UniProtKB/Swiss-Prot Q9Y6K9: Variant p.Met407Val

NF-kappa-B essential modulator
Gene: IKBKG
Chromosomal location: Xq28
Variant information

Variant position:  407
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  Disease [Disclaimer]
The variants are classified into three categories: Disease, Polymorphism and Unclassified.
  • Disease: Variants have been found in patients and disease-association is reported in literature. However, this classification is not a definitive assessment of variant pathogenicity.
  • Polymorphism: No disease-association has been reported.
  • Unclassified: Variants have been found in patients but disease-association remains unclear.

Residue change:  From Methionine (M) to Valine (V) at position 407 (M407V, p.Met407Val).
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:  Similar physico-chemical property. Both residues are medium size and hydrophobic.
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 IP; impairs binding to ubiquitin.
Any additional useful information about the variant.



Sequence information

Variant position:  407
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  419
The length of the canonical sequence.

Location on the sequence:   SPPEEPPDFCCPKCQYQAPD  M DTLQIHVMECIE
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                         SPPEEPPDFCCPKCQYQAPDMDTLQIHVMECIE--

Mouse                         SPPEEPPDFCCPKCQYQAPDMDTLQIHVMECIE

Rat                           SPPEEPPDFCCPKCQYQAPDMDTLQIHVMECIE

Bovine                        SPPDEPPKFCCPKCQYQAPDIDTLQIHVMECIE

Drosophila                    ----------CPICSKSFNALSVLQSHVNDCLD

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 – 419 NF-kappa-B essential modulator
Zinc finger 396 – 417 C2HC-type
Region 251 – 419 Required for interaction with TNFAIP3
Region 382 – 419 Interaction with CYLD
Modified residue 387 – 387 Phosphoserine
Cross 399 – 399 Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)
Mutagenesis 399 – 399 K -> R. Abolishes BCL10-mediated but not RIPK2-mediated ubiquitination. Important decrease in the ubiquitination level; when associated with R-285. No change in the ubiquitination level; when associated with R-115 or R-224.
Mutagenesis 414 – 414 V -> S. Abolishes binding to polyubiquitin.
Mutagenesis 415 – 415 M -> S. Impairs binding to polyubiquitin.
Helix 407 – 416


Literature citations

Genomic rearrangement in NEMO impairs NF-kappaB activation and is a cause of incontinentia pigmenti.
Smahi A.; Courtois G.; Vabres P.; Yamaoka S.; Heuertz S.; Munnich A.; Israel A.; Heiss N.S.; Klauck S.M.; Kioschis P.; Wiemann S.; Poustka A.; Esposito T.; Bardaro T.; Gianfrancesco F.; Ciccodicola A.; D'Urso M.; Woffendin H.; Jakins T.; Donnai D.; Stewart H.; Kenwrick S.J.; Aradhya S.; Yamagata T.; Levy M.; Lewis R.A.; Nelson D.L.;
Nature 405:466-472(2000)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANT IP VAL-407;

The zinc finger of NEMO is a functional ubiquitin-binding domain.
Cordier F.; Grubisha O.; Traincard F.; Veron M.; Delepierre M.; Agou F.;
J. Biol. Chem. 284:2902-2907(2009)
Cited for: UBIQUITIN-BINDING; MUTAGENESIS OF VAL-414 AND MET-415; CHARACTERIZATION OF VARIANT IP VAL-407;

A recurrent deletion in the ubiquitously expressed NEMO (IKK-gamma) gene accounts for the vast majority of incontinentia pigmenti mutations.
Aradhya S.; Woffendin H.; Jakins T.; Bardaro T.; Esposito T.; Smahi A.; Shaw C.; Levy M.; Munnich A.; D'Urso M.; Lewis R.A.; Kenwrick S.; Nelson D.L.;
Hum. Mol. Genet. 10:2171-2179(2001)
Cited for: VARIANTS IP LYS-57 AND VAL-407;

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.