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UniProtKB/Swiss-Prot Q9BT09: Variant p.Gly125Arg

Protein canopy homolog 3
Gene: CNPY3
Variant information

Variant position:  125
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  Unclassified
The variants are classified into three categories: Disease, Polymorphism and Unclassified.
  • Disease: Variants implicated in disease according to literature reports.
  • Polymorphism: Variants not reported to be implicated in disease.
  • Unclassified: Variants with uncertain implication in disease according to literature reports. Evidence against or in favor of a pathogenic role is limited and/or conflicting.

Residue change:  From Glycine (G) to Arginine (R) at position 125 (G125R, p.Gly125Arg).
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 glycine (G) to large size and basic (R)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  -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

Involvement in disease:  Epileptic encephalopathy, early infantile, 60 (EIEE60) [MIM:617929]: A form of epileptic encephalopathy, a heterogeneous group of severe childhood onset epilepsies characterized by refractory seizures, neurodevelopmental impairment, and poor prognosis. Development is normal prior to seizure onset, after which cognitive and motor delays become apparent. EIEE60 is an autosomal recessive condition characterized by onset of seizures in the first months of life. {ECO:0000269|PubMed:29394991}. Note=The disease is caused by mutations affecting the gene represented in this entry.
The name and a short description of the disease associated with the variant. For more information about the disease, the user can refer to OMIM, following the link provided after the disease acronym.

Variant description:  In EIEE60; unknown pathological significance.
Any additional useful information about the variant.

Other resources:  
Links to websites of interest for the variant.



Sequence information

Variant position:  125
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  278
The length of the canonical sequence.

Location on the sequence:   KRLLDYSLHKERTGSNRFAK  G MSETFETLHNLVHKGVKVVM
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                         KRLLDYSLHKERTGSNRFAKGMSETFETLHNLVHKGVKVVM

Mouse                         KRLLDYSLHKERTGSNRFAKGMSETFETLHNLVHKGVKVVM

Pig                           KRLLDYSLHKERTGSNRFAKGMSETFETLHNLVHKGVKVVM

Bovine                        KRLLDYSLHKERTGSNRFAKGMSETFETLHNLVHKGVKVVM

Xenopus laevis                SRLLEYNLHKERTGSNRFAKGMSETFQTLHHLVHKGVKVVM

Xenopus tropicalis            SRLLEYNLHKERSGSNRFAKGMSETFQTLHHLVHKGVKVVM

Zebrafish                     SRIMQYNLHKERDGSNRFAKGMSETFSTLHNLVNKGVKVVM

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 31 – 278 Protein canopy homolog 3
Domain 47 – 271 Saposin B-type
Disulfide bond 49 – 206
Disulfide bond 52 – 194
Disulfide bond 104 – 166
Alternative sequence 55 – 278 Missing. In isoform 2.


Literature citations

Biallelic Variants in CNPY3, Encoding an Endoplasmic Reticulum Chaperone, Cause Early-Onset Epileptic Encephalopathy.
Mutoh H.; Kato M.; Akita T.; Shibata T.; Wakamoto H.; Ikeda H.; Kitaura H.; Aoto K.; Nakashima M.; Wang T.; Ohba C.; Miyatake S.; Miyake N.; Kakita A.; Miyake K.; Fukuda A.; Matsumoto N.; Saitsu H.;
Am. J. Hum. Genet. 102:321-329(2018)
Cited for: INVOLVEMENT IN EIEE60; VARIANT EIEE60 ARG-125;

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.