Sequence Ontology

A shared vocabulary for biological sequence features and annotations

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coding_sequence_variant

SO:0001580

Definition: A sequence variant that changes the coding sequence.

Comments and references

Definition references: SO:ke

Synonyms

ScopeValue
exactJannovar:coding_sequence_variant
exactSeattleseq:coding
exactVAAST:coding_sequence_variant
exactVEP:coding_sequence_variant
exactcoding sequence variant
exactcoding variant
exactcodon variant
exactcodon_variant
exactsnpEff:CDS
relatedsnpEff:CODON_CHANGE

Identifiers and subsets

Accession: SO:0001580

Persistent URL: http://purl.obolibrary.org/obo/SO_0001580

Alternate IDs: SO:0001581

Subsets: None

Cross references: http://snp.gs.washington.edu/SeattleSeqAnnotation137/HelpHowToUse.jsp, http://snpeff.sourceforge.net/SnpEff_manual.html, http:www.ensembl.org/info/genome/variation/predicted_data.html#consequences

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:0001580 Ontology neighborhood graph for SO:0001580 coding_sequence_variant. Parent, child, and related nodes can be activated to open their term pages. SO:0001968 coding_transcript_variant SO:0001968 coding_transcript_variant SO:0001791 exon_variant SO:0001791 exon_variant SO:0001580 coding_sequence_variant SO:0001580 coding_sequence_variant SO:0001818 protein_altering_variant SO:0001818 protein_altering_variant SO:0001819 synonymous_variant SO:0001819 synonymous_variant SO:0001590 terminator_codon_variant SO:0001590 terminator_codon_variant SO:0001582 initiator_codon_variant SO:0001582 initiator_codon_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: coding_sequence_variant
Initial definition captured.
Initial parents: SO:0001791, SO:0001968
92e3cae