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:

US

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 Arginine (R) to Tryptophan (W) at position 89 (R89W, p.Arg89Trp).

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 large size and basic (R) to large size and aromatic (W)

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:

Found in two consanguineous families with intellectual disability; unknown pathological significance.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs201402934 [ dbSNP | Ensembl ]

Sequence information

Variant position:

89

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

Protein sequence length:

652

The length of the canonical sequence.

Location on the sequence:

RFRPFTFSQSTPIGLDRVGR R RQMRASNVSSDGGTEPSALV

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                         RFRPFTFSQSTPIGLDRVGRRRQMRASNVSSDGGTEPSALV

Mouse                         RLRPFTFSQSTPIGLDRVGRRRQMKTSNVSSDGGAESSALV

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	1 – 652	Spermatogenesis-associated protein 13
Region	81 – 108	Disordered
Modified residue	78 – 78	Phosphoserine
Alternative sequence	1 – 96	MTSASPEDQNAPVGCPKGARRRRPISVIGGVSLYGTNQTEELDNLLTQPASRPPMPAHQVPPYKAVSARFRPFTFSQSTPIGLDRVGRRRQMRASN -> MVARGEIARFWSLESLHL. In isoform 2.
Alternative sequence	1 – 96	MTSASPEDQNAPVGCPKGARRRRPISVIGGVSLYGTNQTEELDNLLTQPASRPPMPAHQVPPYKAVSARFRPFTFSQSTPIGLDRVGRRRQMRASN -> MGFIIHIQQVKKQRKKLDQGLILKKEKYRKEKKCASLSFE. In isoform 3.

Literature citations

Mapping autosomal recessive intellectual disability: combined microarray and exome sequencing identifies 26 novel candidate genes in 192 consanguineous families.
Harripaul R.; Vasli N.; Mikhailov A.; Rafiq M.A.; Mittal K.; Windpassinger C.; Sheikh T.I.; Noor A.; Mahmood H.; Downey S.; Johnson M.; Vleuten K.; Bell L.; Ilyas M.; Khan F.S.; Khan V.; Moradi M.; Ayaz M.; Naeem F.; Heidari A.; Ahmed I.; Ghadami S.; Agha Z.; Zeinali S.; Qamar R.; Mozhdehipanah H.; John P.; Mir A.; Ansar M.; French L.; Ayub M.; Vincent J.B.;
Mol. Psychiatry 23:973-984(2018)
Cited for: VARIANT TRP-89;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q96N96: Variant p.Arg89Trp