UniProtKB/SwissProt variant VAR

Variant information

Variant position:

47

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 Aspartate (D) to Tyrosine (Y) at position 47 (D47Y, p.Asp47Tyr).

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 medium size and acidic (D) to large size and aromatic (Y)

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 SEDT; loss-of-function mutation.

Any additional useful information about the variant.

Sequence information

Variant position:

47

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

Protein sequence length:

140

The length of the canonical sequence.

Location on the sequence:

KAESKDDHRHLNQFIAHAAL D LVDENMWLSNNMYLKTVDKF

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.

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 – 140	Trafficking protein particle complex subunit 2

Literature citations

Human wild-type SEDL protein functionally complements yeast Trs20p but some naturally occurring SEDL mutants do not.
Gecz J.; Shaw M.A.; Bellon J.R.; de Barros Lopes M.;
Gene 320:137-144(2003)
Cited for: CHARACTERIZATION OF VARIANT SEDL TYR-47;

SEDLIN forms homodimers: characterisation of SEDLIN mutations and their interactions with transcription factors MBP1, PITX1 and SF1.
Jeyabalan J.; Nesbit M.A.; Galvanovskis J.; Callaghan R.; Rorsman P.; Thakker R.V.;
PLoS ONE 5:E10646-E10646(2010)
Cited for: SELF-ASSOCIATION; INTERACTION WITH ENO1; PITX1 AND SF1; SUBCELLULAR LOCATION; CHARACTERIZATION OF VARIANTS SEDL TYR-47; LEU-73; SER-83 AND ASP-130;

The molecular basis of X-linked spondyloepiphyseal dysplasia tarda.
Gedeon A.K.; Tiller G.E.; Le Merrer M.; Heuertz S.; Tranebjaerg L.; Chitayat D.; Robertson S.; Glass I.A.; Savarirayan R.; Cole W.G.; Rimoin D.L.; Kousseff B.G.; Ohashi H.; Zabel B.; Munnich A.; Gecz J.; Mulley J.C.;
Am. J. Hum. Genet. 68:1386-1397(2001)
Cited for: VARIANTS SEDT TYR-47; LEU-73 AND ASP-130;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P0DI81: Variant p.Asp47Tyr