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NM_152296.5(ATP1A3):c.2116G>A (p.Gly706Arg) AND Cerebellar ataxia-areflexia-pes cavus-optic atrophy-sensorineural hearing loss syndrome

Germline classification:
Likely pathogenic (1 submission)
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:
RCV002510573.3

Allele description [Variation Report for NM_152296.5(ATP1A3):c.2116G>A (p.Gly706Arg)]

NM_152296.5(ATP1A3):c.2116G>A (p.Gly706Arg)

Gene:
ATP1A3:ATPase Na+/K+ transporting subunit alpha 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19q13.2
Genomic location:
Preferred name:
NM_152296.5(ATP1A3):c.2116G>A (p.Gly706Arg)
HGVS:
  • NC_000019.10:g.41975776C>T
  • NG_008015.1:g.23455G>A
  • NM_001256213.2:c.2149G>A
  • NM_001256214.2:c.2155G>A
  • NM_152296.5:c.2116G>AMANE SELECT
  • NP_001243142.1:p.Gly717Arg
  • NP_001243143.1:p.Gly719Arg
  • NP_689509.1:p.Gly706Arg
  • LRG_1186t1:c.2116G>A
  • LRG_1186:g.23455G>A
  • LRG_1186p1:p.Gly706Arg
  • NC_000019.9:g.42479928C>T
  • NM_001256214.1:c.2155G>A
  • NM_152296.4:c.2116G>A
Protein change:
G706R
Links:
dbSNP: rs782175860
NCBI 1000 Genomes Browser:
rs782175860
Molecular consequence:
  • NM_001256213.2:c.2149G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001256214.2:c.2155G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_152296.5:c.2116G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Cerebellar ataxia-areflexia-pes cavus-optic atrophy-sensorineural hearing loss syndrome (CAPOS)
Synonyms:
CEREBELLAR ATAXIA, AREFLEXIA, PES CAVUS, OPTIC ATROPHY, AND SENSORINEURAL HEARING LOSS; Cerebellar ataxia, areflexia, pes cavus, optic atrophy and sensorinural hearing loss; CAPOS syndrome
Identifiers:
MONDO: MONDO:0011038; MedGen: C1832466; Orphanet: 1171; OMIM: 601338

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002820296Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenicgermlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV002820296.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The missense variant p.G706R in ATP1A3 (NM_152296.5) has been previously reported as a de novo mutation in patient with alternating hemiplegia of childhood (Yang et al, 2014). It has been submitted to the ClinVar database as Pathogenic. The p.G706R variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. The p.G706R missense variant is predicted to be damaging by both SIFT and PolyPhen2. The glycine residue at codon 706 of ATP1A3 is conserved in all mammalian species. The nucleotide c.2116 in ATP1A3 is predicted to be conserved by GERP++ and PhyloP across 100 vertebrates. Hence the above variant is classified as Likely Pathogenic as currently variant is being evaluated by proband solo exome.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 23, 2024