NM_022089.4(ATP13A2):c.1306+5G>A AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jan 25, 2024
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:: RCV004719607.1

Allele description [Variation Report for NM_022089.4(ATP13A2):c.1306+5G>A]

NM_022089.4(ATP13A2):c.1306+5G>A

Gene:

ATP13A2:ATPase cation transporting 13A2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p36.13

Genomic location:

Preferred name:

NM_022089.4(ATP13A2):c.1306+5G>A

HGVS:

NC_000001.11:g.16996381C>T
NG_009054.1:g.20548G>A
NM_001141973.3:c.1291+5G>A
NM_001141974.3:c.1291+5G>A
NM_022089.4:c.1306+5G>AMANE SELECT
LRG_834t1:c.1306+5G>A
LRG_834:g.20548G>A
NC_000001.10:g.17322876C>T
NM_022089.3:c.1306+5G>A

Nucleotide change:

IVS13, G-A, +5

Links:

OMIM: 610513.0002; dbSNP: rs786205056

NCBI 1000 Genomes Browser:

rs786205056

Molecular consequence:

NM_001141973.3:c.1291+5G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001141974.3:c.1291+5G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_022089.4:c.1306+5G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005324961	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Jan 25, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005324961

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Jan 25, 2024)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV005324961.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Published functional studies suggest a damaging effect, with exon skipping of in-frame exon 13 (PMID: 16964263); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 25525159, 21724849, 23499937, 22296644, 16964263, 21696388)

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

Last Updated: Oct 8, 2024

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