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UniProtKB/Swiss-Prot O60832: Variant p.Glu41Lys

H/ACA ribonucleoprotein complex subunit DKC1
Gene: DKC1
Chromosomal location: Xq28
Variant information

Variant position:  41
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  Disease [Disclaimer]
The variants are classified into three categories: Disease, Polymorphism and Unclassified.
  • Disease: Variants implicated in disease according to literature reports.
  • Polymorphism: Variants not reported to be implicated in disease.
  • Unclassified: Variants with uncertain implication in disease according to literature reports. Evidence against or in favor of a pathogenic role is limited and/or conflicting.

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

Involvement in disease:  Dyskeratosis congenita, X-linked (DKCX) [MIM:305000]: A rare, progressive bone marrow failure syndrome characterized by the triad of reticulated skin hyperpigmentation, nail dystrophy, and mucosal leukoplakia. Early mortality is often associated with bone marrow failure, infections, fatal pulmonary complications, or malignancy. {ECO:0000269|PubMed:10364516, ECO:0000269|PubMed:15304085, ECO:0000269|PubMed:17417794, ECO:0000269|PubMed:18802941, ECO:0000269|PubMed:19734544, ECO:0000269|PubMed:19879169, ECO:0000269|PubMed:21602826, ECO:0000269|PubMed:25219674, ECO:0000269|PubMed:9590285}. Note=The disease is caused by mutations affecting the gene represented in this entry. Reduced rRNA pseudouridine levels in cells from patients (PubMed:25219674). {ECO:0000269|PubMed:25219674}.
The name and a short description of the disease associated with the variant. For more information about the disease, the user can refer to OMIM, following the link provided after the disease acronym.

Variant description:  In DKCX.
Any additional useful information about the variant.

Other resources:  
Links to websites of interest for the variant.



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.

TypePositionsDescription
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];

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.