NM_001111125.3(IQSEC2):c.296del (p.His99fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 1, 2017
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:: RCV000485376.1

Allele description [Variation Report for NM_001111125.3(IQSEC2):c.296del (p.His99fs)]

NM_001111125.3(IQSEC2):c.296del (p.His99fs)

Gene:

IQSEC2:IQ motif and Sec7 domain ArfGEF 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xp11.22

Genomic location:

Preferred name:

NM_001111125.3(IQSEC2):c.296del (p.His99fs)

HGVS:

NC_000023.11:g.53320828del
NG_021296.2:g.5523del
NM_001111125.3:c.296delMANE SELECT
NP_001104595.1:p.His99fs
LRG_1194t1:c.296del
LRG_1194:g.5523del
LRG_1194p1:p.His99fs
NC_000023.10:g.53350026del
NM_001111125.1:c.296delA

Protein change:

H99fs

Links:

dbSNP: rs1064793152

NCBI 1000 Genomes Browser:

rs1064793152

Molecular consequence:

NM_001111125.3:c.296del - 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
SCV000565071	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Mar 1, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000565071

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Mar 1, 2017)

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, SCV000565071.4

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

Description

The c.296delA variant in the IQSEC2 gene has been reported previously in an individual with seizures and developmental delay (Yavarna et al., 2015). The c.296delA variant causes a frameshift starting with codon Histidine 99, changes this amino acid to a Proline residue, and creates a premature Stop codon at position 107 of the new reading frame, denoted p.His99ProfsX107. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.296delA variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpret c.296delA 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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