NM_139058.3(ARX):c.1129del (p.Gln377fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 17, 2019
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:: RCV001009066.1

Allele description [Variation Report for NM_139058.3(ARX):c.1129del (p.Gln377fs)]

NM_139058.3(ARX):c.1129del (p.Gln377fs)

Gene:

ARX:aristaless related homeobox [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xp21.3

Genomic location:

Preferred name:

NM_139058.3(ARX):c.1129del (p.Gln377fs)

HGVS:

NC_000023.11:g.25007431del
NG_008281.1:g.13519del
NM_139058.3:c.1129delMANE SELECT
NP_620689.1:p.Gln377fs
NC_000023.10:g.25025548del
NM_139058.2:c.1129delC

Protein change:

Q377fs

Links:

dbSNP: rs1601946658

NCBI 1000 Genomes Browser:

rs1601946658

Molecular consequence:

NM_139058.3:c.1129del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV001168876	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Jan 17, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001168876

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Jan 17, 2019)

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, SCV001168876.1

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

Description

The c.1129delC variant in the ARX gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.1129delC variant causes a frameshift starting with codon Glutamine 377, changes this amino acid to an Arginine residue, and creates a premature Stop codon at position 86 of the new reading frame, denoted p.Gln377ArgfsX86. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.1129delC variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.1129delC as 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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