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NC_000001.10:g.(?_955543)_(3350385_?)del AND Left ventricular noncompaction 8

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 22, 2019
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:
RCV001033604.1

Allele description

NC_000001.10:g.(?_955543)_(3350385_?)del

Genes:
  • ATAD3A:ATPase family AAA domain containing 3A [Gene - OMIM - HGNC]
  • ATAD3B:ATPase family AAA domain containing 3B [Gene - OMIM - HGNC]
  • ATAD3C:ATPase family AAA domain containing 3C [Gene - OMIM - HGNC]
  • ACAP3:ArfGAP with coiled-coil, ankyrin repeat and PH domains 3 [Gene - HGNC]
  • C1QTNF12:C1q and TNF related 12 [Gene - OMIM - HGNC]
  • FAAP20:FA core complex associated protein 20 [Gene - OMIM - HGNC]
  • GNB1:G protein subunit beta 1 [Gene - OMIM - HGNC]
  • MIB2:MIB E3 ubiquitin protein ligase 2 [Gene - OMIM - HGNC]
  • MORN1:MORN repeat containing 1 [Gene - HGNC]
  • NADK:NAD kinase [Gene - OMIM - HGNC]
  • PRDM16:PR/SET domain 16 [Gene - OMIM - HGNC]
  • SKI:SKI proto-oncogene [Gene - OMIM - HGNC]
  • SSU72:SSU72 homolog, RNA polymerase II CTD phosphatase [Gene - OMIM - HGNC]
  • TNFRSF14:TNF receptor superfamily member 14 [Gene - OMIM - HGNC]
  • TNFRSF18:TNF receptor superfamily member 18 [Gene - OMIM - HGNC]
  • TNFRSF4:TNF receptor superfamily member 4 [Gene - OMIM - HGNC]
  • ACTRT2:actin related protein T2 [Gene - OMIM - HGNC]
  • AGRN:agrin [Gene - OMIM - HGNC]
  • ANKRD65:ankyrin repeat domain 65 [Gene - HGNC]
  • AURKAIP1:aurora kinase A interacting protein 1 [Gene - OMIM - HGNC]
  • B3GALT6:beta-1,3-galactosyltransferase 6 [Gene - OMIM - HGNC]
  • CALML6:calmodulin like 6 [Gene - OMIM - HGNC]
  • CPTP:ceramide-1-phosphate transfer protein [Gene - OMIM - HGNC]
  • C1orf159:chromosome 1 open reading frame 159 [Gene - HGNC]
  • CFAP74:cilia and flagella associated protein 74 [Gene - OMIM - HGNC]
  • CCNL2:cyclin L2 [Gene - OMIM - HGNC]
  • CDK11A:cyclin dependent kinase 11A [Gene - OMIM - HGNC]
  • CDK11B:cyclin dependent kinase 11B [Gene - OMIM - HGNC]
  • DVL1:dishevelled segment polarity protein 1 [Gene - OMIM - HGNC]
  • FNDC10:fibronectin type III domain containing 10 [Gene - HGNC]
  • GABRD:gamma-aminobutyric acid type A receptor subunit delta [Gene - OMIM - HGNC]
  • HES5:hes family bHLH transcription factor 5 [Gene - OMIM - HGNC]
  • INTS11:integrator complex subunit 11 [Gene - OMIM - HGNC]
  • MMP23B:matrix metallopeptidase 23B [Gene - OMIM - HGNC]
  • MXRA8:matrix remodeling associated 8 [Gene - OMIM - HGNC]
  • MMEL1:membrane metalloendopeptidase like 1 [Gene - OMIM - HGNC]
  • MIR200A:microRNA 200a [Gene - OMIM - HGNC]
  • MIR200B:microRNA 200b [Gene - OMIM - HGNC]
  • MIR429:microRNA 429 [Gene - OMIM - HGNC]
  • MRPL20:mitochondrial ribosomal protein L20 [Gene - OMIM - HGNC]
  • PANK4:pantothenate kinase 4 (inactive) [Gene - OMIM - HGNC]
  • PRXL2B:peroxiredoxin like 2B [Gene - HGNC]
  • PEX10:peroxisomal biogenesis factor 10 [Gene - OMIM - HGNC]
  • PLCH2:phospholipase C eta 2 [Gene - OMIM - HGNC]
  • PRKCZ:protein kinase C zeta [Gene - OMIM - HGNC]
  • PUSL1:pseudouridine synthase like 1 [Gene - HGNC]
  • RER1:retention in endoplasmic reticulum sorting receptor 1 [Gene - OMIM - HGNC]
  • RNF223:ring finger protein 223 [Gene - HGNC]
  • SCNN1D:sodium channel epithelial 1 subunit delta [Gene - OMIM - HGNC]
  • SLC35E2A:solute carrier family 35 member E2A [Gene - HGNC]
  • SLC35E2B:solute carrier family 35 member E2B [Gene - OMIM - HGNC]
  • SDF4:stromal cell derived factor 4 [Gene - OMIM - HGNC]
  • TAS1R3:taste 1 receptor member 3 [Gene - OMIM - HGNC]
  • TTC34:tetratricopeptide repeat domain 34 [Gene - HGNC]
  • TMEM240:transmembrane protein 240 [Gene - OMIM - HGNC]
  • TMEM52:transmembrane protein 52 [Gene - HGNC]
  • TMEM88B:transmembrane protein 88B [Gene - HGNC]
  • TTLL10:tubulin tyrosine ligase like 10 [Gene - HGNC]
  • UBE2J2:ubiquitin conjugating enzyme E2 J2 [Gene - OMIM - HGNC]
  • VWA1:von Willebrand factor A domain containing 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
1p36.33-36.32
Genomic location:
Chr1: 955543 - 3350385 (on Assembly GRCh37)
Preferred name:
NC_000001.10:g.(?_955543)_(3350385_?)del
HGVS:
NC_000001.10:g.(?_955543)_(3350385_?)del

Condition(s)

Name:
Left ventricular noncompaction 8 (LVNC8)
Identifiers:
MONDO: MONDO:0014152; MedGen: C3809288; Orphanet: 154; Orphanet: 54260; OMIM: 615373

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001196911Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(May 22, 2019) 		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 Invitae, SCV001196911.1

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

Description

A gross deletion of the genomic region encompassing the full coding sequence of the PRDM16 gene has been identified. The boundaries of this event are unknown as the deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals with PRDM16-related conditions. The current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in PRDM16 cause 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: Mar 26, 2023