Enum: G2PVariantType
The types of variants associated with the curated gene-disease pair reported in the publication. All terms are Sequence Ontology terms. Where G2P uses a label that differs from the current SO label, the G2P label is recorded as an alias. Descriptions are the SO text definitions where SO provides one.
The NMD-qualified types have two parents in SO, so they are modelled with the base variant as is_a and the NMD qualifier as a mixin. LinkML preserves both, but as of linkml 1.9.5 the OWL generator emits only the is_a parent as rdfs:subClassOf and drops the mixin, so the NMD axis is additionally recorded in the nmd_status annotation to keep it available in every generated artifact. If a later linkml emits permissible-value mixins, that annotation is redundant and can go.
Permissible Values
| Value | Title | Meaning | Description | Nmd Status | Variant Type Group |
|---|---|---|---|---|---|
| NMD_TRIGGERING | NMD_triggering_variant | SO:0002319 | 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. | NMD_VARIANTS | |
| NMD_ESCAPING | NMD_escaping_variant | SO:0002320 | A sequence variant that leads to a change in the location of a termination codon in a transcript but allows the transcript to escape 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. | NMD_VARIANTS | |
| STOP_GAINED_NMD_TRIGGERING | stop_gained_NMD_triggering | SO:0002321 | A stop_gained (SO:0001587) variant that is degraded by nonsense-mediated decay (NMD). | NMD_TRIGGERING | NMD_VARIANTS |
| STOP_GAINED_NMD_ESCAPING | stop_gained_NMD_escaping | SO:0002322 | A stop_gained (SO:0001587) variant that allows the transcript to escape nonsense-mediated decay (NMD). | NMD_ESCAPING | NMD_VARIANTS |
| FRAMESHIFT_VARIANT_NMD_TRIGGERING | frameshift_variant_NMD_triggering | SO:0002323 | A frameshift_variant (SO:0001589) that is degraded by nonsense-mediated decay (NMD). | NMD_TRIGGERING | NMD_VARIANTS |
| FRAMESHIFT_VARIANT_NMD_ESCAPING | frameshift_variant_NMD_escaping | SO:0002324 | A frameshift_variant (SO:0001589) that allows the transcript to escape nonsense-mediated decay (NMD). | NMD_ESCAPING | NMD_VARIANTS |
| SPLICE_DONOR_VARIANT_NMD_TRIGGERING | splice_donor_variant_NMD_triggering | SO:0002325 | A splice_donor_variant (SO:0001575) that is degraded by nonsense-mediated decay (NMD). | NMD_TRIGGERING | NMD_VARIANTS |
| SPLICE_DONOR_VARIANT_NMD_ESCAPING | splice_donor_variant_NMD_escaping | SO:0002326 | A splice_donor_variant (SO:0001575) that allows the transcript to escape nonsense-mediated decay (NMD). | NMD_ESCAPING | NMD_VARIANTS |
| SPLICE_ACCEPTOR_VARIANT_NMD_TRIGGERING | splice_acceptor_variant_NMD_triggering | SO:0002327 | A splice_acceptor_variant (SO:0001574) that is degraded by nonsense-mediated decay (NMD). | NMD_TRIGGERING | NMD_VARIANTS |
| SPLICE_ACCEPTOR_VARIANT_NMD_ESCAPING | splice_acceptor_variant_NMD_escaping | SO:0002328 | A splice_acceptor_variant (SO:0001574) that allows the transcript to escape nonsense-mediated decay (NMD). | NMD_ESCAPING | NMD_VARIANTS |
| SPLICE_REGION_VARIANT | splice_region_variant | SO:0001630 | A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron. | SPLICE_VARIANTS | |
| SPLICE_ACCEPTOR_VARIANT | splice_acceptor_variant | SO:0001574 | A splice variant that changes the 2 base region at the 3' end of an intron. | SPLICE_VARIANTS | |
| SPLICE_DONOR_VARIANT | splice_donor_variant | SO:0001575 | A splice variant that changes the 2 base pair region at the 5' end of an intron. | SPLICE_VARIANTS | |
| FIVE_PRIME_UTR_VARIANT | 5_prime_UTR_variant | SO:0001623 | A UTR variant of the 5' UTR. | REGULATORY_VARIANTS | |
| THREE_PRIME_UTR_VARIANT | 3_prime_UTR_variant | SO:0001624 | A UTR variant of the 3' UTR. | REGULATORY_VARIANTS | |
