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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot O14686: Variant p.Ser5498Phe

Histone-lysine N-methyltransferase 2D
Gene: KMT2D
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Variant information Variant position: help 5498 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 Serine (S) to Phenylalanine (F) at position 5498 (S5498F, p.Ser5498Phe). 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 small size and polar (S) to large size and aromatic (F) 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 KABUK1. Any additional useful information about the variant.


Sequence information Variant position: help 5498 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 5537 The length of the canonical sequence.
Location on the sequence: help APNCVAEVVTFDKEDKIIII S SRRIPKGEELTYDYQFDFED 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                         APNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFED

Mouse                         APNCVAEVVTFDKEDKIIIISSRRIPKGEELTYDYQFDFED
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 – 5537 Histone-lysine N-methyltransferase 2D
Domain 5397 – 5513 SET
Beta strand 5491 – 5500



Literature citations
A mutation screen in patients with Kabuki syndrome.
Li Y.; Boegershausen N.; Alanay Y.; Simsek Kiper P.O.; Plume N.; Keupp K.; Pohl E.; Pawlik B.; Rachwalski M.; Milz E.; Thoenes M.; Albrecht B.; Prott E.C.; Lehmkuehler M.; Demuth S.; Utine G.E.; Boduroglu K.; Frankenbusch K.; Borck G.; Gillessen-Kaesbach G.; Yigit G.; Wieczorek D.; Wollnik B.;
Hum. Genet. 130:715-724(2011)
Cited for: VARIANTS KABUK1 LEU-543; GLN-647; MET-1192; ARG-1453; VAL-1718; GLN-5154 AND PHE-5498; MLL2 mutation detection in 86 patients with Kabuki syndrome: a genotype-phenotype study.
Makrythanasis P.; van Bon B.W.; Steehouwer M.; Rodriguez-Santiago B.; Simpson M.; Dias P.; Anderlid B.M.; Arts P.; Bhat M.; Augello B.; Biamino E.; Bongers E.M.; Del Campo M.; Cordeiro I.; Cueto-Gonzalez A.M.; Cusco I.; Deshpande C.; Frysira E.; Izatt L.; Flores R.; Galan E.; Gener B.; Gilissen C.; Granneman S.M.; Hoyer J.; Yntema H.G.; Kets C.M.; Koolen D.A.; Marcelis C.L.; Medeira A.; Micale L.; Mohammed S.; de Munnik S.A.; Nordgren A.; Psoni S.; Reardon W.; Revencu N.; Roscioli T.; Ruiterkamp-Versteeg M.; Santos H.G.; Schoumans J.; Schuurs-Hoeijmakers J.H.; Silengo M.C.; Toledo L.; Vendrell T.; van der Burgt I.; van Lier B.; Zweier C.; Reymond A.; Trembath R.C.; Perez-Jurado L.; Dupont J.; de Vries B.B.; Brunner H.G.; Veltman J.A.; Merla G.; Antonarakis S.E.; Hoischen A.;
Clin. Genet. 84:539-545(2013)
Cited for: VARIANTS KABUK1 HIS-170; LEU-170; GLN-647; ARG-1380; ARG-1471; ARG-3876; SER-3897; CYS-5030; CYS-5048; HIS-5048; CYS-5214; TRP-5432 AND PHE-5498; VARIANTS LEU-2557; LEU-2652 AND PRO-4010;
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.