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NM_003560.4(PLA2G6):c.1556G>C (p.Ser519Thr) AND Infantile neuroaxonal dystrophy

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 22, 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:
RCV002250928.1

Allele description [Variation Report for NM_003560.4(PLA2G6):c.1556G>C (p.Ser519Thr)]

NM_003560.4(PLA2G6):c.1556G>C (p.Ser519Thr)

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.1556G>C (p.Ser519Thr)
HGVS:
  • NC_000022.11:g.38123130C>G
  • NG_007094.3:g.96649G>C
  • NM_001004426.3:c.1394G>C
  • NM_001199562.3:c.1394G>C
  • NM_001349864.2:c.1556G>C
  • NM_001349865.2:c.1394G>C
  • NM_001349866.2:c.1394G>C
  • NM_001349867.2:c.1022G>C
  • NM_001349868.2:c.878G>C
  • NM_001349869.2:c.860G>C
  • NM_003560.4:c.1556G>CMANE SELECT
  • NP_001004426.1:p.Ser465Thr
  • NP_001186491.1:p.Ser465Thr
  • NP_001336793.1:p.Ser519Thr
  • NP_001336794.1:p.Ser465Thr
  • NP_001336795.1:p.Ser465Thr
  • NP_001336796.1:p.Ser341Thr
  • NP_001336797.1:p.Ser293Thr
  • NP_001336798.1:p.Ser287Thr
  • NP_003551.2:p.Ser519Thr
  • LRG_1015t1:c.1556G>C
  • LRG_1015:g.96649G>C
  • LRG_1015p1:p.Ser519Thr
  • NC_000022.10:g.38519137C>G
  • NM_003560.2:c.1556G>C
Protein change:
S287T
Links:
dbSNP: rs2145721790
NCBI 1000 Genomes Browser:
rs2145721790
Molecular consequence:
  • NM_001004426.3:c.1394G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001199562.3:c.1394G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349864.2:c.1556G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349865.2:c.1394G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349866.2:c.1394G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349867.2:c.1022G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349868.2:c.878G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349869.2:c.860G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003560.4:c.1556G>C - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Infantile neuroaxonal dystrophy (NBIA2A)
Synonyms:
NEURODEGENERATION WITH BRAIN IRON ACCUMULATION 2A; Seitelberger disease; Infantile neuroaxonal dystrophy 1
Identifiers:
MONDO: MONDO:0024457; MedGen: C0270724; Orphanet: 35069; OMIM: 256600

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV0025211443billion
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(May 22, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not 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 3billion, SCV002521144.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

The variant is not observed in the gnomAD v2.1.1 dataset. Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.89; 3Cnet: 0.98). Therefore, this variant is classified as uncertain significanceaccording to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Oct 8, 2024