| REGULATORY_REGION_VARIANT | regulatory_region_variant | SO:0001566 | A sequence variant located within a regulatory region. | REGULATORY_VARIANTS | |
| START_LOST | start_lost | SO:0002012 | A codon variant that changes at least one base of the canonical start codon. | PROTEIN_CHANGING_VARIANTS | |
| STOP_GAINED | stop_gained | SO:0001587 | A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened polypeptide. | PROTEIN_CHANGING_VARIANTS | |
| STOP_LOST | stop_lost | SO:0001578 | A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript. | PROTEIN_CHANGING_VARIANTS | |
| FRAMESHIFT_VARIANT | frameshift_variant | SO:0001589 | A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three. | PROTEIN_CHANGING_VARIANTS | |
| MISSENSE_VARIANT | missense_variant | SO:0001583 | A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved. | PROTEIN_CHANGING_VARIANTS | |
| INFRAME_INSERTION | inframe_insertion | SO:0001821 | An inframe non synonymous variant that inserts bases into in the coding sequence. | PROTEIN_CHANGING_VARIANTS | |
| INFRAME_DELETION | inframe_deletion | SO:0001822 | An inframe non synonymous variant that deletes bases from the coding sequence. | PROTEIN_CHANGING_VARIANTS | |
| SYNONYMOUS_VARIANT | synonymous_variant | SO:0001819 | A sequence variant where there is no resulting change to the encoded amino acid. | OTHER_VARIANTS | |
| INTRON_VARIANT | intron_variant | SO:0001627 | A transcript variant occurring within an intron. | OTHER_VARIANTS | |
| INTERGENIC_VARIANT | intergenic_variant | SO:0001628 | A sequence variant located in the intergenic region, between genes. | OTHER_VARIANTS | |
| NON_CODING_TRANSCRIPT_VARIANT | non_coding_transcript_variant | SO:0001619 | A transcript variant of a non coding RNA gene. | OTHER_VARIANTS | |
| SHORT_TANDEM_REPEAT_CHANGE | short_tandem_repeat_change | SO:0002161 | A sequence variant where the copies of a short tandem repeat (STR) feature are either contracted or expanded. SO:0002161 carries no text definition; this description is taken from the SO term comment. | OTHER_VARIANTS | |
| COPY_NUMBER_VARIATION | copy_number_variation | SO:0001019 | A variation that increases or decreases the copy number of a given region. | OTHER_VARIANTS | |
| WHOLE_PARTIAL_GENE_DELETION | transcript_ablation | SO:0001893 | A feature ablation whereby the deleted region includes a transcript feature. Used by G2P to record whole or partial gene deletions. | OTHER_VARIANTS | |
| WHOLE_PARTIAL_GENE_DUPLICATION | transcript_amplification | SO:0001889 | A feature amplification of a region containing a transcript. Used by G2P to record whole or partial gene duplications. | OTHER_VARIANTS |
Slots
| Name | Description |
|---|---|
| g2p_variant_type | The type of variant associated with a curated gene-disease pair |
Identifier and Mapping Information
Annotations
| property | value |
|---|---|
| stewards | https://www.ebi.ac.uk/gene2phenotype |
| publishers | https://www.ebi.ac.uk/gene2phenotype |
| source | https://www.ebi.ac.uk/gene2phenotype/about/terminology#variant-types-section |
| standard | Sequence Ontology |
Schema Source
- from schema: https://w3id.org/valuesets
LinkML Source
name: G2PVariantType
instantiates:
- valuesets_meta:ValueSetEnumDefinition
annotations:
stewards:
tag: stewards
value: https://www.ebi.ac.uk/gene2phenotype
publishers:
tag: publishers
value: https://www.ebi.ac.uk/gene2phenotype
source:
tag: source
value: https://www.ebi.ac.uk/gene2phenotype/about/terminology#variant-types-section
standard:
tag: standard
value: Sequence Ontology
description: 'The types of variants associated with the curated gene-disease pair
reported in the publication. All terms are Sequence Ontology terms. Where G2P uses
a label that differs from the current SO label, the G2P label is recorded as an
alias. Descriptions are the SO text definitions where SO provides one.
