NM_139058.3(ARX):c.590G>A (p.Gly197Asp) AND not provided

Germline classification:: Likely benign (1 submission)
Last evaluated:: May 8, 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:: RCV001576440.11

Allele description [Variation Report for NM_139058.3(ARX):c.590G>A (p.Gly197Asp)]

NM_139058.3(ARX):c.590G>A (p.Gly197Asp)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

Xp21.3

Genomic location:

Preferred name:

NM_139058.3(ARX):c.590G>A (p.Gly197Asp)

HGVS:

NC_000023.11:g.25013405C>T
NG_008281.1:g.7544G>A
NM_139058.3:c.590G>AMANE SELECT
NP_620689.1:p.Gly197Asp
NC_000023.10:g.25031522C>T
NM_139058.2:c.590G>A

Protein change:

G197D

Links:

dbSNP: rs398124513

NCBI 1000 Genomes Browser:

rs398124513

Molecular consequence:

NM_139058.3:c.590G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Mus musculus ubiquitin-conjugating enzyme E2 variant 2 (Ube2v2), transcript vari...
Mus musculus ubiquitin-conjugating enzyme E2 variant 2 (Ube2v2), transcript variant 2, mRNA
gi|226823222|ref|NM_001159351.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001803630	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (May 8, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001803630

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely benign
(May 8, 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, SCV001803630.1

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

Description

A variant of uncertain significance has been identified in the ARX gene. The G197D variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The G197D variant is not observed in large population cohorts (Lek et al., 2016). The G197D variant 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. In-silico analyses, including protein predictors and evolutionary conservation, support that this variant does not alter protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign 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: Oct 13, 2024

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