NM_021926.4(ALX4):c.16dup (p.Cys6fs) AND Parietal foramina 2

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: May 10, 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:: RCV002266523.1

Allele description [Variation Report for NM_021926.4(ALX4):c.16dup (p.Cys6fs)]

NM_021926.4(ALX4):c.16dup (p.Cys6fs)

Gene:

ALX4:ALX homeobox 4 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

11p11.2

Genomic location:

Preferred name:

NM_021926.4(ALX4):c.16dup (p.Cys6fs)

HGVS:

NC_000011.10:g.44310048dup
NG_015809.1:g.5120dup
NM_021926.4:c.16dupMANE SELECT
NP_068745.2:p.Cys6fs
LRG_1256t1:c.16dup
LRG_1256:g.5120dup
LRG_1256p1:p.Cys6fs
NC_000011.9:g.44331598dup
NM_021926.3:c.16dupT

Protein change:

C6fs

Links:

dbSNP: rs746479735

NCBI 1000 Genomes Browser:

rs746479735

Molecular consequence:

NM_021926.4:c.16dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Parietal foramina 2 (PFM2)
Identifiers:: MONDO: MONDO:0012309; MedGen: C1865044; Orphanet: 60015; OMIM: 609597

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002547543	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely pathogenic (May 10, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002547543

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely pathogenic
(May 10, 2022)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002547543.1

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

Description

Variant summary: ALX4 c.16dupT (p.Cys6LeufsX30) 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. The variant allele was found at a frequency of 1.4e-05 in 215370 control chromosomes (gnomAD). To our knowledge, no occurrence of c.16dupT in individuals affected with Parietal Foramina 2 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 16, 2024

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