UniProtKB/SwissProt variant VAR

Variant information

Variant position:

41

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

Type of variant:

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:

From Glutamate (E) to Lysine (K) at position 41 (E41K, p.Glu41Lys).

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 medium size and acidic (E) to large size and basic (K)

The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:

1

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:

In DKCX.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs121912302 [ dbSNP | Ensembl ]

Sequence information

Variant position:

41

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

Protein sequence length:

514

The length of the canonical sequence.

Location on the sequence:

SLPEEDVAEIQHAEEFLIKP E SKVAKLDTSQWPLLLKNFDK

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                         SLPEEDVAEIQHAEEFLIKPESKVAKLDTSQWPLLLKNFDK

Mouse                         PLQEDDVAEIQHAEEFLIKPESKVAQLDTSQWPLLLKNFDK

Rat                           PLPEADVAEIQHAEDFLIKPESKAAQLDTSQWPLLLKNFDR

Chicken                       SLPDEDVADIQHTEEFLIKPESRVAQLDTSQWPLLLKNFDK

Caenorhabditis elegans        KLEGDDLAEAQQKGSFQLPSSNETAKLDASQWPLLLKNYDK

Drosophila                    PLDGDDIGTLQKQGNFQIKPSSKIAELDTSQWPLLLKNFDK

Slime mold                    KSSEKSTQEVEQ----VIKPE-KTPILDTSKWPLLLKNYDQ

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 – 514	H/ACA ribonucleoprotein complex subunit DKC1
Modified residue	21 – 21	Phosphoserine
Cross	39 – 39	Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)
Cross	43 – 43	Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)

Literature citations

X-linked dyskeratosis congenita is predominantly caused by missense mutations in the DKC1 gene.
Knight S.W.; Heiss N.S.; Vulliamy T.J.; Greschner S.; Stavrides G.; Pai G.S.; Lestringant G.; Varma N.; Mason P.J.; Dokal I.; Poustka A.;
Am. J. Hum. Genet. 65:50-58(1999)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); VARIANTS DKCX VAL-2; GLU-39; LYS-41; THR-65; ALA-66; VAL-321; ILE-350; THR-350; VAL-353 AND ARG-402;

Uncovering global SUMOylation signaling networks in a site-specific manner.
Hendriks I.A.; D'Souza R.C.; Yang B.; Verlaan-de Vries M.; Mann M.; Vertegaal A.C.;
Nat. Struct. Mol. Biol. 21:927-936(2014)
Cited for: SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-413; IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS];

Mapping of SUMO sites and analysis of SUMOylation changes induced by external stimuli.
Impens F.; Radoshevich L.; Cossart P.; Ribet D.;
Proc. Natl. Acad. Sci. U.S.A. 111:12432-12437(2014)
Cited for: SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-413; IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS];

SUMO-2 orchestrates chromatin modifiers in response to DNA damage.
Hendriks I.A.; Treffers L.W.; Verlaan-de Vries M.; Olsen J.V.; Vertegaal A.C.;
Cell Rep. 10:1778-1791(2015)
Cited for: SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-413; IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS];

System-wide analysis of SUMOylation dynamics in response to replication stress reveals novel small ubiquitin-like modified target proteins and acceptor lysines relevant for genome stability.
Xiao Z.; Chang J.G.; Hendriks I.A.; Sigurdsson J.O.; Olsen J.V.; Vertegaal A.C.;
Mol. Cell. Proteomics 14:1419-1434(2015)
Cited for: SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-413; IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS];

Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation.
Hendriks I.A.; Lyon D.; Young C.; Jensen L.J.; Vertegaal A.C.; Nielsen M.L.;
Nat. Struct. Mol. Biol. 24:325-336(2017)
Cited for: SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-20; LYS-39; LYS-43; LYS-191; LYS-394; LYS-413; LYS-424; LYS-433 AND LYS-467; IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS];

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot O60832: Variant p.Glu41Lys