UniProtKB/SwissProt variant VAR

Variant information

Variant position:

50

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

Type of variant:

LB/B

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 50 (A50T, p.Ala50Thr).

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

Other resources:

Links to websites of interest for the variant.

Variant rs11571143 [ dbSNP | Ensembl ]

Sequence information

Variant position:

50

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

Protein sequence length:

933

The length of the canonical sequence.

Location on the sequence:

RPAAGPFPGSQTSDTLPEVS A IPISLDGLLFPRPCQGQDPS

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                         RPAAGPFPGSQTSDTLPEVSAIPISL-----------DGLLFPRPCQGQDPS

Gorilla                       RPAAGPYPGSQTSDTLPEVSAIPISL-----------DGLL

                              RRDGGRLRASQTSDAPRVAAAAAAAAAAASAAPSAPSDRLL

Chimpanzee                    RPAAGPFPGSQTSDTLPEVSAIPISL-----------DGLL

Mouse                         RLDSGPFQGSQHSDVSSVVSPIPISL-----------DGLL

Rat                           RLDPDPFQGSQHSDASSVVSPIPISL-----------DRLL

Rabbit                        RPDPGPFQGSQTSEASSVVSAIPISL-----------DGLL

Chicken                       AP---PSRG--------EAEGIDVAL-----------DGLL

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 – 933	Progesterone receptor
Region	1 – 566	Modulating, Pro-Rich
Region	1 – 164	AF3; mediates transcriptional activation (in isoform B)
Region	1 – 157	Disordered
Alternative sequence	1 – 594	Missing. In isoform 3.
Alternative sequence	1 – 164	Missing. In isoform A.
Alternative sequence	17 – 635	Missing. In isoform 4.
Mutagenesis	55 – 55	L -> A. Reduces transcriptional activation; when associated with A-58 and A-59.
Mutagenesis	58 – 58	L -> A. Reduces transcriptional activation; when associated with A-55 and A-59.
Mutagenesis	59 – 59	L -> A. Reduces transcriptional activation; when associated with A-55 and A-58.

Literature citations

Submission
NIEHS SNPs program;
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANTS THR-50; VAL-120; LEU-186; ARG-301; THR-344; SER-444; LEU-529; PRO-536; VAL-651 AND LEU-865;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P06401: Variant p.Ala50Thr