The NMD-qualified types have two parents in SO, so they are modelled with the base
variant as is_a and the NMD qualifier as a mixin. LinkML preserves both, but as
of linkml 1.9.5 the OWL generator emits only the is_a parent as rdfs:subClassOf
and drops the mixin, so the NMD axis is additionally recorded in the nmd_status
annotation to keep it available in every generated artifact. If a later linkml emits
permissible-value mixins, that annotation is redundant and can go.'
title: G2P Variant Type
from_schema: https://w3id.org/valuesets
contributors:
- orcid:0000-0002-6601-2165
- https://github.com/anthropics/claude-code
status: STANDARD
rank: 1000
permissible_values:
NMD_TRIGGERING:
text: NMD_TRIGGERING
description: 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.
meaning: SO:0002319
annotations:
variant_type_group:
tag: variant_type_group
value: NMD_VARIANTS
title: NMD_triggering_variant
aliases:
- NMD_triggering
NMD_ESCAPING:
text: NMD_ESCAPING
description: A sequence variant that leads to a change in the location of a termination
codon in a transcript but allows the transcript to escape 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.
meaning: SO:0002320
annotations:
variant_type_group:
tag: variant_type_group
value: NMD_VARIANTS
title: NMD_escaping_variant
aliases:
- NMD_escaping
STOP_GAINED_NMD_TRIGGERING:
text: STOP_GAINED_NMD_TRIGGERING
description: A stop_gained (SO:0001587) variant that is degraded by nonsense-mediated
decay (NMD).
meaning: SO:0002321
is_a: STOP_GAINED
mixins:
- NMD_TRIGGERING
annotations:
variant_type_group:
tag: variant_type_group
value: NMD_VARIANTS
nmd_status:
tag: nmd_status
value: NMD_TRIGGERING
title: stop_gained_NMD_triggering
STOP_GAINED_NMD_ESCAPING:
text: STOP_GAINED_NMD_ESCAPING
description: A stop_gained (SO:0001587) variant that allows the transcript to
escape nonsense-mediated decay (NMD).
meaning: SO:0002322
is_a: STOP_GAINED
mixins:
- NMD_ESCAPING
annotations:
variant_type_group:
tag: variant_type_group
value: NMD_VARIANTS
nmd_status:
tag: nmd_status
value: NMD_ESCAPING
title: stop_gained_NMD_escaping
FRAMESHIFT_VARIANT_NMD_TRIGGERING:
text: FRAMESHIFT_VARIANT_NMD_TRIGGERING
description: A frameshift_variant (SO:0001589) that is degraded by nonsense-mediated
decay (NMD).
meaning: SO:0002323
is_a: FRAMESHIFT_VARIANT
mixins:
- NMD_TRIGGERING
annotations:
variant_type_group:
tag: variant_type_group
value: NMD_VARIANTS
nmd_status:
tag: nmd_status
value: NMD_TRIGGERING
title: frameshift_variant_NMD_triggering
FRAMESHIFT_VARIANT_NMD_ESCAPING:
text: FRAMESHIFT_VARIANT_NMD_ESCAPING
description: A frameshift_variant (SO:0001589) that allows the transcript to escape
nonsense-mediated decay (NMD).
meaning: SO:0002324
is_a: FRAMESHIFT_VARIANT
mixins:
- NMD_ESCAPING
annotations:
variant_type_group:
tag: variant_type_group
value: NMD_VARIANTS
nmd_status:
tag: nmd_status
value: NMD_ESCAPING
title: frameshift_variant_NMD_escaping
SPLICE_DONOR_VARIANT_NMD_TRIGGERING:
text: SPLICE_DONOR_VARIANT_NMD_TRIGGERING
description: A splice_donor_variant (SO:0001575) that is degraded by nonsense-mediated
decay (NMD).
meaning: SO:0002325
is_a: SPLICE_DONOR_VARIANT
mixins:
- NMD_TRIGGERING
annotations:
variant_type_group:
tag: variant_type_group
value: NMD_VARIANTS
nmd_status:
tag: nmd_status
value: NMD_TRIGGERING
title: splice_donor_variant_NMD_triggering
SPLICE_DONOR_VARIANT_NMD_ESCAPING:
text: SPLICE_DONOR_VARIANT_NMD_ESCAPING
description: A splice_donor_variant (SO:0001575) that allows the transcript to
escape nonsense-mediated decay (NMD).
