Sequence Ontology

A shared vocabulary for biological sequence features and annotations

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missense_variant

SO:0001583

Definition: A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved.

Comments and references

EBI term: Non-synonymous SNPs. SNPs that are located in the coding sequence and result in an amino acid change in the encoded peptide sequence. A change that causes a non_synonymous_codon can be more than 3 bases - for example 4 base substitution.

Definition references: EBI:fc, EBI:gr, SO:ke

Synonyms

ScopeValue
exactJannovar:missense_variant
exactSeattleseq:missense
exactVAAST:missense_variant
exactVAT:nonsynonymous
exactVEP:missense_variant
exactmissense
exactmissense codon
exactsnpEff:NON_SYNONYMOUS_CODING
relatedANNOVAR:nonsynonymous SNV
relatedSeattleseq:missense-near-splice
relatedVAAST:non_synonymous_codon

Identifiers and subsets

Accession: SO:0001583

Persistent URL: http://purl.obolibrary.org/obo/SO_0001583

Alternate IDs: SO:0001584, SO:0001783

Subsets: None

Cross references: http://en.wikipedia.org/wiki/Missense_mutation, http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp, http://snpeff.sourceforge.net/SnpEff_manual.html, http://vat.gersteinlab.org/formats.php, http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences, loinc:LA6698-0

History summary

Term history is reconstructed from the Git-era ontology files by comparing ontology classes across revisions. Earlier SVN-era changes will be added at a future date.

First seen in Git-era editable history: 2016-12-05 in commit 92e3cae

Most recent Git-era change: 2022-04-25 in commit 476626e

Number of changes: 2

Ontology neighborhood diagram

Ontology neighborhood for SO:0001583 Ontology neighborhood graph for SO:0001583 missense_variant. Parent, child, and related nodes can be activated to open their term pages. SO:0001992 nonsynonymous_variant SO:0001992 nonsynonymous_variant SO:0001583 missense_variant SO:0001583 missense_variant SO:0001585 conservative_missense_variant SO:0001585 conservative_missense_variant SO:0001586 non_conservative_missense_variant SO:0001586 non_conservative_missense_variant
The local DAG shows nearby parent, child, and related terms. Each node links to its own term page.

Relationships

Parents

Children

Change history

This timeline summarizes changes identified in SO’s GitHub commit history, including updates to labels, definitions, parent terms, synonyms, subsets, and obsoletion status. It is a best-effort reconstruction and may not include every change to a term. Since only history from GitHub is included at the moment, any term added before the migration from SVN to Git will show as being created in 2016. This will be addressed once SVN history is incorporated.

DateChangeSummaryEvidence
2022-04-25xref removedCross reference removed: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html476626e
2016-12-05createdTerm introduced into the editable ontology history
Initial label: missense_variant
Initial definition captured.
Initial parent: SO:0001992
92e3cae