NM_006420.3(ARFGEF2):c.1958+1G>A AND Periventricular heterotopia with microcephaly, autosomal recessive

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 1, 2013
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV000074502.4

Allele description [Variation Report for NM_006420.3(ARFGEF2):c.1958+1G>A]

NM_006420.3(ARFGEF2):c.1958+1G>A

Gene:

ARFGEF2:ADP ribosylation factor guanine nucleotide exchange factor 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

20q13.13

Genomic location:

Preferred name:

NM_006420.3(ARFGEF2):c.1958+1G>A

HGVS:

NC_000020.11:g.48976200G>A
NG_011490.2:g.59463G>A
NM_001410846.1:c.1955+1G>A
NM_006420.3:c.1958+1G>AMANE SELECT
NC_000020.10:g.47592737G>A
NM_006420.2:c.1958+1G>A

Nucleotide change:

IVS14DS, G-A, +1

Links:

OMIM: 605371.0003; dbSNP: rs398122523

NCBI 1000 Genomes Browser:

rs398122523

Molecular consequence:

NM_001410846.1:c.1955+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_006420.3:c.1958+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: Periventricular heterotopia with microcephaly, autosomal recessive (ARPHM)
Synonyms:: PERIVENTRICULAR NODULAR HETEROTOPIA 2; Heterotopia, periventricular, autosomal recessive; Periventricular heterotopia with microcephaly
Identifiers:: MONDO: MONDO:0011966; MedGen: C1842563; Orphanet: 2149; OMIM: 608097

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000108587	OMIM	no assertion criteria provided	Pathogenic (Nov 1, 2013)	germline	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000108587

OMIM

no assertion criteria provided

Pathogenic
(Nov 1, 2013)

germline

literature only

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

West syndrome, microcephaly, grey matter heterotopia and hypoplasia of corpus callosum due to a novel ARFGEF2 mutation.

Banne E, Atawneh O, Henneke M, Brockmann K, Gärtner J, Elpeleg O, Edvardson S.

J Med Genet. 2013 Nov;50(11):772-5. doi: 10.1136/jmedgenet-2013-101752. Epub 2013 Jun 28.

PubMed [citation]

PMID:: 23812912

Details of each submission

From OMIM, SCV000108587.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In 5 members of a consanguineous Palestinian family with periventricular heterotopia with microcephaly (608097), Banne et al. (2013) identified a homozygous G-to-A transition in intron 14 of the ARFGEF2 gene (c.1958+1G-A), resulting in the elimination of 44 nucleotides of the patients' cDNA. The mutation was found by homozygosity mapping combined with whole-exome sequencing and segregated with the disorder in the family. It was not present in the dbSNP (build 132) database or among in-house database variants. The patients had severely delayed psychomotor development, microcephaly, and infantile seizures associated with hypsarrhythmia on EEG, consistent with a clinical diagnosis of West syndrome. Brain MRI showed periventricular heterotopia and thin corpus callosum. No other organ systems were affected.

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

Last Updated: Jun 10, 2023

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