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UniProtKB/Swiss-Prot Q53T94: Variant p.Ala6Ser

TATA box-binding protein-associated factor RNA polymerase I subunit B
Gene: TAF1B
Variant information

Variant position:  6
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 Serine (S) at position 6 (A6S, p.Ala6Ser).
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 small size and polar (S)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  1
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:  6
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  588
The length of the canonical sequence.

Location on the sequence:   MDLEE  A EEFKERCTQCAAVSWGLTDE
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                         MDL--EEAEEFKERCTQCAAVSWGLTDE

Mouse                         MDV--EEVKAFRDRCSQCAAVSWGLT

Rat                           MDV--EQMKAFTDRCSQCAAVSWGLT

Bovine                        MDL--EEAREFRERCSQCAAVSWGLT

Chicken                       MDE--EDAGDFNERCAQCSEVNWGLT

Xenopus laevis                MEA--EDGRGYNVPCPQCSEINWAIS

Xenopus tropicalis            MEE--EDARGYNKPCPQCSEVNWAIS

Zebrafish                     MDE--QITGGYSEPCGQCAAVDWGVS

Caenorhabditis elegans        MHS------AKNEKCNACGGYRFSVN

Drosophila                    MEEVLETMQLENMHCDVCEGTTFQER

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.

Chain 1 – 588 TATA box-binding protein-associated factor RNA polymerase I subunit B
Zinc finger 4 – 39 RRN7-type
Metal binding 13 – 13 Zinc
Metal binding 16 – 16 Zinc
Modified residue 1 – 1 N-acetylmethionine
Alternative sequence 1 – 255 Missing. In isoform 3.
Mutagenesis 13 – 13 C -> A. Abolishes Pol I transcription but not recruitment of SL1/TIF-IB complex to rDNA promoters.

Literature citations

Reconstitution of transcription factor SL1: exclusive binding of TBP by SL1 or TFIID subunits.
Comai L.; Zomerdijk J.C.B.M.; Beckmann H.; Zhou S.; Admon A.; Tjian R.;
Science 266:1966-1972(1994)
Cited for: NUCLEOTIDE SEQUENCE [MRNA]; PROTEIN SEQUENCE OF 11-20; 42-56; 93-110; 123-135; 264-276; 281-289; 311-321; 331-340; 396-407; 429-444; 448-466 AND 471-480; FUNCTION; INTERACTION WITH TBP; TAF1A AND TAF1C; VARIANTS SER-6; ILE-282; ALA-351 AND ASP-462;

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
The MGC Project Team;
Genome Res. 14:2121-2127(2004)

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.