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UniProtKB/Swiss-Prot Q8N3U4: Variant p.Arg604Gln

Cohesin subunit SA-2
Gene: STAG2
Variant information

Variant position:  604
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  US
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 Arginine (R) to Glutamine (Q) at position 604 (R604Q, p.Arg604Gln).
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 large size and basic (R) to medium size and polar (Q)
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 MKMS; unknown pathological significance.
Any additional useful information about the variant.



Sequence information

Variant position:  604
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  1231
The length of the canonical sequence.

Location on the sequence:   KVTNLLQLPQYFDLEIYTTG  R LEKHLDALLRQIRNIVEKHT
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                         KVTNLLQLPQYFDLEIYTTGRLEKHLDALLRQIRNIVEKHT

Mouse                         KVTNLLQLPQYFDLEIYTTGRLEKHLDALLRQIRNIVEKHT

Xenopus laevis                KVTNLLQLPQYFDLEIYTTGRLEKHLEALLRQIRNIVEKHT

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 1 – 1231 Cohesin subunit SA-2
Modified residue 607 – 607 N6-acetyllysine


Literature citations

De novo loss-of-function variants in STAG2 are associated with developmental delay, microcephaly, and congenital anomalies.
Mullegama S.V.; Klein S.D.; Mulatinho M.V.; Senaratne T.N.; Singh K.; Nguyen D.C.; Gallant N.M.; Strom S.P.; Ghahremani S.; Rao N.P.; Martinez-Agosto J.A.;
Am. J. Med. Genet. A 173:1319-1327(2017)
Cited for: FUNCTION; INVOLVEMENT IN MKMS; VARIANTS MKMS 69-ARG--PHE-1231 DEL AND GLN-604; CHARACTERIZATION OF VARIANT MKMS 69-ARG--PHE-1231 DEL;

Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies.
Yuan B.; Neira J.; Pehlivan D.; Santiago-Sim T.; Song X.; Rosenfeld J.; Posey J.E.; Patel V.; Jin W.; Adam M.P.; Baple E.L.; Dean J.; Fong C.T.; Hickey S.E.; Hudgins L.; Leon E.; Madan-Khetarpal S.; Rawlins L.; Rustad C.F.; Stray-Pedersen A.; Tveten K.; Wenger O.; Diaz J.; Jenkins L.; Martin L.; McGuire M.; Pietryga M.; Ramsdell L.; Slattery L.; Abid F.; Bertuch A.A.; Grange D.; Immken L.; Schaaf C.P.; Van Esch H.; Bi W.; Cheung S.W.; Breman A.M.; Smith J.L.; Shaw C.; Crosby A.H.; Eng C.; Yang Y.; Lupski J.R.; Xiao R.; Liu P.;
Genet. Med. 21:663-675(2019)
Cited for: VARIANTS MKMS 140-GLN--PHE-1231 DEL; CYS-159; 535-CYS--PHE-1231 DEL AND GLN-604;

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.