Sequence Ontology

A shared vocabulary for biological sequence features and annotations

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NMD_triggering_variant

SO:0002319

Definition: A sequence variant that leads to a change in the location of a termination codon in a transcript that leads to nonsense-mediated decay (NMD). The change in location of a termination codon can be caused by several different types of sequence variants, including stop_gained (SO:0001587), frameshift_variant (SO:0001589), splice_donor_variant (SO:0001575), and splice_acceptor_variant (SO:0001574) types of variants.

Comments and references

Added as per request from Ang Roberts as part of GenCC November 2020.

Definition references: GenCC:AR

Synonyms

ScopeValue
exactNMD triggering variant
exactnonsense-mediated decay triggering variant

Identifiers and subsets

Accession: SO:0002319

Persistent URL: http://purl.obolibrary.org/obo/SO_0002319

Alternate IDs: None

Subsets: None

Cross references: None

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: 2020-12-30 in commit 5e13381

Most recent Git-era change: 2020-12-30 in commit 5e13381

Number of changes: 1

Ontology neighborhood diagram

Ontology neighborhood for SO:0002319 Ontology neighborhood graph for SO:0002319 NMD_triggering_variant. Parent, child, and related nodes can be activated to open their term pages. SO:0002218 functionally_abnormal SO:0002218 functionally_abnormal SO:0002319 NMD_triggering_variant SO:0002319 NMD_triggering_variant SO:0002327 splice_acceptor_variant_NMD_triggering SO:0002327 splice_acceptor_variant_NMD_triggering SO:0002325 splice_donor_variant_NMD_triggering SO:0002325 splice_donor_variant_NMD_triggering SO:0002323 frameshift_variant_NMD_triggering SO:0002323 frameshift_variant_NMD_triggering SO:0002321 stop_gained_NMD_triggering SO:0002321 stop_gained_NMD_triggering
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
2020-12-30createdTerm introduced into the editable ontology history
Initial label: NMD_triggering_variant
Initial definition captured.
Initial parent: SO:0002218
5e13381
#521