO:0000269|PubMed:24931394}. Note=The disease is caused by mutations affecting the gene represented in this entry.

The name and a short description of the disease associated with the variant. For more information about the disease, the user can refer to OMIM, following the link provided after the disease acronym.

Variant description:

In IMD23; decreased phosphoacetylglucosamine mutase activity; no effect on protein abundance.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs267608261 [ dbSNP | Ensembl ]

Sequence information

Variant position:

502

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

Protein sequence length:

542

The length of the canonical sequence.

Location on the sequence:

NDLVKKYKLSRAFVRPSGTE D VVRVYAEADSQESADHLAHE

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                         NDLVKKYKLSRAFVRPSGTEDVVRVYAEADSQESADHLAHE

Mouse                         NDLVKKYTLARAFVRPSGTEDIVRVYAEANSQESADRLAYE

Pig                           NDLVKKYKLSRAFVRPSGTEDVVRVYAEADSQENADSLAYE

Baker's yeast                 DLVVAKYPMGRSFVRASGTEDAVRVYAECKDSSKLGQFCDE

Fission yeast                 DALVAKYEKGRSFVRASGTEDVVRVYAEASTKQAADELCEK

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 – 542	Phosphoacetylglucosamine mutase
Binding site	505 – 505	Substrate

Literature citations

Hypomorphic homozygous mutations in phosphoglucomutase 3 (PGM3) impair immunity and increase serum IgE levels.
Sassi A.; Lazaroski S.; Wu G.; Haslam S.M.; Fliegauf M.; Mellouli F.; Patiroglu T.; Unal E.; Ozdemir M.A.; Jouhadi Z.; Khadir K.; Ben-Khemis L.; Ben-Ali M.; Ben-Mustapha I.; Borchani L.; Pfeifer D.; Jakob T.; Khemiri M.; Asplund A.C.; Gustafsson M.O.; Lundin K.E.; Falk-Soerqvist E.; Moens L.N.; Gungor H.E.; Engelhardt K.R.; Dziadzio M.; Stauss H.; Fleckenstein B.; Meier R.; Prayitno K.; Maul-Pavicic A.; Schaffer S.; Rakhmanov M.; Henneke P.; Kraus H.; Eibel H.; Koelsch U.; Nadifi S.; Nilsson M.; Bejaoui M.; Schaeffer A.A.; Smith C.I.; Dell A.; Barbouche M.R.; Grimbacher B.;
J. Allergy Clin. Immunol. 133:1410-1419(2014)
Cited for: FUNCTION; CATALYTIC ACTIVITY; PATHWAY; INVOLVEMENT IN IMD23; VARIANTS IMD23 SER-83; GLU-340 DEL AND TYR-502; CHARACTERIZATION OF VARIANTS IMD23 SER-83; GLU-340 DEL AND TYR-502;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot O95394: Variant p.Asp502Tyr