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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q14683: Variant p.Arg496His

Structural maintenance of chromosomes protein 1A
Gene: SMC1A
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Variant information Variant position: help 496 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 Histidine (H) at position 496 (R496H, p.Arg496His). 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 polar (H) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help 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

Variant description: help In CDLS2; affects the affinity of SMC hinge dimers for DNA; mutated hinge dimers bind DNA with higher affinity than wild-type proteins. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 496 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 1233 The length of the canonical sequence.
Location on the sequence: help ELNQVMEQLGDARIDRQESS R QQRKAEIMESIKRLYPGSVY 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                         ELNQVMEQLGDARIDRQESSRQQRKAEIMESIKRLYPGSVY

Mouse                         ELNQVMEQLGDARIDRQESSRQQRKAEIMESIKRLYPGSVY

Rat                           ELNQVMEQLGDARIDRQESSRQQRKAEIMESIKRLYPGSVY

Bovine                        ELNQVMEQLGDARIDRQESSRQQRKAEIMESIKRLYPGSVY

Xenopus laevis                ELNQVMEQLGDARIDRQESSRQQRKAEIMESIKRLYPGSVY

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 – 1233 Structural maintenance of chromosomes protein 1A
Coiled coil 163 – 503



Literature citations
Mutations in cohesin complex members SMC3 and SMC1A cause a mild variant of Cornelia de Lange syndrome with predominant mental retardation.
Deardorff M.A.; Kaur M.; Yaeger D.; Rampuria A.; Korolev S.; Pie J.; Gil-Rodriguez C.; Arnedo M.; Loeys B.; Kline A.D.; Wilson M.; Lillquist K.; Siu V.; Ramos F.J.; Musio A.; Jackson L.S.; Dorsett D.; Krantz I.D.;
Am. J. Hum. Genet. 80:485-494(2007)
Cited for: VARIANTS CDLS2 58-VAL--ARG-62 DEL; VAL-133; HIS-196; CYS-496; HIS-496; TRP-711; GLN-790 AND LEU-1122; Cornelia de Lange syndrome mutations in SMC1A or SMC3 affect binding to DNA.
Revenkova E.; Focarelli M.L.; Susani L.; Paulis M.; Bassi M.T.; Mannini L.; Frattini A.; Delia D.; Krantz I.; Vezzoni P.; Jessberger R.; Musio A.;
Hum. Mol. Genet. 18:418-427(2009)
Cited for: CHARACTERIZATION OF VARIANTS CDLS2 ALA-493; CYS-496 AND HIS-496; GENOMIC INSTABILITY OF CDLS CELL LINES TO IONIZING RADIATION; SMC1A expression and mechanism of pathogenicity in probands with X-Linked Cornelia de Lange syndrome.
Liu J.; Feldman R.; Zhang Z.; Deardorff M.A.; Haverfield E.V.; Kaur M.; Li J.R.; Clark D.; Kline A.D.; Waggoner D.J.; Das S.; Jackson L.G.; Krantz I.D.;
Hum. Mutat. 30:1535-1542(2009)
Cited for: VARIANTS CDLS2 58-VAL--ARG-62 DEL; VAL-133; LYS-141; HIS-196; LYS-268 DEL; SER-306 DEL; GLN-398; CYS-496; HIS-496; GLU-683 DEL; GLY-693; TRP-711; PHE-781; GLN-790; GLY-816; GLN-1049; LEU-1122 AND TRP-1123;
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.