UniProtKB/SwissProt variant VAR

Variant information

Variant position:

89

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

Type of variant:

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:

From Proline (P) to Leucine (L) at position 89 (P89L, p.Pro89Leu).

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:

Similar physico-chemical property. Both residues are medium size and hydrophobic.

The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:

-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:

In AUTS20; risk factor for disease development; decreased function in dendritic spine formation; decreased protein abundance; does not localize to the plasma membrane but is retained in the endoplasmic reticulum.

Any additional useful information about the variant.

Sequence information

Variant position:

89

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

Protein sequence length:

863

The length of the canonical sequence.

Location on the sequence:

LNNEILGPVIQFLGVPYAAP P TGERRFQPPEPPSPWSDIRN

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                         LNNEILGPVIQFLGVPYAAPPTGERRFQPPEPPSPWSDI-RN

Mouse                         LNNEILGPVIQFLGVPYAAPPTGEHRFQPPEPPSPWSDI-R

Rat                           LNNEILGPVIQFLGVPYAAPPTGEHRFQPPEPPSPWSDI-R

Caenorhabditis elegans        PEGDDLPPVAQYLGIPYGVAPTGQYRFNMAISAAKWTHMPK

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.

Type	Positions	Description
Chain	46 – 863	Neuroligin-1
Topological domain	46 – 717	Extracellular
Glycosylation	109 – 109	N-linked (GlcNAc...) (complex) asparagine

Literature citations

Functional significance of rare neuroligin 1 variants found in autism.
Nakanishi M.; Nomura J.; Ji X.; Tamada K.; Arai T.; Takahashi E.; Bucan M.; Takumi T.;
PLoS Genet. 13:e1006940-e1006940(2017)
Cited for: FUNCTION; SUBCELLULAR LOCATION; TISSUE SPECIFICITY; VARIANTS AUTS20 LEU-89; ILE-90; PRO-309; GLU-337 AND TYR-835; VARIANT HIS-756; CHARACTERIZATION OF VARIANTS AUTS20 LEU-89; ILE-90; PRO-309; GLU-337 AND TYR-835; CHARACTERIZATION OF VARIANT HIS-756;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q8N2Q7: Variant p.Pro89Leu