NC_000016.9:g.(?_256302)_(633035_?)del AND Epilepsy

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 19, 2022
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:: RCV003113402.4

Allele description [Variation Report for NC_000016.9:g.(?_256302)_(633035_?)del]

NC_000016.9:g.(?_256302)_(633035_?)del

Genes:

DECR2:2,4-dienoyl-CoA reductase 2 [Gene - OMIM - HGNC]
LUC7L:LUC7 like [Gene - OMIM - HGNC]
NHLRC4:NHL repeat containing 4 [Gene - HGNC]
NME4:NME/NM23 nucleoside diphosphate kinase 4 [Gene - OMIM - HGNC]
RAB11FIP3:RAB11 family interacting protein 3 [Gene - OMIM - HGNC]
ARHGDIG:Rho GDP dissociation inhibitor gamma [Gene - OMIM - HGNC]
AXIN1:axin 1 [Gene - OMIM - HGNC]
CAPN15:calpain 15 [Gene - OMIM - HGNC]
FAM234A:family with sequence similarity 234 member A [Gene - HGNC]
MRPL28:mitochondrial ribosomal protein L28 [Gene - OMIM - HGNC]
PIGQ:phosphatidylinositol glycan anchor biosynthesis class Q [Gene - OMIM - HGNC]
PGAP6:post-GPI attachment to proteins 6 [Gene - OMIM - HGNC]
PRR35:proline rich 35 [Gene - HGNC]
PDIA2:protein disulfide isomerase family A member 2 [Gene - OMIM - HGNC]
RGS11:regulator of G protein signaling 11 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16p13.3

Genomic location:

Chr16: 256302 - 633035 (on Assembly GRCh37)

Preferred name:

NC_000016.9:g.(?_256302)_(633035_?)del

HGVS:

NC_000016.9:g.(?_256302)_(633035_?)del

Condition(s)

Name:: Epilepsy
Synonyms:: Seizure Disorders; Seizure disorder
Identifiers:: MONDO: MONDO:0005027; MeSH: D004827; MedGen: C0014544

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003793670	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 19, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 24463883, 25558065, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003793670

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 19, 2022)

germline

clinical testing

PubMed (3)
[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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Clinical whole-genome sequencing in severe early-onset epilepsy reveals new genes and improves molecular diagnosis.

Martin HC, Kim GE, Pagnamenta AT, Murakami Y, Carvill GL, Meyer E, Copley RR, Rimmer A, Barcia G, Fleming MR, Kronengold J, Brown MR, Hudspith KA, Broxholme J, Kanapin A, Cazier JB, Kinoshita T, Nabbout R; WGS500 Consortium, Bentley D, McVean G, Heavin S, et al.

Hum Mol Genet. 2014 Jun 15;23(12):3200-11. doi: 10.1093/hmg/ddu030. Epub 2014 Jan 25.

PubMed [citation]

PMID:: 24463883
PMCID:: PMC4030775

Accelerating novel candidate gene discovery in neurogenetic disorders via whole-exome sequencing of prescreened multiplex consanguineous families.

Alazami AM, Patel N, Shamseldin HE, Anazi S, Al-Dosari MS, Alzahrani F, Hijazi H, Alshammari M, Aldahmesh MA, Salih MA, Faqeih E, Alhashem A, Bashiri FA, Al-Owain M, Kentab AY, Sogaty S, Al Tala S, Temsah MH, Tulbah M, Aljelaify RF, Alshahwan SA, Seidahmed MZ, et al.

Cell Rep. 2015 Jan 13;10(2):148-61. doi: 10.1016/j.celrep.2014.12.015. Epub 2014 Dec 31.

PubMed [citation]

PMID:: 25558065

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003793670.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the PIGQ gene has been identified. Loss-of-function variants in PIGQ are known to be pathogenic (PMID: 24463883, 25558065). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with PIGQ-related conditions. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024

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