VCV001303247.2 - ClinVar

NM_001195248.2(APTX):c.809C>T (p.Ser270Phe)

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.

(1)

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.

Uncertain significance

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001195248.2(APTX):c.809C>T (p.Ser270Phe)

Variation ID: 1303247 Accession: VCV001303247.2

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 9p21.1 9: 32974523 (GRCh38) [ NCBI UCSC ] 9: 32974521 (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	Nov 6, 2021	Mar 4, 2023	Nov 10, 2020

HGVS

Nucleotide	Protein	Molecular consequence
NM_001195248.2:c.809C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001182177.2:p.Ser270Phe	missense
NM_001195249.2:c.809C>T	NP_001182178.1:p.Ser270Phe	missense
NM_001195250.2:c.647C>T	NP_001182179.2:p.Ser216Phe	missense
NM_001195251.2:c.809C>T	NP_001182180.1:p.Ser270Phe	missense
NM_001195252.2:c.593C>T	NP_001182181.2:p.Ser198Phe	missense
NM_001195254.2:c.647C>T	NP_001182183.1:p.Ser216Phe	missense
NM_001368995.1:c.809C>T	NP_001355924.1:p.Ser270Phe	missense
NM_001368996.1:c.809C>T	NP_001355925.1:p.Ser270Phe	missense
NM_001368997.1:c.809C>T	NP_001355926.1:p.Ser270Phe	missense
NM_001368998.1:c.809C>T	NP_001355927.1:p.Ser270Phe	missense
NM_001368999.1:c.809C>T	NP_001355928.1:p.Ser270Phe	missense
NM_001369000.1:c.647C>T	NP_001355929.1:p.Ser216Phe	missense
NM_001369001.1:c.647C>T	NP_001355930.1:p.Ser216Phe	missense
NM_001369002.1:c.545C>T	NP_001355931.1:p.Ser182Phe	missense
NM_001369003.1:c.545C>T	NP_001355932.1:p.Ser182Phe	missense
NM_001369004.1:c.545C>T	NP_001355933.1:p.Ser182Phe	missense
NM_001369005.1:c.545C>T	NP_001355934.1:p.Ser182Phe	missense
NM_001369006.1:c.545C>T	NP_001355935.1:p.Ser182Phe	missense
NM_001370669.1:c.545C>T	NP_001357598.1:p.Ser182Phe	missense
NM_001370670.1:c.545C>T	NP_001357599.1:p.Ser182Phe	missense
NM_001370673.1:c.545C>T	NP_001357602.1:p.Ser182Phe	missense
NM_175069.3:c.809C>T	NP_778239.2:p.Ser270Phe	missense
NM_175073.3:c.809C>T	NP_778243.1:p.Ser270Phe	missense
NR_036577.2:n.760C>T		non-coding transcript variant
NR_160920.1:n.648C>T		non-coding transcript variant
NR_160921.1:n.779C>T		non-coding transcript variant
NR_160922.1:n.1010C>T		non-coding transcript variant
NR_160923.1:n.814C>T		non-coding transcript variant
NR_160924.1:n.819C>T		non-coding transcript variant
NR_160925.1:n.1015C>T		non-coding transcript variant
NR_160926.1:n.805C>T		non-coding transcript variant
NR_160927.1:n.898C>T		non-coding transcript variant
NR_160928.1:n.788C>T		non-coding transcript variant
NR_160929.1:n.702C>T		non-coding transcript variant
NR_160930.1:n.755C>T		non-coding transcript variant
NR_160931.1:n.994C>T		non-coding transcript variant
NC_000009.12:g.32974523G>A
NC_000009.11:g.32974521G>A
NG_012821.2:g.55609C>T

... more HGVS ... less HGVS

Protein change

S182F, S198F, S216F, S270F

Other names

Canonical SPDI

NC_000009.12:32974522: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.

Trans-Omics for Precision Medicine (TOPMed) 0.00000

Links

dbSNP: rs1828859707 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	Uncertain significance (1)	criteria provided, single submitter	Nov 10, 2020	RCV001756746.2

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.
Uncertain significance (Nov 10, 2020)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV001987698.2 First in ClinVar: Nov 06, 2021 Last updated: Mar 04, 2023	Comment: Reported previously in an individual with ataxia with oculomotor apraxia who also harbored a APTX splicing variant, although parental studies were not performed to determine … (more) Reported previously in an individual with ataxia with oculomotor apraxia who also harbored a APTX splicing variant, although parental studies were not performed to determine the phase of these two variants (Laurencin et al., 2015; Renaud et al., 2018); Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 25845762, 29356829) (less)

Comment:

Reported previously in an individual with ataxia with oculomotor apraxia who also harbored a APTX splicing variant, although parental studies were not performed to determine the phase of these two variants (Laurencin et al., 2015; Renaud et al., 2018); Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 25845762, 29356829)

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.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs1828859707 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Dec 25, 2023

ClinVar Genomic variation as it relates to human health

NM_001195248.2(APTX):c.809C>T (p.Ser270Phe)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs1828859707 ...