X-25013659-TGCCGCCGCCGCCGCCGCCGCC-TGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC

Variant names:

• chrX-25013659-T-TGCCGCCGCCGCCGCCGCCGCC
• rs387906492
• NM_139058.3:c.315_335dupGGCGGCGGCGGCGGCGGCGGC

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 10P and 1B. PM2 PP5_Very_Strong BP3

The NM_139058.3(ARX):​c.315_335dupGGCGGCGGCGGCGGCGGCGGC​(p.Ala106_Ala112dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency: Genomes: not found (cov: 22)
• Consequence: ARX NM_139058.3 disruptive_inframe_insertion
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:12
• Conservation: PhyloP100: 1.33

Genes affected

ARX (HGNC:18060): (aristaless related homeobox) This gene is a homeobox-containing gene expressed during development. The expressed protein contains two conserved domains, a C-peptide (or aristaless domain) and the prd-like class homeobox domain. It is a member of the group-II aristaless-related protein family whose members are expressed primarily in the central and/or peripheral nervous system. This gene is thought to be involved in CNS development. Expansion of a polyalanine tract and other mutations in this gene cause X-linked cognitive disability and epilepsy. [provided by RefSeq, Jul 2016]

ACMG classification

Verdict is Likely_pathogenic. Variant got 9 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant X-25013659-T-TGCCGCCGCCGCCGCCGCCGCC is Pathogenic according to our data. Variant chrX-25013659-T-TGCCGCCGCCGCCGCCGCCGCC is described in ClinVar as [Likely_pathogenic]. Clinvar id is 11186.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP3: Nonframeshift variant in repetitive region in NM_139058.3

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARX	NM_139058.3	c.315_335dupGGCGGCGGCGGCGGCGGCGGC	p.Ala106_Ala112dup	disruptive_inframe_insertion	Exon 2 of 5	ENST00000379044.5	NP_620689.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARX	ENST00000379044.5	c.315_335dupGGCGGCGGCGGCGGCGGCGGC	p.Ala106_Ala112dup	disruptive_inframe_insertion	Exon 2 of 5	1	NM_139058.3	ENSP00000368332.4

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 22

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:12

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Developmental and epileptic encephalopathy, 1 Pathogenic:3

Jul 31, 2007

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

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Centogene AG - the Rare Disease Company

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 22, 2022

3billion, Medical Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant has been reported as pathogenic more than twice (ClinVar ID: VCV000011186), along with assertion criteria based on the ACMG guidelines. It is absent from the gnomAD v2.1.1 dataset. Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline. -

not provided Pathogenic:3

Jan 28, 2021

Athena Diagnostics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This duplication results in the addition of 7 alanines within the first poly-alanine tract of the ARX gene, and has been referred to by various nomenclatures in published literature, including (GCG)10+7, c.333_334(GCG)7, and c.330ins(GCG)7 (see PMID: 26029707). This variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). This variant has been identified in multiple unrelated males with ARX-related disease, including both maternally inherited and apparent de novo cases. Assessment of experimental evidence suggests this variant results in abnormal protein function. Expression of this variant results in protein mislocalization and aggregation, and increased cell death (PMID: PMID: 17490853, 21496008). Mice carrying this variant display severe seizures and learning impairments (PMID: 19605412). -

Sep 07, 2016

Eurofins Ntd Llc (ga)

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is the most common pathogenic repeat allele of the first poly-alanine tract (referred to as PA1) within exon 2 of the ARX gene. This repeat allele has been reported with various nomenclatures in multiple individuals with ARX-related diseases including intellectual disability, Ohtahara syndrome and EIEE.1-4 References: Stromme et al. Nat Genet. 2002 Apr;30(4):441-5 Absoud et al. Dev Med Child Neurol. 2010 Mar;52(3):305-7. Kitamura et al. Hum Mol Genet. 2009 Oct 1;18(19):3708-24 Marques et al. Mol Genet Genomic Med. 2015 May;3(3):203-14 -

