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UniProtKB/Swiss-Prot P43034: Variant p.Gly162Ser

Platelet-activating factor acetylhydrolase IB subunit alpha
Gene: PAFAH1B1
Variant information

Variant position:  162
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 Glycine (G) to Serine (S) at position 162 (G162S, p.Gly162Ser).
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 small size and polar (S)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  0
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:  Lissencephaly 1 (LIS1) [MIM:607432]: A classical lissencephaly. It is characterized by agyria or pachygyria and disorganization of the clear neuronal lamination of normal six-layered cortex. The cortex is abnormally thick and poorly organized with 4 primitive layers. Associated with enlarged and dysmorphic ventricles and often hypoplasia of the corpus callosum. {ECO:0000269|PubMed:11163258, ECO:0000269|PubMed:11502906, ECO:0000269|PubMed:15007136, ECO:0000269|PubMed:15173193, ECO:0000269|PubMed:9063735}. 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 LIS1.
Any additional useful information about the variant.

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



Sequence information

Variant position:  162
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  410
The length of the canonical sequence.

Location on the sequence:   FERTLKGHTDSVQDISFDHS  G KLLASCSADMTIKLWDFQGF
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                         FERTLKGHTDSVQDIS-----FDHSGK----LLASCSADMTIKLWDFQ-GF

Chimpanzee                    FERTLKGHTDSVQDIS-----FDHSGK----LLASCSADMT

Mouse                         FERTLKGHTDSVQDIS-----FDHSGK----LLASCSADMT

Rat                           FERTLKGHTDSVQDIS-----FDHSGK----LLASCSADMT

Pig                           FERTLKGHTDSVQDIS-----FDHSGK----LLASCSADMT

Bovine                        FERTLKGHTDSVEDIS-----FDHSGK----LLASCSADMT

Cat                           FERTLKGHTDSVQDIS-----FDHSGK----LLASCSADMT

Chicken                       FERTLKGHTDSVQDIS-----FDHTGK----LLASCSADMT

Xenopus laevis                FERTLKGHTDSVQDIS-----FDHSGK----LLASCSADMT

Xenopus tropicalis            FERTLKGHTDSVQDIS-----FDHSGK----LLASCSADMT

Caenorhabditis elegans        LERTLKGHTDAVNDIA-----IDAAGK----QLVSCSSDLS

Drosophila                    YERSLKGHTDSVQDVA-----FDAQGK----LLASCSADLS

Slime mold                    FERTLKGHTNAVQDID-----FDKTGN----LLASCSADLT

Baker's yeast                 PLASLQSHTKAITSMDVLFTNYTNSSKKNYLVIVTASKDLQ

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 – 410 Platelet-activating factor acetylhydrolase IB subunit alpha
Repeat 148 – 187 WD 2
Region 83 – 410 Interaction with dynein and dynactin
Alternative sequence 134 – 170 Missing. In isoform 2.


Literature citations

LIS1 missense mutations cause milder lissencephaly phenotypes including a child with normal IQ.
Leventer R.J.; Cardoso C.; Ledbetter D.H.; Dobyns W.B.;
Neurology 57:416-422(2001)
Cited for: VARIANTS LIS1 SER-31; SER-162 AND HIS-317;

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.