VCV000004427.1 - ClinVar

NM_001195248.2(APTX):c.841del (p.Ser281fs)

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.

Pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001195248.2(APTX):c.841del (p.Ser281fs)

Variation ID: 4427 Accession: VCV000004427.1

Type and length

Deletion, 1 bp

Location

Cytogenetic: 9p21.1 9: 32974491 (GRCh38) [ NCBI UCSC ] 9: 32974489 (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	Apr 4, 2013	Apr 4, 2013	Oct 1, 2001

HGVS

Nucleotide	Protein	Molecular consequence
NM_001195248.2:c.841del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001182177.2:p.Ser281fs	frameshift
NM_001195249.2:c.841del	NP_001182178.1:p.Ser281fs	frameshift
NM_001195250.2:c.679del	NP_001182179.2:p.Ser227fs	frameshift
NM_001195251.2:c.841del	NP_001182180.1:p.Ser281fs	frameshift
NM_001195252.2:c.625del	NP_001182181.2:p.Ser209fs	frameshift
NM_001195254.2:c.679del	NP_001182183.1:p.Ser227fs	frameshift
NM_001368995.1:c.841del	NP_001355924.1:p.Ser281fs	frameshift
NM_001368996.1:c.841del	NP_001355925.1:p.Ser281fs	frameshift
NM_001368997.1:c.841del	NP_001355926.1:p.Ser281fs	frameshift
NM_001368998.1:c.841del	NP_001355927.1:p.Ser281fs	frameshift
NM_001368999.1:c.841del	NP_001355928.1:p.Ser281fs	frameshift
NM_001369000.1:c.679del	NP_001355929.1:p.Ser227fs	frameshift
NM_001369001.1:c.679del	NP_001355930.1:p.Ser227fs	frameshift
NM_001369002.1:c.577del	NP_001355931.1:p.Ser193fs	frameshift
NM_001369003.1:c.577del	NP_001355932.1:p.Ser193fs	frameshift
NM_001369004.1:c.577del	NP_001355933.1:p.Ser193fs	frameshift
NM_001369005.1:c.577del	NP_001355934.1:p.Ser193fs	frameshift
NM_001369006.1:c.577del	NP_001355935.1:p.Ser193fs	frameshift
NM_001370669.1:c.577del	NP_001357598.1:p.Ser193fs	frameshift
NM_001370670.1:c.577del	NP_001357599.1:p.Ser193fs	frameshift
NM_001370673.1:c.577del	NP_001357602.1:p.Ser193fs	frameshift
NM_175069.3:c.841del	NP_778239.2:p.Ser281fs	frameshift
NM_175073.2:c.840del		frameshift
NM_175073.3:c.841del	NP_778243.1:p.Ser281fs	frameshift
NR_036577.2:n.792del		non-coding transcript variant
NR_160920.1:n.680del		non-coding transcript variant
NR_160921.1:n.811del		non-coding transcript variant
NR_160922.1:n.1042del		non-coding transcript variant
NR_160923.1:n.846del		non-coding transcript variant
NR_160924.1:n.851del		non-coding transcript variant
NR_160925.1:n.1047del		non-coding transcript variant
NR_160926.1:n.837del		non-coding transcript variant
NR_160927.1:n.930del		non-coding transcript variant
NR_160928.1:n.820del		non-coding transcript variant
NR_160929.1:n.734del		non-coding transcript variant
NR_160930.1:n.787del		non-coding transcript variant
NR_160931.1:n.1026del		non-coding transcript variant
NC_000009.12:g.32974492del
NC_000009.11:g.32974490del
NG_012821.2:g.55641del

... more HGVS ... less HGVS

Protein change

S209fs, S193fs, S281fs, S227fs

Other names

Canonical SPDI

NC_000009.12:32974490:AA: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

ClinGen: CA253145 OMIM: 606350.0003 dbSNP: rs587776594 VarSome

Comment on variant

NCBI staff reviewed the sequence information reported in PubMed 11586299 to determine the location of this variant on the current reference sequence. The 318delT is mapped on mRNA FLJ20157 (GenBank AK000164.1), which corresponds to 840delT on NM_175073.2.

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.
Ataxia, early-onset, with oculomotor apraxia and hypoalbuminemia	Pathogenic (1)	no assertion criteria provided	Oct 1, 2001	RCV000004677.2

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 (Oct 01, 2001)	no assertion criteria provided Method: literature only	ATAXIA, EARLY-ONSET, WITH OCULOMOTOR APRAXIA AND HYPOALBUMINEMIA Affected status: not provided Allele origin: germline	OMIM Accession: SCV000024851.1 First in ClinVar: Apr 04, 2013 Last updated: Apr 04, 2013	Publications: PubMed (1) PubMed: 11586299 Comment on evidence: In one pedigree, Date et al. (2001) observed that members with EAOH (208920) were homozygous for a 318delT single-nucleotide deletion resulting in a frameshift with … (more) In one pedigree, Date et al. (2001) observed that members with EAOH (208920) were homozygous for a 318delT single-nucleotide deletion resulting in a frameshift with a premature stop. In 3 pedigrees, the 167insT (606350.0001), P32L (606350.0002), and 318delT mutations were present in compound heterozygous state. (less)

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
Early-onset ataxia with ocular motor apraxia and hypoalbuminemia is caused by mutations in a new HIT superfamily gene.	Date H	Nature genetics	2001	PMID: 11586299

Text-mined citations for rs587776594 ...

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 Apr 25, 2022

ClinVar Genomic variation as it relates to human health

NM_001195248.2(APTX):c.841del (p.Ser281fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs587776594 ...