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NC_000006.11:g.(?_33131435)_(33419703_?)dup AND Intellectual disability, autosomal dominant 5

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 20, 2018
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:
RCV000817954.3

Allele description [Variation Report for NC_000006.11:g.(?_33131435)_(33419703_?)dup]

NC_000006.11:g.(?_33131435)_(33419703_?)dup

Genes:
  • HCG25:HLA complex group 25 [Gene - HGNC]
  • LOC129389491:MPRA-validated peak5757 silencer [Gene]
  • PHF1:PHD finger protein 1 [Gene - OMIM - HGNC]
  • SYNGAP1-AS1:SYNGAP1 antisense RNA 1 [Gene - HGNC]
  • LOC123620086:Sharpr-MPRA regulatory region 3790 [Gene]
  • TAPBP:TAP binding protein [Gene - OMIM - HGNC]
  • VPS52:VPS52 subunit of GARP complex [Gene - OMIM - HGNC]
  • WDR46:WD repeat domain 46 [Gene - OMIM - HGNC]
  • B3GALT4:beta-1,3-galactosyltransferase 4 [Gene - OMIM - HGNC]
  • COL11A2:collagen type XI alpha 2 chain [Gene - OMIM - HGNC]
  • CUTA:cutA divalent cation tolerance homolog [Gene - OMIM - HGNC]
  • DAXX:death domain associated protein [Gene - OMIM - HGNC]
  • HSD17B8:hydroxysteroid 17-beta dehydrogenase 8 [Gene - OMIM - HGNC]
  • KIFC1:kinesin family member C1 [Gene - OMIM - HGNC]
  • MIR219A1:microRNA 219a-1 [Gene - OMIM - HGNC]
  • MIR5004:microRNA 5004 [Gene - HGNC]
  • MIR6834:microRNA 6834 [Gene - HGNC]
  • MIR6873:microRNA 6873 [Gene - HGNC]
  • PFDN6:prefoldin subunit 6 [Gene - OMIM - HGNC]
  • RGL2:ral guanine nucleotide dissociation stimulator like 2 [Gene - OMIM - HGNC]
  • RXRB:retinoid X receptor beta [Gene - OMIM - HGNC]
  • RPS18:ribosomal protein S18 [Gene - OMIM - HGNC]
  • RING1:ring finger protein 1 [Gene - OMIM - HGNC]
  • SMIM40:small integral membrane protein 40 [Gene - HGNC]
  • SLC39A7:solute carrier family 39 member 7 [Gene - OMIM - HGNC]
  • SYNGAP1:synaptic Ras GTPase activating protein 1 [Gene - OMIM - HGNC]
  • LOC105375022:uncharacterized LOC105375022 [Gene]
  • ZBTB22:zinc finger and BTB domain containing 22 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
6p21.32
Genomic location:
Preferred name:
NC_000006.11:g.(?_33131435)_(33419703_?)dup
HGVS:
NC_000006.11:g.(?_33131435)_(33419703_?)dup

Condition(s)

Name:
Intellectual disability, autosomal dominant 5 (MRD5)
Synonyms:
INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL DOMINANT 5
Identifiers:
MONDO: MONDO:0012960; MedGen: C2675473; OMIM: 612621

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000958541Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Aug 20, 2018) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000958541.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant results in a copy number gain of the genomic region encompassing the full coding sequence of the SYNGAP1 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 SYNGAP1-related disease. 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024