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UniProtKB/Swiss-Prot Q13428: Variant p.Ala1390Val

Treacle protein
Gene: TCOF1
Variant information

Variant position:  1390
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  LB/B
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 Alanine (A) to Valine (V) at position 1390 (A1390V, p.Ala1390Val).
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 hydrophobic (A) to medium size and hydrophobic (V)
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

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



Sequence information

Variant position:  1390
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  1488
The length of the canonical sequence.

Location on the sequence:   GEGGEASVSPEKTSTTSKGK  A KRDKASGDVKEKKGKGSLGS
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                         GEGGEASVSPEKTSTTSKGKAKRDKASGDVKEKKGKGSLGS

Mouse                         PRA--SAVSPEKAPMTSKAKSKLDKGSAG---GKGKGSPGP

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 – 1488 Treacle protein
Region 1322 – 1488 Disordered
Compositional bias 1385 – 1425 Basic and acidic residues
Modified residue 1376 – 1376 Phosphoserine
Modified residue 1378 – 1378 Phosphoserine
Modified residue 1407 – 1407 Phosphoserine
Modified residue 1410 – 1410 Phosphoserine
Alternative sequence 959 – 1488 Missing. In isoform 5.


Literature citations

The mutational spectrum in Treacher Collins syndrome reveals a predominance of mutations that create a premature-termination codon.
Edwards S.J.; Gladwin A.J.; Dixon M.J.;
Am. J. Hum. Genet. 60:515-524(1997)
Cited for: VARIANTS LEU-516; ALA-887; VAL-1390 AND GLY-1432; VARIANT TCS1 ARG-53;

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.