NM_001195248.2(APTX):c.874+6_874+7del AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 1, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001919721.3

Allele description

NM_001195248.2(APTX):c.874+6_874+7del

Gene:

APTX:aprataxin [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

9p21.1

Genomic location:

Preferred name:

NM_001195248.2(APTX):c.874+6_874+7del

HGVS:

NC_000009.12:g.32974452_32974453del
NG_012821.2:g.55680_55681del
NM_001195248.2:c.874+6_874+7delMANE SELECT
NM_001195249.2:c.874+6_874+7del
NM_001195250.2:c.712+6_712+7del
NM_001195251.2:c.874+6_874+7del
NM_001195252.2:c.658+6_658+7del
NM_001195254.2:c.712+6_712+7del
NM_001368995.1:c.874+6_874+7del
NM_001368996.1:c.874+6_874+7del
NM_001368997.1:c.874+6_874+7del
NM_001368998.1:c.874+6_874+7del
NM_001368999.1:c.874+6_874+7del
NM_001369000.1:c.712+6_712+7del
NM_001369001.1:c.712+6_712+7del
NM_001369002.1:c.610+6_610+7del
NM_001369003.1:c.610+6_610+7del
NM_001369004.1:c.610+6_610+7del
NM_001369005.1:c.610+6_610+7del
NM_001369006.1:c.610+6_610+7del
NM_001370669.1:c.610+6_610+7del
NM_001370670.1:c.610+6_610+7del
NM_001370673.1:c.610+6_610+7del
NM_175069.3:c.874+6_874+7del
NM_175073.3:c.874+6_874+7del
NC_000009.11:g.32974449_32974450del
NC_000009.11:g.32974450_32974451del

Links:

dbSNP: rs1483847207

NCBI 1000 Genomes Browser:

rs1483847207

Molecular consequence:

NM_001195248.2:c.874+6_874+7del - intron variant - [Sequence Ontology: SO:0001627]
NM_001195249.2:c.874+6_874+7del - intron variant - [Sequence Ontology: SO:0001627]
NM_001195250.2:c.712+6_712+7del - intron variant - [Sequence Ontology: SO:0001627]
NM_001195251.2:c.874+6_874+7del - intron variant - [Sequence Ontology: SO:0001627]
NM_001195252.2:c.658+6_658+7del - intron variant - [Sequence Ontology: SO:0001627]
NM_001195254.2:c.712+6_712+7del - intron variant - [Sequence Ontology: SO:0001627]
NM_001368995.1:c.874+6_874+7del - intron variant - [Sequence Ontology: SO:0001627]
NM_001368996.1:c.874+6_874+7del - intron variant - [Sequence Ontology: SO:0001627]
NM_001368997.1:c.874+6_874+7del - intron variant - [Sequence Ontology: SO:0001627]
NM_001368998.1:c.874+6_874+7del - intron variant - [Sequence Ontology: SO:0001627]
NM_001368999.1:c.874+6_874+7del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369000.1:c.712+6_712+7del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369001.1:c.712+6_712+7del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369002.1:c.610+6_610+7del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369003.1:c.610+6_610+7del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369004.1:c.610+6_610+7del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369005.1:c.610+6_610+7del - intron variant - [Sequence Ontology: SO:0001627]
NM_001369006.1:c.610+6_610+7del - intron variant - [Sequence Ontology: SO:0001627]
NM_001370669.1:c.610+6_610+7del - intron variant - [Sequence Ontology: SO:0001627]
NM_001370670.1:c.610+6_610+7del - intron variant - [Sequence Ontology: SO:0001627]
NM_001370673.1:c.610+6_610+7del - intron variant - [Sequence Ontology: SO:0001627]
NM_175069.3:c.874+6_874+7del - intron variant - [Sequence Ontology: SO:0001627]
NM_175073.3:c.874+6_874+7del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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sodium/calcium exchanger 3 isoform X4 [Homo sapiens]
sodium/calcium exchanger 3 isoform X4 [Homo sapiens]
gi|2462541411|ref|XP_054232605.1|

Protein
sodium/calcium exchanger 3 isoform X7 [Homo sapiens]
sodium/calcium exchanger 3 isoform X7 [Homo sapiens]
gi|2462541415|ref|XP_054232607.1|

Protein
Same Parent, Connectivity for PubChem Compound (Select 138461123) (3)
PubChem Compound
Chromosome neighbors for GEO Profiles (Select 132379512) (20)
GEO Profiles
Model organism or animal sample from Grammomys cometes
Model organism or animal sample from Grammomys cometes

biosample

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002165120	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 1, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17576681, 9536098, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002165120

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 1, 2022)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]

PMID:: 17576681
PMCID:: PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]

PMID:: 9536098

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV002165120.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant is present in population databases (no rsID available, gnomAD 0.006%). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. ClinVar contains an entry for this variant (Variation ID: 1395461). This variant has not been reported in the literature in individuals affected with APTX-related conditions. This sequence change falls in intron 8 of the APTX gene. It does not directly change the encoded amino acid sequence of the APTX protein. It affects a nucleotide within the consensus splice site.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 20, 2024

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