NM_001139.3(ALOX12B):c.252C>A (p.Cys84Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 10, 2015
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:: RCV000267897.1

Allele description [Variation Report for NM_001139.3(ALOX12B):c.252C>A (p.Cys84Ter)]

NM_001139.3(ALOX12B):c.252C>A (p.Cys84Ter)

Gene:

ALOX12B:arachidonate 12-lipoxygenase, 12R type [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_001139.3(ALOX12B):c.252C>A (p.Cys84Ter)

HGVS:

NC_000017.11:g.8086116G>T
NG_007099.1:g.6588C>A
NG_007099.2:g.6601C>A
NM_001139.3:c.252C>AMANE SELECT
NP_001130.1:p.Cys84Ter
LRG_1264t1:c.252C>A
LRG_1264:g.6601C>A
LRG_1264p1:p.Cys84Ter
NC_000017.10:g.7989434G>T
NM_001139.2:c.252C>A

Protein change:

C84*

Links:

dbSNP: rs886041394

NCBI 1000 Genomes Browser:

rs886041394

Molecular consequence:

NM_001139.3:c.252C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000329978	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Dec 10, 2015)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000329978

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Dec 10, 2015)

germline

clinical testing

Citation Link

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

Details of each submission

From GeneDx, SCV000329978.6

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

Description

While the nonsense variant C84X in the ALOX12B gene has not been previously reported to be pathogenic, it is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. Other loss-of-function variants downstream of C84X were observed in association with autosomal recessive congenital ichthyosis (Stenson et al., 2014). Moreover, this nonsense variant 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 and/or benign variant in these populations.Therefore, we consider C84X to be a pathogenic variant.

#	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: Apr 23, 2022

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