NM_003560.4(PLA2G6):c.1506G>C (p.Lys502Asn) AND Neurodegeneration with brain iron accumulation 2B

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jul 20, 2016
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:: RCV000502668.6

Allele description [Variation Report for NM_003560.4(PLA2G6):c.1506G>C (p.Lys502Asn)]

NM_003560.4(PLA2G6):c.1506G>C (p.Lys502Asn)

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.1506G>C (p.Lys502Asn)

HGVS:

NC_000022.11:g.38123180C>G
NG_007094.3:g.96599G>C
NM_001004426.3:c.1344G>C
NM_001199562.3:c.1344G>C
NM_001349864.2:c.1506G>C
NM_001349865.2:c.1344G>C
NM_001349866.2:c.1344G>C
NM_001349867.2:c.972G>C
NM_001349868.2:c.828G>C
NM_001349869.2:c.810G>C
NM_003560.4:c.1506G>CMANE SELECT
NP_001004426.1:p.Lys448Asn
NP_001186491.1:p.Lys448Asn
NP_001336793.1:p.Lys502Asn
NP_001336794.1:p.Lys448Asn
NP_001336795.1:p.Lys448Asn
NP_001336796.1:p.Lys324Asn
NP_001336797.1:p.Lys276Asn
NP_001336798.1:p.Lys270Asn
NP_003551.2:p.Lys502Asn
LRG_1015t1:c.1506G>C
LRG_1015:g.96599G>C
LRG_1015p1:p.Lys502Asn
NC_000022.10:g.38519187C>G
NG_007094.2:g.87511G>C
NM_003560.2:c.1506G>C

Protein change:

K270N

Links:

dbSNP: rs1555988382

NCBI 1000 Genomes Browser:

rs1555988382

Molecular consequence:

NM_001004426.3:c.1344G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001199562.3:c.1344G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001349864.2:c.1506G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001349865.2:c.1344G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001349866.2:c.1344G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001349867.2:c.972G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001349868.2:c.828G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001349869.2:c.810G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_003560.4:c.1506G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Neurodegeneration with brain iron accumulation 2B
Synonyms:: NEUROAXONAL DYSTROPHY, ATYPICAL; NEURODEGENERATION WITH BRAIN IRON ACCUMULATION, PLA2G6-RELATED; aNAD; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0012444; MedGen: C1857747; Orphanet: 35069; OMIM: 610217

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000596432	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jul 20, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000596432

Genetic Services Laboratory, University of Chicago

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jul 20, 2016)

germline

clinical testing

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

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

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 Genetic Services Laboratory, University of Chicago, SCV000596432.1

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

#	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: Nov 25, 2023

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