UniProtKB/SwissProt variant VAR

Variant information

Variant position:

144

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 Serine (S) to Cysteine (C) at position 144 (S144C, p.Ser144Cys).

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 polar (S) to medium size and polar (C)

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.

Variant rs766737607 [ dbSNP | Ensembl ]

Sequence information

Variant position:

144

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

Protein sequence length:

3661

The length of the canonical sequence.

Location on the sequence:

GSRALATKDMRKSQERSMSY S DESRLSNLLRRITREDDRDR

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                         GSRALATKDMRKSQERSMSYSDESRLSNLLRRITREDDRDR

Mouse                         GSRALATKDMRKSQERSMSYSDESRLSNLLRRITREDDRDR

Zebrafish                     GNRALATKDMRKSQDRPLAHSEESRLANLLRRASREDDRER

Caenorhabditis elegans        LA------------------GKVIRLVGVL-----------

Drosophila                    HRKAYQCKGDTIN---PMANGEDLRLSKIIRRLINENNPTV

Slime mold                    TATATAITPTPIT----TSQSTSSSMLNLPLKVGKE-----

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 – 3661	Serine/threonine-protein kinase SMG1
Region	1 – 1977	Interaction with SMG8 and SMG9
Region	116 – 144	Disordered
Alternative sequence	1 – 1269	Missing. In isoform 4.
Alternative sequence	1 – 630	Missing. In isoform 3.
Beta strand	143 – 148

Literature citations

The mRNA surveillance protein hSMG-1 functions in genotoxic stress response pathways in mammalian cells.
Brumbaugh K.M.; Otterness D.M.; Geisen C.; Oliveira V.; Brognard J.; Li X.; Lejeune F.; Tibbetts R.S.; Maquat L.E.; Abraham R.T.;
Mol. Cell 14:585-598(2004)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2); FUNCTION; PHOSPHORYLATION OF TP53; TISSUE SPECIFICITY; SUBCELLULAR LOCATION; ACTIVITY REGULATION; MUTAGENESIS OF ASP-2335; VARIANTS CYS-144 AND LYS-612;

Patterns of somatic mutation in human cancer genomes.
Greenman C.; Stephens P.; Smith R.; Dalgliesh G.L.; Hunter C.; Bignell G.; Davies H.; Teague J.; Butler A.; Stevens C.; Edkins S.; O'Meara S.; Vastrik I.; Schmidt E.E.; Avis T.; Barthorpe S.; Bhamra G.; Buck G.; Choudhury B.; Clements J.; Cole J.; Dicks E.; Forbes S.; Gray K.; Halliday K.; Harrison R.; Hills K.; Hinton J.; Jenkinson A.; Jones D.; Menzies A.; Mironenko T.; Perry J.; Raine K.; Richardson D.; Shepherd R.; Small A.; Tofts C.; Varian J.; Webb T.; West S.; Widaa S.; Yates A.; Cahill D.P.; Louis D.N.; Goldstraw P.; Nicholson A.G.; Brasseur F.; Looijenga L.; Weber B.L.; Chiew Y.-E.; DeFazio A.; Greaves M.F.; Green A.R.; Campbell P.; Birney E.; Easton D.F.; Chenevix-Trench G.; Tan M.-H.; Khoo S.K.; Teh B.T.; Yuen S.T.; Leung S.Y.; Wooster R.; Futreal P.A.; Stratton M.R.;
Nature 446:153-158(2007)
Cited for: VARIANTS [LARGE SCALE ANALYSIS] THR-35; CYS-126; CYS-144; TYR-151; ASN-160; VAL-167; GLY-320; SER-465; ARG-546; SER-588; LYS-612; CYS-753; CYS-809; CYS-812; ILE-829; ASP-832; GLY-952; SER-969; LEU-1016; GLN-1029; SER-1072; HIS-1103; ARG-1275; PRO-1292; VAL-1332; PRO-1358; THR-1418; CYS-2171; SER-2258; LYS-2345; GLU-2730; SER-2889; ALA-2899; THR-3239 AND GLN-3583;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q96Q15: Variant p.Ser144Cys