meaning: SO:0002326
is_a: SPLICE_DONOR_VARIANT
mixins:
- NMD_ESCAPING
annotations:
variant_type_group:
tag: variant_type_group
value: NMD_VARIANTS
nmd_status:
tag: nmd_status
value: NMD_ESCAPING
title: splice_donor_variant_NMD_escaping
SPLICE_ACCEPTOR_VARIANT_NMD_TRIGGERING:
text: SPLICE_ACCEPTOR_VARIANT_NMD_TRIGGERING
description: A splice_acceptor_variant (SO:0001574) that is degraded by nonsense-mediated
decay (NMD).
meaning: SO:0002327
is_a: SPLICE_ACCEPTOR_VARIANT
mixins:
- NMD_TRIGGERING
annotations:
variant_type_group:
tag: variant_type_group
value: NMD_VARIANTS
nmd_status:
tag: nmd_status
value: NMD_TRIGGERING
title: splice_acceptor_variant_NMD_triggering
SPLICE_ACCEPTOR_VARIANT_NMD_ESCAPING:
text: SPLICE_ACCEPTOR_VARIANT_NMD_ESCAPING
description: A splice_acceptor_variant (SO:0001574) that allows the transcript
to escape nonsense-mediated decay (NMD).
meaning: SO:0002328
is_a: SPLICE_ACCEPTOR_VARIANT
mixins:
- NMD_ESCAPING
annotations:
variant_type_group:
tag: variant_type_group
value: NMD_VARIANTS
nmd_status:
tag: nmd_status
value: NMD_ESCAPING
title: splice_acceptor_variant_NMD_escaping
SPLICE_REGION_VARIANT:
text: SPLICE_REGION_VARIANT
description: A sequence variant in which a change has occurred within the region
of the splice site, either within 1-3 bases of the exon or 3-8 bases of the
intron.
meaning: SO:0001630
annotations:
variant_type_group:
tag: variant_type_group
value: SPLICE_VARIANTS
title: splice_region_variant
SPLICE_ACCEPTOR_VARIANT:
text: SPLICE_ACCEPTOR_VARIANT
description: A splice variant that changes the 2 base region at the 3' end of
an intron.
meaning: SO:0001574
annotations:
variant_type_group:
tag: variant_type_group
value: SPLICE_VARIANTS
title: splice_acceptor_variant
SPLICE_DONOR_VARIANT:
text: SPLICE_DONOR_VARIANT
description: A splice variant that changes the 2 base pair region at the 5' end
of an intron.
meaning: SO:0001575
annotations:
variant_type_group:
tag: variant_type_group
value: SPLICE_VARIANTS
title: splice_donor_variant
FIVE_PRIME_UTR_VARIANT:
text: FIVE_PRIME_UTR_VARIANT
description: A UTR variant of the 5' UTR.
meaning: SO:0001623
annotations:
variant_type_group:
tag: variant_type_group
value: REGULATORY_VARIANTS
title: 5_prime_UTR_variant
THREE_PRIME_UTR_VARIANT:
text: THREE_PRIME_UTR_VARIANT
description: A UTR variant of the 3' UTR.
meaning: SO:0001624
annotations:
variant_type_group:
tag: variant_type_group
value: REGULATORY_VARIANTS
title: 3_prime_UTR_variant
REGULATORY_REGION_VARIANT:
text: REGULATORY_REGION_VARIANT
description: A sequence variant located within a regulatory region.
meaning: SO:0001566
annotations:
variant_type_group:
tag: variant_type_group
value: REGULATORY_VARIANTS
title: regulatory_region_variant
START_LOST:
text: START_LOST
description: A codon variant that changes at least one base of the canonical start
codon.
meaning: SO:0002012
annotations:
variant_type_group:
tag: variant_type_group
value: PROTEIN_CHANGING_VARIANTS
title: start_lost
STOP_GAINED:
text: STOP_GAINED
description: A sequence variant whereby at least one base of a codon is changed,
resulting in a premature stop codon, leading to a shortened polypeptide.
meaning: SO:0001587
annotations:
variant_type_group:
tag: variant_type_group
value: PROTEIN_CHANGING_VARIANTS
title: stop_gained
STOP_LOST:
text: STOP_LOST
description: A sequence variant where at least one base of the terminator codon
(stop) is changed, resulting in an elongated transcript.
