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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q9UID3: Variant p.Arg490Cys

Vacuolar protein sorting-associated protein 51 homolog
Gene: VPS51
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Variant information Variant position: help 490 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 Arginine (R) to Cysteine (C) at position 490 (R490C, p.Arg490Cys). 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 basic (R) to medium size and polar (C) 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 PCH13; impaired association with VPS50 and VPS53 subunits; reduced levels of assembled GARP and EARP complexes. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 490 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 782 The length of the canonical sequence.
Location on the sequence: help KEVSFSNKPYFRGEFCSQGV R EGLIVGFVHSMCQTAQSFCD 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                         KEVSFSNKP--YFRGEFCSQGVREGLIVGFVHSMCQTAQSFCD

Mouse                         KEVSFSNKP--YFRGEFCSQGVREGLIVGFIRSMCQTAQSF

Bovine                        KEVSFSNKP--YFRGEFCSQGVRESLIVGFIRSMCQTAQSF

Chicken                       RDVAFASLP--YFKGEFCVEAVREGLVVAFVRWLCRTARGF

Xenopus laevis                KDVAFSNKA--YFKGEFCSQGVREGLIVAFITSVCQTARQF

Xenopus tropicalis            KDVAFSDKP--YFKGEFCSQGVREGLIVAFIKSVCQTARQF

Zebrafish                     KDITFSNKP--YFKGEFCSQGVREGLVVSFIKFICQSSRQY

Caenorhabditis elegans        SDVTFANLPPDEFRQSFSFNA-HERLLVQAFHRFSELADEY

Drosophila                    TDWSFNIKA--EHKGALCVEGIRENLLIGFLRHIAKVMCGF

Slime mold                    TETQFLSS---YQDTIFTKIQVKLQQFFLFLVNIHFLEYLD

Baker's yeast                 -----------------------------------------

Fission yeast                 -----------------------------------------
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 – 782 Vacuolar protein sorting-associated protein 51 homolog



Literature citations
A neurodevelopmental disorder caused by mutations in the VPS51 subunit of the GARP and EARP complexes.
Gershlick D.C.; Ishida M.; Jones J.R.; Bellomo A.; Bonifacino J.S.; Everman D.B.;
Hum. Mol. Genet. 28:1548-1560(2019)
Cited for: VARIANT PCH13 CYS-490; INVOLVEMENT IN PCH13; CHARACTERIZATION OF VARIANT PCH13 CYS-490; INTERACTION WITH VSP50 AND VSP53;
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.