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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P78527: Variant p.Leu3062Arg

DNA-dependent protein kinase catalytic subunit
Gene: PRKDC
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Variant information Variant position: help 3062 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 Leucine (L) to Arginine (R) at position 3062 (L3062R, p.Leu3062Arg). 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 hydrophobic (L) to large size and basic (R) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help -2 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 IMD26; shows increased long palindromic (P)-nucleotide stretches in the immunoglobulin coding joints indicating a defect in hairpin opening and insufficient DCLRE1C activation. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 3062 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 4128 The length of the canonical sequence.
Location on the sequence: help PYMIRSKLKLLLQGEADQSL L TFIDKAMHGELQKAILELHY 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                         PYMIRSKLKLLLQGEADQSLLTFIDKAMHGELQKAILELHY

                              PYMIRSKLKLLLQGEADQSLLTFIDEAVNKDLQKALIELHY

Mouse                         PYVIRSKLKLLLQGEGNQSLLTFVDEAMNKELQKTVLELQY

Chicken                       PYIIRSKLKLLLNGENDQTLLTFIDEAMKTEQKKALIEMHY

Xenopus laevis                PYMIRSKLKMLLGGNNDQTLLTFVDEAMKVEQRKVLMETFY

Slime mold                    SYFFEFNLKV---KENWNYLYQFIADLANTKQYQ-YLENKF
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 – 4128 DNA-dependent protein kinase catalytic subunit
Domain 2906 – 3539 FAT
Region 2436 – 3212 KIP-binding
Helix 3061 – 3068



Literature citations
A DNA-PKcs mutation in a radiosensitive T-B- SCID patient inhibits Artemis activation and nonhomologous end-joining.
van der Burg M.; Ijspeert H.; Verkaik N.S.; Turul T.; Wiegant W.W.; Morotomi-Yano K.; Mari P.O.; Tezcan I.; Chen D.J.; Zdzienicka M.Z.; van Dongen J.J.; van Gent D.C.;
J. Clin. Invest. 119:91-98(2009)
Cited for: INVOLVEMENT IN IMD26; VARIANT IMD26 ARG-3062;
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.