UniProtKB/Swiss-Prot P00973: Variant p.Gly162Ser

• Variant information
• Sequence information
• Literature citations
• All

Variant information

Variant position: 162 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 Glycine (G) to Serine (S) at position 162 (G162S, p.Gly162Ser). 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 glycine (G) to small size and polar (S) 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
Polymorphism: Polymorphism dbSNP:rs10774671 is associated with protection against severe COVID-19 disease (PubMed:34581622, PubMed:33633408). In humans, the OAS1 protein is expressed as two major forms designated p46 and p42. The longer p46 isoform is generated by alternative splicing to an exon downstream of the terminal exon used by the p42 isoform. Although all human genotypes contain the exon that completes the transcript encoding p46, an intronic SNP (rs10774671) determines OAS1 exon usage. Alleles with a G at this SNP (G alleles) specify expression of the p46 isoform and some p42, whereas alleles with A at this position predominantly encode the p42 isoform and cannot express the p46 isoform (PubMed:34581622). The p42 isoform, which is the most common isoform in humans (~61% of alleles), has no detectable anti-SARS-CoV-2 activity. The p46 isoform has anti-SARS-CoV-2 activity (PubMed:34581622). Additional information on the polymorphism described.
Other resources: Links to websites of interest for the variant.

• Variant rs1131454 [ dbSNP | Ensembl ]

Sequence information

Variant position: 162 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: 400 The length of the canonical sequence.
Location on the sequence: GEGVEFDVLPAFDALGQLTG G YKPNPQIYVKLIEECTDLQK 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 – 400	2'-5'-oligoadenylate synthase 1
Binding site	148 – 148
Site	158 – 158	Interaction with dsRNA
Mutagenesis	148 – 148	D -> A. Strongly reduced enzyme activity.
Beta strand	161 – 163

Literature citations

Structure of two forms of the interferon-induced (2'-5') oligo A synthetase of human cells based on cDNAs and gene sequences.
Benech P.; Mory Y.; Revel M.; Chebath J.;
EMBO J. 4:2249-2256(1985)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORMS P42 AND P46); VARIANTS ASP-31; SER-162; THR-352 AND THR-361; Full-length sequence and expression of the 42 kDa 2-5A synthetase induced by human interferon.
Wathelet M.G.; Moutschen S.; Cravador A.; Dewit L.; Defilippi P.; Huez G.A.; Content J.;
FEBS Lett. 196:113-120(1986)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM P42); CATALYTIC ACTIVITY; SUBCELLULAR LOCATION; VARIANT SER-162; Structure and expression of a cloned cDNA for human (2'-5')oligoadenylate synthetase.
Shiojiri S.; Fukunaga R.; Ichii Y.; Sokawa Y.;
J. Biochem. 99:1455-1464(1986)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM P42); CATALYTIC ACTIVITY; SUBCELLULAR LOCATION; VARIANT SER-162; Cloning, sequencing, and expression of two murine 2'-5'-oligoadenylate synthetases. Structure-function relationships.
Ghosh S.K.; Kusari J.; Bandyopadhyay S.K.; Samanta H.; Kumar R.; Sen G.C.;
J. Biol. Chem. 266:15293-15299(1991)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORMS P48 AND P42); VARIANT SER-162; The mammalian 2'-5' oligoadenylate synthetase gene family: evidence for concerted evolution of paralogous Oas1 genes in Rodentia and Artiodactyla.
Perelygin A.A.; Zharkikh A.A.; Scherbik S.V.; Brinton M.A.;
J. Mol. Evol. 63:562-576(2006)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM P48); VARIANTS SER-162; THR-352 AND THR-361; Complete sequencing and characterization of 21,243 full-length human cDNAs.
Ota T.; Suzuki Y.; Nishikawa T.; Otsuki T.; Sugiyama T.; Irie R.; Wakamatsu A.; Hayashi K.; Sato H.; Nagai K.; Kimura K.; Makita H.; Sekine M.; Obayashi M.; Nishi T.; Shibahara T.; Tanaka T.; Ishii S.; Yamamoto J.; Saito K.; Kawai Y.; Isono Y.; Nakamura Y.; Nagahari K.; Murakami K.; Yasuda T.; Iwayanagi T.; Wagatsuma M.; Shiratori A.; Sudo H.; Hosoiri T.; Kaku Y.; Kodaira H.; Kondo H.; Sugawara M.; Takahashi M.; Kanda K.; Yokoi T.; Furuya T.; Kikkawa E.; Omura Y.; Abe K.; Kamihara K.; Katsuta N.; Sato K.; Tanikawa M.; Yamazaki M.; Ninomiya K.; Ishibashi T.; Yamashita H.; Murakawa K.; Fujimori K.; Tanai H.; Kimata M.; Watanabe M.; Hiraoka S.; Chiba Y.; Ishida S.; Ono Y.; Takiguchi S.; Watanabe S.; Yosida M.; Hotuta T.; Kusano J.; Kanehori K.; Takahashi-Fujii A.; Hara H.; Tanase T.-O.; Nomura Y.; Togiya S.; Komai F.; Hara R.; Takeuchi K.; Arita M.; Imose N.; Musashino K.; Yuuki H.; Oshima A.; Sasaki N.; Aotsuka S.; Yoshikawa Y.; Matsunawa H.; Ichihara T.; Shiohata N.; Sano S.; Moriya S.; Momiyama H.; Satoh N.; Takami S.; Terashima Y.; Suzuki O.; Nakagawa S.; Senoh A.; Mizoguchi H.; Goto Y.; Shimizu F.; Wakebe H.; Hishigaki H.; Watanabe T.; Sugiyama A.; Takemoto M.; Kawakami B.; Yamazaki M.; Watanabe K.; Kumagai A.; Itakura S.; Fukuzumi Y.; Fujimori Y.; Komiyama M.; Tashiro H.; Tanigami A.; Fujiwara T.; Ono T.; Yamada K.; Fujii Y.; Ozaki K.; Hirao M.; Ohmori Y.; Kawabata A.; Hikiji T.; Kobatake N.; Inagaki H.; Ikema Y.; Okamoto S.; Okitani R.; Kawakami T.; Noguchi S.; Itoh T.; Shigeta K.; Senba T.; Matsumura K.; Nakajima Y.; Mizuno T.; Morinaga M.; Sasaki M.; Togashi T.; Oyama M.; Hata H.; Watanabe M.; Komatsu T.; Mizushima-Sugano J.; Satoh T.; Shirai Y.; Takahashi Y.; Nakagawa K.; Okumura K.; Nagase T.; Nomura N.; Kikuchi H.; Masuho Y.; Yamashita R.; Nakai K.; Yada T.; Nakamura Y.; Ohara O.; Isogai T.; Sugano S.;
Nat. Genet. 36:40-45(2004)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM P42); VARIANT SER-162; Cloning of human full-length CDSs in BD Creator(TM) system donor vector.
Kalnine N.; Chen X.; Rolfs A.; Halleck A.; Hines L.; Eisenstein S.; Koundinya M.; Raphael J.; Moreira D.; Kelley T.; LaBaer J.; Lin Y.; Phelan M.; Farmer A.;
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM P42); VARIANT SER-162; Submission
Suzuki Y.; Sugano S.; Totoki Y.; Toyoda A.; Takeda T.; Sakaki Y.; Tanaka A.; Yokoyama S.;
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM P42); VARIANT SER-162; 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 P42); VARIANT SER-162;