meaning: SO:0001578
annotations:
variant_type_group:
tag: variant_type_group
value: PROTEIN_CHANGING_VARIANTS
title: stop_lost
FRAMESHIFT_VARIANT:
text: FRAMESHIFT_VARIANT
description: A sequence variant which causes a disruption of the translational
reading frame, because the number of nucleotides inserted or deleted is not
a multiple of three.
meaning: SO:0001589
annotations:
variant_type_group:
tag: variant_type_group
value: PROTEIN_CHANGING_VARIANTS
title: frameshift_variant
MISSENSE_VARIANT:
text: MISSENSE_VARIANT
description: A sequence variant, that changes one or more bases, resulting in
a different amino acid sequence but where the length is preserved.
meaning: SO:0001583
annotations:
variant_type_group:
tag: variant_type_group
value: PROTEIN_CHANGING_VARIANTS
title: missense_variant
INFRAME_INSERTION:
text: INFRAME_INSERTION
description: An inframe non synonymous variant that inserts bases into in the
coding sequence.
meaning: SO:0001821
annotations:
variant_type_group:
tag: variant_type_group
value: PROTEIN_CHANGING_VARIANTS
title: inframe_insertion
INFRAME_DELETION:
text: INFRAME_DELETION
description: An inframe non synonymous variant that deletes bases from the coding
sequence.
meaning: SO:0001822
annotations:
variant_type_group:
tag: variant_type_group
value: PROTEIN_CHANGING_VARIANTS
title: inframe_deletion
SYNONYMOUS_VARIANT:
text: SYNONYMOUS_VARIANT
description: A sequence variant where there is no resulting change to the encoded
amino acid.
meaning: SO:0001819
annotations:
variant_type_group:
tag: variant_type_group
value: OTHER_VARIANTS
title: synonymous_variant
INTRON_VARIANT:
text: INTRON_VARIANT
description: A transcript variant occurring within an intron.
meaning: SO:0001627
annotations:
variant_type_group:
tag: variant_type_group
value: OTHER_VARIANTS
title: intron_variant
INTERGENIC_VARIANT:
text: INTERGENIC_VARIANT
description: A sequence variant located in the intergenic region, between genes.
meaning: SO:0001628
annotations:
variant_type_group:
tag: variant_type_group
value: OTHER_VARIANTS
title: intergenic_variant
NON_CODING_TRANSCRIPT_VARIANT:
text: NON_CODING_TRANSCRIPT_VARIANT
description: A transcript variant of a non coding RNA gene.
meaning: SO:0001619
annotations:
variant_type_group:
tag: variant_type_group
value: OTHER_VARIANTS
title: non_coding_transcript_variant
SHORT_TANDEM_REPEAT_CHANGE:
text: SHORT_TANDEM_REPEAT_CHANGE
description: A sequence variant where the copies of a short tandem repeat (STR)
feature are either contracted or expanded. SO:0002161 carries no text definition;
this description is taken from the SO term comment.
meaning: SO:0002161
annotations:
variant_type_group:
tag: variant_type_group
value: OTHER_VARIANTS
title: short_tandem_repeat_change
COPY_NUMBER_VARIATION:
text: COPY_NUMBER_VARIATION
description: A variation that increases or decreases the copy number of a given
region.
meaning: SO:0001019
annotations:
variant_type_group:
tag: variant_type_group
value: OTHER_VARIANTS
title: copy_number_variation
WHOLE_PARTIAL_GENE_DELETION:
text: WHOLE_PARTIAL_GENE_DELETION
description: A feature ablation whereby the deleted region includes a transcript
feature. Used by G2P to record whole or partial gene deletions.
meaning: SO:0001893
annotations:
variant_type_group:
tag: variant_type_group
value: OTHER_VARIANTS
title: transcript_ablation
aliases:
- whole_partial_gene_deletion
WHOLE_PARTIAL_GENE_DUPLICATION:
text: WHOLE_PARTIAL_GENE_DUPLICATION
description: A feature amplification of a region containing a transcript. Used
by G2P to record whole or partial gene duplications.
meaning: SO:0001889
annotations:
variant_type_group:
tag: variant_type_group
value: OTHER_VARIANTS
title: transcript_amplification
aliases:
- whole_partial_gene_duplication