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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P49642: Variant p.Cys301Arg

DNA primase small subunit
Gene: PRIM1
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Variant information Variant position: help 301 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: help 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: help From Cysteine (C) to Arginine (R) at position 301 (C301R, p.Cys301Arg). 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: help Change from medium size and polar (C) to large size and basic (R) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help -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: help In PDIL; loss of function in DNA replication initiation; contrary to the wild type, the mutant does not rescue reduced cell proliferation, prolonged S-phase and impaired DNA replication when transfected in patient cells. Any additional useful information about the variant.


Sequence information Variant position: help 301 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 420 The length of the canonical sequence.
Location on the sequence: help NNIKNDKYGPWLEWEIMLQY C FPRLDINVSKGINHLLKSPF 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: help The multiple alignment of the region surrounding the variant against various orthologous sequences. 
Human                         NNIKNDKYGPW------LEWE----IMLQYCFPRLDINVSKGINHLLKSPF

Mouse                         QNMKNDKCGPW------LEWE----VMLQYCFPRLDVNVSK

Caenorhabditis elegans        RKSLSPKDGLLDFKMQGRDRNYLLYFVLQRCYPRLDVNVST

Drosophila                    NSMRTSTTSAWSRKLKNIVAE----IQLGLLYPRLDINVTR

Baker's yeast                 KGPKQDSHII---KLRECKED----LVLMTLYPKLDVEVTK

Fission yeast                 IASISPSVIAI------AKQD----IVLTYLYPRLDVEVSR
Sequence annotation in neighborhood: help 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 – 420 DNA primase small subunit
Binding site 306 – 306
Binding site 306 – 306
Mutagenesis 306 – 306 D -> A. Loss of primase activity.
Mutagenesis 306 – 306 D -> N. Decreases the binding affinity for NTPs.
Mutagenesis 315 – 315 H -> A. Decreases the binding affinity for NTPs. Loss of primase activity.
Mutagenesis 318 – 318 K -> A. Decreases the binding affinity for NTPs. Loss of primase activity.
Helix 291 – 301



Literature citations
PRIM1 deficiency causes a distinctive primordial dwarfism syndrome.
Parry D.A.; Tamayo-Orrego L.; Carroll P.; Marsh J.A.; Greene P.; Murina O.; Uggenti C.; Leitch A.; Kaposzta R.; Mero G.; Nagy A.; Orlik B.; Kovacs-Paszthy B.; Quigley A.J.; Riszter M.; Rankin J.; Reijns M.A.M.; Szakszon K.; Jackson A.P.;
Genes Dev. 34:1520-1533(2020)
Cited for: VARIANT PDIL ARG-301; INVOLVEMENT IN PDIL; CHARACTERIZATION OF VARIANT PDIL ARG-301; FUNCTION;
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.