NC_000017.10:g.(?_6328780)_(7128416_?)dup AND Developmental and epileptic encephalopathy, 25

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 29, 2020
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:: RCV001320321.1

Allele description [Variation Report for NC_000017.10:g.(?_6328780)_(7128416_?)dup]

NC_000017.10:g.(?_6328780)_(7128416_?)dup

Genes:

BCL6B:BCL6B transcription repressor [Gene - OMIM - HGNC]
CLEC10A:C-type lectin domain containing 10A [Gene - OMIM - HGNC]
FBXO39:F-box protein 39 [Gene - OMIM - HGNC]
KIAA0753:KIAA0753 [Gene - OMIM - HGNC]
PIMREG:PICALM interacting mitotic regulator [Gene - OMIM - HGNC]
PITPNM3:PITPNM family member 3 [Gene - OMIM - HGNC]
XAF1:XIAP associated factor 1 [Gene - OMIM - HGNC]
ACADVL:acyl-CoA dehydrogenase very long chain [Gene - OMIM - HGNC]
ALOX12:arachidonate 12-lipoxygenase, 12S type [Gene - OMIM - HGNC]
AIPL1:aryl hydrocarbon receptor interacting protein like 1 [Gene - OMIM - HGNC]
ASGR1:asialoglycoprotein receptor 1 [Gene - OMIM - HGNC]
ASGR2:asialoglycoprotein receptor 2 [Gene - OMIM - HGNC]
C17orf100:chromosome 17 open reading frame 100 [Gene - HGNC]
C17orf49:chromosome 17 open reading frame 49 [Gene - OMIM - HGNC]
DLG4:discs large MAGUK scaffold protein 4 [Gene - OMIM - HGNC]
MED31:mediator complex subunit 31 [Gene - HGNC]
MIR195:microRNA 195 [Gene - OMIM - HGNC]
MIR497HG:mir-497-195 cluster host gene [Gene - HGNC]
RNASEK:ribonuclease K [Gene - OMIM - HGNC]
SLC13A5:solute carrier family 13 member 5 [Gene - OMIM - HGNC]
SLC16A11:solute carrier family 16 member 11 [Gene - OMIM - HGNC]
SLC16A13:solute carrier family 16 member 13 [Gene - HGNC]
TEKT1:tektin 1 [Gene - OMIM - HGNC]
TXNDC17:thioredoxin domain containing 17 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

17p13.2-13.1

Genomic location:

Chr17: 6328780 - 7128416 (on Assembly GRCh37)

Preferred name:

NC_000017.10:g.(?_6328780)_(7128416_?)dup

HGVS:

NC_000017.10:g.(?_6328780)_(7128416_?)dup

Condition(s)

Name:: Developmental and epileptic encephalopathy, 25 (DEE25)
Synonyms:: Epileptic encephalopathy, early infantile, 25; Developmental and epileptic encephalopathy 25, with amelogenesis imperfecta; Epileptic encephalopathy, early infantile, 25, with amelogenesis imperfecta
Identifiers:: MONDO: MONDO:0014392; MedGen: C4014621; Orphanet: 442835; OMIM: 615905

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001511101	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 29, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001511101

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 29, 2020)

germline

clinical testing

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001511101.1

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

Description

This variant results in a copy number gain of the genomic region encompassing the full coding sequence of the SLC13A5 gene. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals with SLC13A5-related conditions. Experimental studies are not available for this variant, and the functional significance of a copy number gain of this gene is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Aug 5, 2023

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