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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q8IY18: Variant p.His990Asp

Structural maintenance of chromosomes protein 5
Gene: SMC5
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Variant information Variant position: help 990 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 Histidine (H) to Aspartate (D) at position 990 (H990D, p.His990Asp). 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 polar (H) to medium size and acidic (D) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help -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: help In ATELS2; loss-of-function variant; unable to rescue microcephaly and aberrant craniofacial patterning in zebrafish lacking SMC5; does not relocalize efficiently to sites of laser irradiation-induced DNA damage; no effect on interaction with SLF2, SMC6 and NSMCE2. Any additional useful information about the variant.


Sequence information Variant position: help 990 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 1101 The length of the canonical sequence.
Location on the sequence: help GIRIRVKFRSSTQLHELTPH H QSGGERSVSTMLYLMALQEL 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                         GIRIRVKFRSSTQLHELTPHHQSGGERSVSTMLYLMALQEL

Mouse                         GIRIRVKFRSSTQLHELTPHHQSGGERSVSTMLYLMALQEL

Chicken                       GIRIRVKFHNFTDLHELTPYHQSGGEKSVSTVLYLMALQEL

Xenopus laevis                GIRIRVKFRSSTQLHELTPHHQSGGERSVSTMLYLMALQEL

Zebrafish                     GIRIQVQFRRNTRMHELTPHHQSGGERSVTTMLYLMSLQEL

Caenorhabditis elegans        GIMIMVCFRKGESMKRLDNKVQSGGERSVATMLYLLALQQL

Baker's yeast                 KIEIMVKFRDNAPLKKLDSHTQSGGERAVSTVLYMIALQEF

Fission yeast                 YIDILVQFREEEGLQKLTGQRQSGGERSVSTIMYLLSLQGL
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 – 1101 Structural maintenance of chromosomes protein 5



Literature citations
Pathogenic variants in SLF2 and SMC5 cause segmented chromosomes and mosaic variegated hyperploidy.
Grange L.J.; Reynolds J.J.; Ullah F.; Isidor B.; Shearer R.F.; Latypova X.; Baxley R.M.; Oliver A.W.; Ganesh A.; Cooke S.L.; Jhujh S.S.; McNee G.S.; Hollingworth R.; Higgs M.R.; Natsume T.; Khan T.; Martos-Moreno G.A.; Chupp S.; Mathew C.G.; Parry D.; Simpson M.A.; Nahavandi N.; Yueksel Z.; Drasdo M.; Kron A.; Vogt P.; Jonasson A.; Seth S.A.; Gonzaga-Jauregui C.; Brigatti K.W.; Stegmann A.P.A.; Kanemaki M.; Josifova D.; Uchiyama Y.; Oh Y.; Morimoto A.; Osaka H.; Ammous Z.; Argente J.; Matsumoto N.; Stumpel C.T.R.M.; Taylor A.M.R.; Jackson A.P.; Bielinsky A.K.; Mailand N.; Le Caignec C.; Davis E.E.; Stewart G.S.;
Nat. Commun. 13:6664-6664(2022)
Cited for: VARIANTS ATELS2 ARG-372 DEL; 425-ARG--SER-1101 DEL AND ASP-990; INVOLVEMENT IN ATELS2; CHARACTERIZATION OF VARIANTS ATELS2 ARG-372 DEL; 425-ARG--SER-1101 DEL AND ASP-990; INTERACTION WITH SMC6; SLF2 AND NSMCE2;
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.