NM_006421.5(ARFGEF1):c.3592-2A>G AND multiple conditions

Germline classification:: Pathogenic (1 submission)
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:: RCV001290723.2

Allele description [Variation Report for NM_006421.5(ARFGEF1):c.3592-2A>G]

NM_006421.5(ARFGEF1):c.3592-2A>G

Gene:

ARFGEF1:ADP ribosylation factor guanine nucleotide exchange factor 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q13.2

Genomic location:

Preferred name:

NM_006421.5(ARFGEF1):c.3592-2A>G

HGVS:

NC_000008.11:g.67227600T>C
NM_001413184.1:c.3592-2A>G
NM_001413185.1:c.3592-2A>G
NM_001413186.1:c.3592-2A>G
NM_001413187.1:c.3592-2A>G
NM_001413188.1:c.2992-2A>G
NM_001413189.1:c.3592-2A>G
NM_001413190.1:c.3586-2A>G
NM_001413191.1:c.3592-2A>G
NM_001413192.1:c.3592-2A>G
NM_001413193.1:c.2992-2A>G
NM_001413194.1:c.3592-2A>G
NM_001413195.1:c.3592-2A>G
NM_001413196.1:c.2167-2A>G
NM_001413197.1:c.2992-2A>G
NM_006421.5:c.3592-2A>GMANE SELECT
NC_000008.10:g.68139835T>C
NM_006421.4:c.3592-2A>G

Links:

dbSNP: rs1839416809

NCBI 1000 Genomes Browser:

rs1839416809

Molecular consequence:

NM_001413184.1:c.3592-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001413185.1:c.3592-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001413186.1:c.3592-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001413187.1:c.3592-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001413188.1:c.2992-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001413189.1:c.3592-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001413190.1:c.3586-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001413191.1:c.3592-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001413192.1:c.3592-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001413193.1:c.2992-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001413194.1:c.3592-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001413195.1:c.3592-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001413196.1:c.2167-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001413197.1:c.2992-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_006421.5:c.3592-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:: Global developmental delay (DD)
Identifiers:: MedGen: C0557874; Human Phenotype Ontology: HP:0001263

Name:: Delayed speech and language development
Identifiers:: MedGen: C0454644; Human Phenotype Ontology: HP:0000750

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001478860	Equipe Genetique des Anomalies du Developpement, Université de Bourgogne	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	de novo	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25741868, 34113008

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001478860

Equipe Genetique des Anomalies du Developpement, Université de Bourgogne

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic

de novo

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	de novo	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Haploinsufficiency of ARFGEF1 is associated with developmental delay, intellectual disability, and epilepsy with variable expressivity.

Thomas Q, Gautier T, Marafi D, Besnard T, Willems M, Moutton S, Isidor B, Cogné B, Conrad S, Tenconi R, Iascone M, Sorlin A, Masurel A, Dabir T, Jackson A, Banka S, Delanne J, Lupski JR, Saadi NW, Alkuraya FS, Zahrani FA, Agrawal PB, et al.

Genet Med. 2021 Oct;23(10):1901-1911. doi: 10.1038/s41436-021-01218-6. Epub 2021 Jun 10.

PubMed [citation]

PMID:: 34113008

Details of each submission

From Equipe Genetique des Anomalies du Developpement, Université de Bourgogne, SCV001478860.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

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

Last Updated: Aug 13, 2023

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