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NM_003560.4(PLA2G6):c.2287C>T (p.Gln763Ter) AND Neurodegeneration with brain iron accumulation

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jun 23, 2021
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:
RCV001532992.1

Allele description [Variation Report for NM_003560.4(PLA2G6):c.2287C>T (p.Gln763Ter)]

NM_003560.4(PLA2G6):c.2287C>T (p.Gln763Ter)

Gene:
PLA2G6:phospholipase A2 group VI [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
22q13.1
Genomic location:
Preferred name:
NM_003560.4(PLA2G6):c.2287C>T (p.Gln763Ter)
Other names:
NM_003560.4(PLA2G6):c.2287C>T; p.Gln763Ter
HGVS:
  • NC_000022.11:g.38112295G>A
  • NG_007094.3:g.107484C>T
  • NG_033059.2:g.3375C>T
  • NM_001004426.3:c.2125C>T
  • NM_001199562.3:c.2125C>T
  • NM_001349864.2:c.2287C>T
  • NM_001349865.2:c.2125C>T
  • NM_001349866.2:c.2125C>T
  • NM_001349867.2:c.1753C>T
  • NM_001349868.2:c.1609C>T
  • NM_001349869.2:c.1591C>T
  • NM_003560.4:c.2287C>TMANE SELECT
  • NP_001004426.1:p.Gln709Ter
  • NP_001186491.1:p.Gln709Ter
  • NP_001336793.1:p.Gln763Ter
  • NP_001336794.1:p.Gln709Ter
  • NP_001336795.1:p.Gln709Ter
  • NP_001336796.1:p.Gln585Ter
  • NP_001336797.1:p.Gln537Ter
  • NP_001336798.1:p.Gln531Ter
  • NP_003551.2:p.Gln763Ter
  • LRG_1015t1:c.2287C>T
  • LRG_1015:g.107484C>T
  • LRG_1015p1:p.Gln763Ter
  • NC_000022.10:g.38508302G>A
  • NG_007094.2:g.98396C>T
  • NM_003560.2:c.2287C>T
Protein change:
Q531*
Links:
dbSNP: rs373493102
NCBI 1000 Genomes Browser:
rs373493102
Molecular consequence:
  • NM_001004426.3:c.2125C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001199562.3:c.2125C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001349864.2:c.2287C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001349865.2:c.2125C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001349866.2:c.2125C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001349867.2:c.1753C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001349868.2:c.1609C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001349869.2:c.1591C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_003560.4:c.2287C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Neurodegeneration with brain iron accumulation (NBIA)
Identifiers:
MONDO: MONDO:0018307; MedGen: C2931845; OMIM: PS234200

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001748827Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely pathogenic
(Jun 23, 2021) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001748827.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: PLA2G6 c.2287C>T (p.Gln763X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been cited in ClinVar as pathogenic by multiple submitters (e.g. c.2370T>G, p.Tyr790X; c.2370_2371delTG, p.Tyr790X) and are reported as disease causing mutations in HGMD (e.g. c.2389C>T, p.Q797X). The variant allele was found at a frequency of 8e-06 in 249528 control chromosomes (gnomAD). To our knowledge, no occurrence of c.2287C>T in individuals affected with Neurodegeneration With Brain Iron Accumulation and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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

Last Updated: May 26, 2024