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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P41229: Variant p.Asp402Tyr

Lysine-specific demethylase 5C
Gene: KDM5C
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Variant information Variant position: help 402 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 Aspartate (D) to Tyrosine (Y) at position 402 (D402Y, p.Asp402Tyr). 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 acidic (D) to large size and aromatic (Y) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help -3 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 MRXSCJ; decreases enzymatic activity. Any additional useful information about the variant.


Sequence information Variant position: help 402 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 1560 The length of the canonical sequence.
Location on the sequence: help AFGFEQATREYTLQSFGEMA D SFKADYFNMPVHMVPTELVE 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                         AFGFEQATREYTLQSFGEMADSFKADYFNMPVHMVPTELVE

                              AFGFEQATREYTLQSFGEMADSFKADYFNMPVHMVPTELVE

Mouse                         AFGFEQATREYTLQSFGEMADSFKADYFNMPVHMVPTELVE

Pig                           AFGFEQATREYTLQSFGEMADSFKADYSNMPVHMVPTELVE
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 – 1560 Lysine-specific demethylase 5C
Helix 394 – 409



Literature citations
The histone H3K4 demethylase SMCX links REST target genes to X-linked mental retardation.
Tahiliani M.; Mei P.; Fang R.; Leonor T.; Rutenberg M.; Shimizu F.; Li J.; Rao A.; Shi Y.;
Nature 447:601-605(2007)
Cited for: FUNCTION; SUBUNIT; MUTAGENESIS OF HIS-514; SUBCELLULAR LOCATION; CHARACTERIZATION OF VARIANTS MRXSCJ GLY-87; TYR-402 AND CYS-751; Mutations in the JARID1C gene, which is involved in transcriptional regulation and chromatin remodeling, cause X-linked mental retardation.
Jensen L.R.; Amende M.; Gurok U.; Moser B.; Gimmel V.; Tzschach A.; Janecke A.R.; Tariverdian G.; Chelly J.; Fryns J.-P.; Van Esch H.; Kleefstra T.; Hamel B.C.J.; Moraine C.; Gecz J.; Turner G.; Reinhardt R.; Kalscheuer V.M.; Ropers H.-H.; Lenzner S.;
Am. J. Hum. Genet. 76:227-236(2005)
Cited for: VARIANTS MRXSCJ PRO-388; TYR-402; LYS-698 AND PHE-731; TISSUE SPECIFICITY; Mutations in the intellectual disability gene KDM5C reduce protein stability and demethylase activity.
Brookes E.; Laurent B.; Ounap K.; Carroll R.; Moeschler J.B.; Field M.; Schwartz C.E.; Gecz J.; Shi Y.;
Hum. Mol. Genet. 24:2861-2872(2015)
Cited for: CHARACTERIZATION OF VARIANTS MRXSCJ TYR-402 AND LEU-480;
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.