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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot A6NHR9: Variant p.Arg479Pro

Structural maintenance of chromosomes flexible hinge domain-containing protein 1
Gene: SMCHD1
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Variant information Variant position: help 479 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 Arginine (R) to Proline (P) at position 479 (R479P, p.Arg479Pro). 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 large size and basic (R) to medium size and hydrophobic (P) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help -2 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 FSHD2; decreased protein level in fibroblasts as compared to wild-type protein. Any additional useful information about the variant.


Sequence information Variant position: help 479 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 2005 The length of the canonical sequence.
Location on the sequence: help FILEKAARGKRPIFECFWNG R LIPYTSVEDFDWCTPPKKRG 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                         FILEKAARGKRPIFECFWNGRLIPYTSVEDFDWCTPPKKRG

Mouse                         FISEKAARGKRPIFECFWNGRLIPYTSVGDFDWCAPPKKRG
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 2 – 2005 Structural maintenance of chromosomes flexible hinge domain-containing protein 1
Region 111 – 702 ATPase activity domain
Alternative sequence 1 – 1065 Missing. In isoform 3.
Beta strand 479 – 486



Literature citations
Digenic inheritance of an SMCHD1 mutation and an FSHD-permissive D4Z4 allele causes facioscapulohumeral muscular dystrophy type 2.
Lemmers R.J.; Tawil R.; Petek L.M.; Balog J.; Block G.J.; Santen G.W.; Amell A.M.; van der Vliet P.J.; Almomani R.; Straasheijm K.R.; Krom Y.D.; Klooster R.; Sun Y.; den Dunnen J.T.; Helmer Q.; Donlin-Smith C.M.; Padberg G.W.; van Engelen B.G.; de Greef J.C.; Aartsma-Rus A.M.; Frants R.R.; de Visser M.; Desnuelle C.; Sacconi S.; Filippova G.N.; Bakker B.; Bamshad M.J.; Tapscott S.J.; Miller D.G.; van der Maarel S.M.;
Nat. Genet. 44:1370-1374(2012)
Cited for: VARIANTS FSHD2 CYS-353; PRO-479; ARG-492; SER-690; ASN-868 AND SER-1554; FUNCTION; INVOLVEMENT IN FSHD2; Inter-individual differences in CpG methylation at D4Z4 correlate with clinical variability in FSHD1 and FSHD2.
Lemmers R.J.; Goeman J.J.; van der Vliet P.J.; van Nieuwenhuizen M.P.; Balog J.; Vos-Versteeg M.; Camano P.; Ramos Arroyo M.A.; Jerico I.; Rogers M.T.; Miller D.G.; Upadhyaya M.; Verschuuren J.J.; Lopez de Munain Arregui A.; van Engelen B.G.; Padberg G.W.; Sacconi S.; Tawil R.; Tapscott S.J.; Bakker B.; van der Maarel S.M.;
Hum. Mol. Genet. 24:659-669(2015)
Cited for: VARIANTS FSHD2 GLU-137; 138-GLN--VAL-2005 DEL; PHE-194; 195-ASN--VAL-2005 DEL; ASP-263; 344-ARG--VAL-2005 DEL; CYS-353; ARG-425; 434-TYR--VAL-2005 DEL; PRO-479; SER-690; SER-716; 731-GLN--VAL-2005 DEL; PRO-748; 780-GLU--VAL-2005 DEL; ASN-849; ASN-868; ILE-1468; SER-1554; 1176-THR-ASP-1177 DELINS MET-HIS; 1795-ARG--VAL-2005 DEL AND 1868-ARG--VAL-2005 DEL;
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.