VCV002571331.14 - ClinVar

NM_001195248.2(APTX):c.739C>T (p.Arg247Ter)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(2)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001195248.2(APTX):c.739C>T (p.Arg247Ter)

Variation ID: 2571331 Accession: VCV002571331.14

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 9p21.1 9: 32984662 (GRCh38) [ NCBI UCSC ] 9: 32984660 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Jul 17, 2023	Oct 20, 2024	Jan 11, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_001195248.2:c.739C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001182177.2:p.Arg247Ter	nonsense
NM_001195249.2:c.739C>T	NP_001182178.1:p.Arg247Ter	nonsense
NM_001195250.2:c.577C>T	NP_001182179.2:p.Arg193Ter	nonsense
NM_001195251.2:c.739C>T	NP_001182180.1:p.Arg247Ter	nonsense
NM_001195252.2:c.523C>T	NP_001182181.2:p.Arg175Ter	nonsense
NM_001195254.2:c.577C>T	NP_001182183.1:p.Arg193Ter	nonsense
NM_001368995.1:c.739C>T	NP_001355924.1:p.Arg247Ter	nonsense
NM_001368996.1:c.739C>T	NP_001355925.1:p.Arg247Ter	nonsense
NM_001368997.1:c.739C>T	NP_001355926.1:p.Arg247Ter	nonsense
NM_001368998.1:c.739C>T	NP_001355927.1:p.Arg247Ter	nonsense
NM_001368999.1:c.739C>T	NP_001355928.1:p.Arg247Ter	nonsense
NM_001369000.1:c.577C>T	NP_001355929.1:p.Arg193Ter	nonsense
NM_001369001.1:c.577C>T	NP_001355930.1:p.Arg193Ter	nonsense
NM_001369002.1:c.475C>T	NP_001355931.1:p.Arg159Ter	nonsense
NM_001369003.1:c.475C>T	NP_001355932.1:p.Arg159Ter	nonsense
NM_001369004.1:c.475C>T	NP_001355933.1:p.Arg159Ter	nonsense
NM_001369005.1:c.475C>T	NP_001355934.1:p.Arg159Ter	nonsense
NM_001369006.1:c.475C>T	NP_001355935.1:p.Arg159Ter	nonsense
NM_001370669.1:c.475C>T	NP_001357598.1:p.Arg159Ter	nonsense
NM_001370670.1:c.475C>T	NP_001357599.1:p.Arg159Ter	nonsense
NM_001370673.1:c.475C>T	NP_001357602.1:p.Arg159Ter	nonsense
NM_175069.3:c.739C>T	NP_778239.2:p.Arg247Ter	nonsense
NM_175071.1:c.217C>T	NP_778241.1:p.Arg73Ter	nonsense
NM_175073.3:c.739C>T	NP_778243.1:p.Arg247Ter	nonsense
NR_036576.1:n.813C>T
NR_036577.2:n.690C>T		non-coding transcript variant
NR_036578.1:n.835C>T
NR_036579.1:n.982C>T
NR_160921.1:n.709C>T		non-coding transcript variant
NR_160922.1:n.940C>T		non-coding transcript variant
NR_160923.1:n.744C>T		non-coding transcript variant
NR_160924.1:n.749C>T		non-coding transcript variant
NR_160925.1:n.945C>T		non-coding transcript variant
NR_160926.1:n.735C>T		non-coding transcript variant
NR_160930.1:n.685C>T		non-coding transcript variant
NR_160931.1:n.924C>T		non-coding transcript variant
NC_000009.12:g.32984662G>A
NC_000009.11:g.32984660G>A
NG_012821.2:g.45470C>T

... more HGVS ... less HGVS

Protein change

R159*, R175*, R193*, R247*, R73*

Other names

Canonical SPDI

NC_000009.12:32984661:G:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
APTX		-	-	GRCh38 GRCh37	289	358

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not provided	Pathogenic (1)	criteria provided, single submitter	Apr 1, 2023	RCV003312732.12
Epilepsy	Pathogenic (1)	criteria provided, single submitter	Jan 11, 2024	RCV003484415.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Jan 11, 2024)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Epilepsy Affected status: yes Allele origin: germline	Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan Accession: SCV004232393.1 First in ClinVar: Jan 26, 2024 Last updated: Jan 26, 2024	Publications: PubMed (1) PubMed: 25741868 Sex: female
Pathogenic (Apr 01, 2023)	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2) Method: clinical testing	not provided Affected status: yes Allele origin: germline	CeGaT Center for Human Genetics Tuebingen Accession: SCV004010825.12 First in ClinVar: Jul 16, 2023 Last updated: Oct 20, 2024	Comment: APTX: PVS1:Strong, PM2, PM3, PP4:Moderate Number of individuals with the variant: 1

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.	Richards S	Genetics in medicine : official journal of the American College of Medical Genetics	2015	PMID: 25741868

Text-mined citations for this variant ...

Record last updated Oct 20, 2024

ClinVar Genomic variation as it relates to human health

NM_001195248.2(APTX):c.739C>T (p.Arg247Ter)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...