NM_001139.2(ALOX12B):c.1562A>G (p.Tyr521Cys) AND not provided

Clinical significance:Pathogenic (Last evaluated: Mar 23, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000413764.1

Allele description

NM_001139.2(ALOX12B):c.1562A>G (p.Tyr521Cys)

Gene:
ALOX12B:arachidonate 12-lipoxygenase, 12R type [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17p13.1
Genomic location:
Preferred name:
NM_001139.2(ALOX12B):c.1562A>G (p.Tyr521Cys)
HGVS:
  • NC_000017.11:g.8075687T>C
  • NG_007099.1:g.17017A>G
  • NM_001139.2:c.1562A>G
  • NP_001130.1:p.Tyr521Cys
  • NC_000017.10:g.7979005T>C
  • O75342:p.Tyr521Cys
Protein change:
Y521C; TYR521CYS
Links:
UniProtKB: O75342#VAR_069556; OMIM: 603741.0012; dbSNP: rs199766569
NCBI 1000 Genomes Browser:
rs199766569
Allele Frequency:
0.00027(C)
Molecular consequence:
  • NM_001139.2:c.1562A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000490400GeneDxcriteria provided, single submitter
Pathogenic
(Mar 23, 2016)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000490400.1

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

Description

The Y521C pathogenic variant in the ALOX12B gene has been reported previously in association with autosomal recessive congenital ichthyosis (ARCI) (Vahlquist et al., 2010; Eckl et al., 2005). It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Y521C is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species and in silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret Y521C as a pathogenic variant.

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

Last Updated: Jul 16, 2018