UniProtKB/SwissProt variant VAR

Variant information

Variant position:

56

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 56 (A56T, p.Ala56Thr).

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 rs28383151 [ dbSNP | Ensembl ]

Sequence information

Variant position:

56

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

Protein sequence length:

336

The length of the canonical sequence.

Location on the sequence:

LTDGHSAWTGTVSESEISQE A DDMAMEKGKYVGELRKALLS

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                         LTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLS

Mouse                         LTDGHSAWTATVSELEISQEADDMAMEKGKYIDELRKALVP

Slime mold                    LTDLTNVWSSNVTTKYIENILKPQGMSFDQYFQLLKKSLLK

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 – 336	DNA repair protein XRCC4
Region	1 – 213	Interaction with IFFO1
Modified residue	53 – 53	Phosphoserine; by PRKDC
Mutagenesis	55 – 55	E -> R. Abolished interaction with NHEJ1/XLF.
Mutagenesis	58 – 58	D -> R. Abolished interaction with NHEJ1/XLF.
Mutagenesis	61 – 61	M -> R. Abolished interaction with NHEJ1/XLF.
Mutagenesis	62 – 62	E -> R. Does not affect interaction with NHEJ1/XLF.
Mutagenesis	65 – 65	K -> E. Strongly decreased interaction with NHEJ1/XLF. Abolished interaction with NHEJ1/XLF; when associated with E-99. Abolished ability to bridge DNA; when associated with E-99. Abolished interaction with NHEJ1/XLF; when associated with E-102.
Mutagenesis	69 – 69	E -> R. Does not affect interaction with NHEJ1/XLF.
Mutagenesis	71 – 71	R -> E. Abolished interaction with NHEJ1/XLF; when associated with E-99.
Mutagenesis	72 – 72	K -> E. Abolished interaction with NHEJ1/XLF; when associated with E-99. Abolished ability to bridge DNA; when associated with E-90 and E-99.
Helix	49 – 58

Literature citations

Submission
NIEHS SNPs program;
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANTS CYS-12; THR-56; THR-134; GLN-142 AND SER-247;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q13426: Variant p.Ala56Thr