Dec 01, 2023

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Alanine repeat expansion in the first polyalanine tract of the ARX protein, extending the allele to 23 repeats; Published functional studies demonstrate a damaging effect as expansions in the first polyalanine repeat track are suggested to interfere with ARX-related regulation of KDM5C resulting in the misregulation of numerous downstream processes (PMID: 23246292); Published mouse models have also displayed severe seizures and learning disabilities (PMID: 19605412); Not observed in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 11889467, 22628459, 36571524, 17664401, 23583054, 21496008, 15726411, 26029707, 17490853, 20300201, 23246292, 19605412) -

Inborn genetic diseases Pathogenic:1

Apr 08, 2017

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.315_335dup21 pathogenic mutation (also known as p.A109_A115dup), located in coding exon 2 of the ARX gene, results from an in-frame duplication of 21 nucleotides at nucleotide positions 315 to 335. This results in the duplication of 7 extra residues (AAAAAAA) between codons 109 and 115, leading to an expansion of the first polyalanine tract from 16 to 23. This mutation was originally reported as (GCG)10+7 in two families with X-linked infantile spasm syndrome and West syndrome (Strømme et al. Nat Genet. 2002 Apr;30(4):441-5). De novo occurrences of the mutation (described as c.333_334ins[GCG]7 and c.333_335dup(GGC)7) were also reported in multiple patients with mental retardation, dystonia, infantile-onset refractory epilepsy, and/or developmental delay (Guerrini et al. Neurology. 2007 Jul 31;69(5):427-33; Mirzaa et al. Pediatr. Neurol. 2013 May;48(5):367-77). In addition, expression of ARX protein harboring the 23 alanines was shown to cause protein aggregation, cell death, and mislocalization (Nasrallah et al. J Cell Biol. 2004 Nov 8;167(3):411-6; Fullston et al. Clin. Genet. 2011 Dec;80(6):510-22). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Intellectual disability, X-linked, with or without seizures, arx-related Pathogenic:1

Jul 10, 2023

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

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: ARX c.315_335dup21 (p.Ala109_Ala115dup) results in an in-frame duplication that is predicted to duplicate 7 amino acids into the encoded protein, resulting in an expansion of the first polyalanine tract of Arx. The variant was absent in 106683 control chromosomes (gnomAD v3.1.2). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.315_335dup21 has been reported in the literature in multiple hemizygotes affected with AXR-Related Disorder, including several de novo occurrences (e.g., Mirzaa_2013, Bertoli-Avella_2021). These data indicate that the variant is very likely be associated with disease. Several publications report experimental evidence evaluating an impact on protein function, finding that the variant lead to protein aggregation, mislocalization, and increased cell death in vitro (e.g., Masrallah_2004), and a mouse model of the variant displayed seizures as well as learning and memory defects (e.g., Kitamura_2009). The following publications have been ascertained in the context of this evaluation (PMID: 32860008, 23583054, 15533998, 19605412). Six submitters have reported clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Intellectual disability, X-linked, with or without seizures, arx-related;C3463992:Developmental and epileptic encephalopathy, 1 Pathogenic:1

Jun 04, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant, c.315_335dup, results in the insertion of 7 amino acid(s) of the ARX protein (p.Ala109_Ala115dup), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the gnomAD database. This variant has been observed in individual(s) with early-onset epilepsy (PMID: 11889467, 15726411, 17664401, 26029707). In at least one individual the variant was observed to be de novo. It has also been observed to segregate with disease in related individuals. This variant is also known as c.333_334ins(GCG)7 and (GCG)10+7. ClinVar contains an entry for this variant (Variation ID: 11186). Algorithms developed to predict the effect of variants on gene product structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects ARX function (PMID: 17490853, 23246292). For these reasons, this variant has been classified as Pathogenic. -

West syndrome Pathogenic:1

Dec 15, 2023

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Zygosity: Hemizygosis -

X-linked lissencephaly with abnormal genitalia Pathogenic:1

Nov 06, 2014

Genetic Services Laboratory, University of Chicago

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Corpus callosum agenesis-abnormal genitalia syndrome;C0796244:Intellectual disability, X-linked, with or without seizures, arx-related;C0796250:Partington syndrome;C1846171:X-linked lissencephaly with abnormal genitalia;C3463992:Developmental and epileptic encephalopathy, 1 Pathogenic:1

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Juno Genomics, Hangzhou Juno Genomics, Inc

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PM2_Supporting+PS4+PP1_Strong+PS3+PM4 -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs387906492; hg19: chrX-25031776;