UniProtKB/SwissProt variant VAR

Variant information

Variant position:

499

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 Valine (V) at position 499 (A499V, p.Ala499Val).

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 hydrophobic (V)

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 rs2228000 [ dbSNP | Ensembl ]

Sequence information

Variant position:

499

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

Protein sequence length:

940

The length of the canonical sequence.

Location on the sequence:

GSKSASRTHRGSHRKDPSLP A ASSSSSSSKRGKKMCSDGEK

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                         GSKSA--------------------------------------------------SRTHRGSH----------------------------------------RKDPSLPAASSSSSSSKRGKKMCSDGEK

Mouse                         GSKSA------------------------------------

Drosophila                    RSKSPKVLISPSFLKKKSDGADSTSDPQKHQMAPETKARIS

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	2 – 940	DNA repair protein complementing XP-C cells
Region	327 – 519	Disordered
Region	496 – 734	Interaction with RAD23B
Compositional bias	496 – 510	Polar residues
Alternative sequence	141 – 940	Missing. In isoform 3.

Literature citations

Purification and cloning of a nucleotide excision repair complex involving the Xeroderma pigmentosum group C protein and a human homologue of yeast RAD23.
Masutani C.; Sugasawa K.; Yanagisawa J.; Sonoyama T.; Ui M.; Enomoto T.; Takio K.; Tanaka K.; van der Spek P.J.; Bootsma D.; Hoeijmakers J.H.J.; Hanaoka F.;
EMBO J. 13:1831-1843(1994)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); PROTEIN SEQUENCE OF 2-55; VARIANTS VAL-499 AND LYS-939;

The human XPC DNA repair gene: arrangement, splice site information content and influence of a single nucleotide polymorphism in a splice acceptor site on alternative splicing and function.
Khan S.G.; Muniz-Medina V.; Shahlavi T.; Baker C.C.; Inui H.; Ueda T.; Emmert S.; Schneider T.D.; Kraemer K.H.;
Nucleic Acids Res. 30:3624-3631(2002)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANTS VAL-499 AND LYS-939; ALTERNATIVE SPLICING;

Submission
NIEHS SNPs program;
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANTS VAL-16; PHE-48; ARG-86; GLN-314; HIS-492; VAL-499; ILE-513; GLU-632; HIS-671; MET-689; GLN-928 AND LYS-939;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q01831: Variant p.Ala499Val