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UniProtKB/Swiss-Prot O00623: Variant p.Ser320Phe

Peroxisome assembly protein 12
Gene: PEX12
Variant information

Variant position:  320
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 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 Serine (S) to Phenylalanine (F) at position 320 (S320F, p.Ser320Phe).
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 small size and polar (S) to large size and aromatic (F)
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:  Peroxisome biogenesis disorder 3B (PBD3B) [MIM:266510]: A peroxisome biogenesis disorder that includes neonatal adrenoleukodystrophy (NALD) and infantile Refsum disease (IRD), two milder manifestations of the Zellweger disease spectrum. The clinical course of patients with the NALD and IRD presentation is variable and may include developmental delay, hypotonia, liver dysfunction, sensorineural hearing loss, retinal dystrophy and vision impairment. Children with the NALD presentation may reach their teens, while patients with the IRD presentation may reach adulthood. The clinical conditions are often slowly progressive in particular with respect to loss of hearing and vision. The biochemical abnormalities include accumulation of phytanic acid, very long chain fatty acids (VLCFA), di- and trihydroxycholestanoic acid and pipecolic acid. {ECO:0000269|PubMed:10562279, ECO:0000269|PubMed:19105186}. 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 PBD3B; attenuates interaction with PEX10 and decreases peroxisomal protein import.
Any additional useful information about the variant.

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



Sequence information

Variant position:  320
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  359
The length of the canonical sequence.

Location on the sequence:   MKTVCPLCRKTRVNDTVLAT  S GYVFCYRCVFHYVRSHQACP
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                         MKTVCPLCRKTRVNDTVLATSGYVFCYRCVFHYVRSHQA-CP

Mouse                         MKTVCPLCRKTRVNDTVLATSGYVFCYRCVFNYVRSHQA-C

Rat                           MKTVCPLCRKARVNDTVLATSGYVFCYRCVFNYVRSHQA-C

Bovine                        MKTVCPLCRKNRVNDTVLATSGYVFCYRCVFHYVRSHQA-C

Caenorhabditis elegans        DTNKCPICLKKRVNDTALFVSGYVFCYTCINQYVNTYNK-C

Drosophila                    QRGECPVCLLSIQTPTACSVSGYVFCWKCIVSHMKEHGT-C

Slime mold                    DKRLCPLCLKERTNPTICG-SGFVFCYPCIFGYVNEHSK-C

Baker's yeast                 VSEACPVCEKTVQNPCVLE-TGYVACYPCAISYLVNNEGHC

Fission yeast                 --DICKICGEKIKNPAVLS-TGFVFCYPCIQVWLQRHPFKC

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 – 359 Peroxisome assembly protein 12
Topological domain 261 – 359 Cytoplasmic
Zinc finger 304 – 343 RING-type; degenerate
Mutagenesis 304 – 304 C -> W. Abolishes interaction with PEX19; when associated with Q-307.
Mutagenesis 307 – 307 C -> Q. Abolishes interaction with PEX19; when associated with W-304.


Literature citations

PEX12 interacts with PEX5 and PEX10 and acts downstream of receptor docking in peroxisomal matrix protein import.
Chang C.C.; Warren D.S.; Sacksteder K.A.; Gould S.J.;
J. Cell Biol. 147:761-774(1999)
Cited for: VARIANT PBD3B PHE-320; CHARACTERIZATION OF VARIANT PBD3B PHE-320; INTERACTION WITH PEX5 AND PEX10;

Identification of novel mutations and sequence variation in the Zellweger syndrome spectrum of peroxisome biogenesis disorders.
Yik W.Y.; Steinberg S.J.; Moser A.B.; Moser H.W.; Hacia J.G.;
Hum. Mutat. 30:E467-E480(2009)
Cited for: VARIANTS PBD-CG3 SER-34; GLN-178 DEL AND GLN-349 DEL; VARIANT PBD3B PHE-320; VARIANT ILE-245;

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.