NM_022089.4(ATP13A2):c.1236G>T (p.Leu412Phe) AND Inborn genetic diseases

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 2, 2019
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:: RCV002365138.2

Allele description [Variation Report for NM_022089.4(ATP13A2):c.1236G>T (p.Leu412Phe)]

NM_022089.4(ATP13A2):c.1236G>T (p.Leu412Phe)

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.1236G>T (p.Leu412Phe)

HGVS:

NC_000001.11:g.16996456C>A
NG_009054.1:g.20473G>T
NM_001141973.3:c.1221G>T
NM_001141974.3:c.1221G>T
NM_022089.4:c.1236G>TMANE SELECT
NP_001135445.1:p.Leu407Phe
NP_001135446.1:p.Leu407Phe
NP_071372.1:p.Leu412Phe
LRG_834t1:c.1236G>T
LRG_834:g.20473G>T
LRG_834p1:p.Leu412Phe
NC_000001.10:g.17322951C>A
NM_022089.2:c.1236G>T

Protein change:

L407F

Molecular consequence:

NM_001141973.3:c.1221G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001141974.3:c.1221G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_022089.4:c.1236G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002662546	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Dec 2, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002662546

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Dec 2, 2019)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Ambry Genetics, SCV002662546.2

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

Description

The p.L412F variant (also known as c.1236G>T), located in coding exon 13 of the ATP13A2 gene, results from a G to T substitution at nucleotide position 1236. The leucine at codon 412 is replaced by phenylalanine, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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: May 1, 2024

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