UniProtKB/Swiss-Prot Q9C0D0: Variant p.Arg521Cys

Phosphatase and actin regulator 1
Gene: PHACTR1
Chromosomal location: 6p24.1
Variant information

Variant position:  521
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  Unclassified
The variants are classified into three categories: Disease, Polymorphism and Unclassified.
  • Disease: Variants have been found in patients and disease-association is reported in literature. However, this classification is not a definitive assessment of variant pathogenicity.
  • Polymorphism: No disease-association has been reported.
  • Unclassified: Variants have been found in patients but disease-association remains unclear.

Residue change:  From Arginine (R) to Cysteine (C) at position 521 (R521C, p.Arg521Cys).
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 large size and basic (R) to medium size and polar (C)
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

Variant description:  Found in a patient with mental retardation, seizures, severely delayed psychomotor development, spastic tetraparesis, joint contractures and scoliosis.
Any additional useful information about the variant.



Sequence information

Variant position:  521
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  580
The length of the canonical sequence.

Location on the sequence:   TRKLSQRPTVEELRERKILI  R FSDYVEVADAQDYDRRADKP
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                         TRKLSQRPTVEELRERKILIRFSDYVEVADAQDYDRRADKP

Mouse                         TRKLSQRPTVEELRERKILIRFSDYVEVADAQDYDRRADKP

Rat                           TRKLSQRPTVEELRERKILIRFSDYVEVADAQDYDRRADKP

Chicken                       TRKLSQRPTVEELRERKILIRFSDYVEVADAQDYDRRADKP

Xenopus laevis                TRKLSQRPTVEELREKKILISFSDYVELADAQDYDRRADKP

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 – 580 Phosphatase and actin regulator 1
Repeat 498 – 523 RPEL 4
Alternative sequence 485 – 580 Missing. In isoform 2.


Literature citations

Diagnostic exome sequencing in persons with severe intellectual disability.
de Ligt J.; Willemsen M.H.; van Bon B.W.; Kleefstra T.; Yntema H.G.; Kroes T.; Vulto-van Silfhout A.T.; Koolen D.A.; de Vries P.; Gilissen C.; del Rosario M.; Hoischen A.; Scheffer H.; de Vries B.B.; Brunner H.G.; Veltman J.A.; Vissers L.E.;
N. Engl. J. Med. 367:1921-1929(2012)
Cited for: VARIANT CYS-521;

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.