UniProtKB/SwissProt variant VAR

Variant information

Variant position:

1021

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 Glutamate (E) to Lysine (K) at position 1021 (E1021K, p.Glu1021Lys).

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 (E) to large size and basic (K)

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 APDS; results in gain of function causing enhanced membrane association and kinase activity.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs397518423 [ dbSNP | Ensembl ]

Sequence information

Variant position:

1021

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

Protein sequence length:

1044

The length of the canonical sequence.

Location on the sequence:

SLALGKTEEEALKHFRVKFN E ALRESWKTKVNWLAHNVSKD

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                         SLALGKTEEEALKHFRVKFNEALRESWKTKVNWLAHNVSKD

Mouse                         SLALGKTEEEALKHFRVKFNEALRESWKTKVNWLAHNVSKD

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 – 1044	Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform
Domain	774 – 1041	PI3K/PI4K
Modified residue	1039 – 1039	Phosphoserine; by autocatalysis
Alternative sequence	302 – 1044	Missing. In isoform 2.
Mutagenesis	1039 – 1039	S -> A. Abolishes autophosphorylation, no effect on lipid kinase activity.
Mutagenesis	1039 – 1039	S -> DE. Abolishes autophosphorylation, reduced lipid kinase activity.
Helix	1008 – 1031

Literature citations

Phosphoinositide 3-kinase delta gene mutation predisposes to respiratory infection and airway damage.
Angulo I.; Vadas O.; Garcon F.; Banham-Hall E.; Plagnol V.; Leahy T.R.; Baxendale H.; Coulter T.; Curtis J.; Wu C.; Blake-Palmer K.; Perisic O.; Smyth D.; Maes M.; Fiddler C.; Juss J.; Cilliers D.; Markelj G.; Chandra A.; Farmer G.; Kielkowska A.; Clark J.; Kracker S.; Debre M.; Picard C.; Pellier I.; Jabado N.; Morris J.A.; Barcenas-Morales G.; Fischer A.; Stephens L.; Hawkins P.; Barrett J.C.; Abinun M.; Clatworthy M.; Durandy A.; Doffinger R.; Chilvers E.R.; Cant A.J.; Kumararatne D.; Okkenhaug K.; Williams R.L.; Condliffe A.; Nejentsev S.;
Science 342:866-871(2013)
Cited for: VARIANT APDS LYS-1021; CHARACTERIZATION OF VARIANT APDS LYS-1021;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot O00329: Variant p.Glu1021Lys