UniProtKB/SwissProt variant VAR

Variant information

Variant position:

38

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 Aspartate (D) to Glutamate (E) at position 38 (D38E, p.Asp38Glu).

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 acidic.

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

BLOSUM score:

2

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.

Variant rs3748043 [ dbSNP | Ensembl ]

Sequence information

Variant position:

38

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

Protein sequence length:

2624

The length of the canonical sequence.

Location on the sequence:

GARGSTASNPQRGRESPRPP D PATDSASKPAEPTDVPTVDF

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                         GARGSTASNPQRGRESPRPPDPATDSASKPAEPTDVPTVDF

Mouse                         GTRGSAAPNPQRGPEAPRPPEPATESAPKPAEPTDVPAVDS

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 – 2624	Transcription factor TFIIIB component B'' homolog
Region	1 – 299	Interaction with ZBTB43
Alternative sequence	1 – 1863	Missing. In isoform 8.
Alternative sequence	1 – 610	Missing. In isoform 5.
Alternative sequence	24 – 43	Missing. In isoform 6.

Literature citations

Different human TFIIIB activities direct RNA polymerase III transcription from TATA-containing and TATA-less promoters.
Schramm L.; Pendergrast P.S.; Sun Y.; Hernandez N.;
Genes Dev. 14:2650-2663(2000)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 3 AND 4); FUNCTION; VARIANTS GLU-38 AND MET-1347;

The transcription factor-like nuclear regulator (TFNR) contains a novel 55-amino-acid motif repeated nine times and maps closely to SMN1.
Kelter A.R.; Herchenbach J.; Wirth B.;
Genomics 70:315-326(2000)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2); NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-2187 (ISOFORM 1); NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 2189-2624 (ISOFORM 2); SUBCELLULAR LOCATION; TISSUE SPECIFICITY; VARIANTS GLU-38; MET-1347 AND LEU-2013;

Prediction of the coding sequences of unidentified human genes. XIX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro.
Nagase T.; Kikuno R.; Hattori A.; Kondo Y.; Okumura K.; Ohara O.;
DNA Res. 7:347-355(2000)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1); VARIANTS GLU-38; CYS-757; ILE-1244; MET-1264; MET-1347 AND GLU-1469;

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)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1); VARIANTS GLU-38; CYS-757; ILE-1244; MET-1264; MET-1347 AND GLU-1469;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot A6H8Y1: Variant p.Asp38Glu