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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q9UBB6: Variant p.Trp498Arg

Neurochondrin
Gene: NCDN
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Variant information Variant position: help 498 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 Tryptophan (W) to Arginine (R) at position 498 (W498R, p.Trp498Arg). 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 aromatic (W) to large size and basic (R) 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 NEDIES; in the neuroblastoma cell line SH-SY5Y, in which NCDN has been knocked out, does not rescue impaired neurite formation following retinoic acid treatment, contrary to wild-type; in these cells, there is markedly decreased phosphorylation of ERK1/ERK2, compared to wild-type, suggesting impaired GRM5 activation. Any additional useful information about the variant.


Sequence information Variant position: help 498 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 729 The length of the canonical sequence.
Location on the sequence: help REILIKEGAPSLLCKYFLQQ W ELTSPGHDTSVLPDSVEIGL 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                         REILIKEGAPSLLCK----YF-LQQWELTS----------------PGHDTSVLPDSVEIGL

Mouse                         REILIKEGAPSLLCK----YF-LQQWELTS-----------

Rat                           REILIKEGAPSLLCK----YF-LQQWELTS-----------

Bovine                        REILIKEGAPSLLCK----YF-LQQWELTS-----------

Chicken                       RDILISEGAPALLCD----YF-LHQWGVLT-----------

Xenopus laevis                RKVLISEGVPALLCD----YF-QLQWDVLF-----------

Drosophila                    RRVLFTHKQDEVLLESLEFYFSIAHWKRPPIPRAERLKRMN
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 2 – 729 Neurochondrin



Literature citations
Monoallelic and bi-allelic variants in NCDN cause neurodevelopmental delay, intellectual disability, and epilepsy.
Fatima A.; Hoeber J.; Schuster J.; Koshimizu E.; Maya-Gonzalez C.; Keren B.; Mignot C.; Akram T.; Ali Z.; Miyatake S.; Tanigawa J.; Koike T.; Kato M.; Murakami Y.; Abdullah U.; Ali M.A.; Fadoul R.; Laan L.; Castillejo-Lopez C.; Liik M.; Jin Z.; Birnir B.; Matsumoto N.; Baig S.M.; Klar J.; Dahl N.;
Am. J. Hum. Genet. 108:739-748(2021)
Cited for: INVOLVEMENT IN NEDIES; FUNCTION; VARIANTS NEDIES GLN-433; GLN-478; ARG-498 AND LEU-652; CHARACTERIZATION OF VARIANTS NEDIES GLN-433; GLU-478; ARG-498 AND LEU-652;
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.