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NC_000011.9:g.(?_532616)_(2906985_?)dup AND Neuronal ceroid lipofuscinosis

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 31, 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:
RCV001032557.1

Allele description [Variation Report for NC_000011.9:g.(?_532616)_(2906985_?)dup]

NC_000011.9:g.(?_532616)_(2906985_?)dup

Genes:
  • BRSK2:BR serine/threonine kinase 2 [Gene - OMIM - HGNC]
  • CD151:CD151 molecule (Raph blood group) [Gene - OMIM - HGNC]
  • CD81:CD81 molecule [Gene - OMIM - HGNC]
  • DEAF1:DEAF1 transcription factor [Gene - OMIM - HGNC]
  • EPS8L2:EPS8 like 2 [Gene - OMIM - HGNC]
  • H19:H19 imprinted maternally expressed transcript [Gene - OMIM - HGNC]
  • HRAS:HRas proto-oncogene, GTPase [Gene - OMIM - HGNC]
  • IGF2-AS:IGF2 antisense RNA [Gene - OMIM - HGNC]
  • INS-IGF2:INS-IGF2 readthrough [Gene - HGNC]
  • KCNQ1DN:KCNQ1 downstream neighbor [Gene - OMIM - HGNC]
  • KCNQ1OT1:KCNQ1 opposite strand/antisense transcript 1 [Gene - OMIM - HGNC]
  • LMNTD2-AS1:LMNTD2 antisense RNA 1 [Gene - HGNC]
  • MIR210HG:MIR210 host gene [Gene - HGNC]
  • MOB2:MOB kinase activator 2 [Gene - OMIM - HGNC]
  • PHRF1:PHD and ring finger domains 1 [Gene - OMIM - HGNC]
  • POLR2L:RNA polymerase II, I and III subunit L [Gene - OMIM - HGNC]
  • RASSF7:Ras association domain family member 7 [Gene - OMIM - HGNC]
  • ASCL2:achaete-scute family bHLH transcription factor 2 [Gene - OMIM - HGNC]
  • AP2A2:adaptor related protein complex 2 subunit alpha 2 [Gene - OMIM - HGNC]
  • CDHR5:cadherin related family member 5 [Gene - OMIM - HGNC]
  • CRACR2B:calcium release activated channel regulator 2B [Gene - OMIM - HGNC]
  • CTSD:cathepsin D [Gene - OMIM - HGNC]
  • CEND1:cell cycle exit and neuronal differentiation 1 [Gene - OMIM - HGNC]
  • CHID1:chitinase domain containing 1 [Gene - OMIM - HGNC]
  • C11orf21:chromosome 11 open reading frame 21 [Gene - OMIM - HGNC]
  • CDKN1C:cyclin dependent kinase inhibitor 1C [Gene - OMIM - HGNC]
  • DRD4:dopamine receptor D4 [Gene - OMIM - HGNC]
  • DUSP8:dual specificity phosphatase 8 [Gene - OMIM - HGNC]
  • GATD1:glutamine amidotransferase class 1 domain containing 1 [Gene - HGNC]
  • IGF2:insulin like growth factor 2 [Gene - OMIM - HGNC]
  • INS:insulin [Gene - OMIM - HGNC]
  • IFITM10:interferon induced transmembrane protein 10 [Gene - OMIM - HGNC]
  • IRF7:interferon regulatory factor 7 [Gene - OMIM - HGNC]
  • KRTAP5-1:keratin associated protein 5-1 [Gene - OMIM - HGNC]
  • KRTAP5-2:keratin associated protein 5-2 [Gene - HGNC]
  • KRTAP5-3:keratin associated protein 5-3 [Gene - HGNC]
  • KRTAP5-4:keratin associated protein 5-4 [Gene - HGNC]
  • KRTAP5-5:keratin associated protein 5-5 [Gene - HGNC]
  • KRTAP5-6:keratin associated protein 5-6 [Gene - HGNC]
  • LMNTD2:lamin tail domain containing 2 [Gene - HGNC]
  • LRRC56:leucine rich repeat containing 56 [Gene - OMIM - HGNC]
  • LSP1:lymphocyte specific protein 1 [Gene - OMIM - HGNC]
  • MIR210:microRNA 210 [Gene - OMIM - HGNC]
  • MRPL23:mitochondrial ribosomal protein L23 [Gene - OMIM - HGNC]
  • MUC2:mucin 2, oligomeric mucus/gel-forming [Gene - OMIM - HGNC]
  • MUC5AC:mucin 5AC, oligomeric mucus/gel-forming [Gene - OMIM - HGNC]
  • MUC5B:mucin 5B, oligomeric mucus/gel-forming [Gene - OMIM - HGNC]
  • MUC6:mucin 6, oligomeric mucus/gel-forming [Gene - OMIM - HGNC]
  • PIDD1:p53-induced death domain protein 1 [Gene - OMIM - HGNC]
  • PNPLA2:patatin like phospholipase domain containing 2 [Gene - OMIM - HGNC]
  • KCNQ1:potassium voltage-gated channel subfamily Q member 1 [Gene - OMIM - HGNC]
  • RPLP2:ribosomal protein lateral stalk subunit P2 [Gene - OMIM - HGNC]
  • SCT:secretin [Gene - OMIM - HGNC]
  • SLC25A22:solute carrier family 25 member 22 [Gene - OMIM - HGNC]
  • SYT8:synaptotagmin 8 [Gene - OMIM - HGNC]
  • TSPAN32:tetraspanin 32 [Gene - OMIM - HGNC]
  • TSPAN4:tetraspanin 4 [Gene - OMIM - HGNC]
  • TOLLIP:toll interacting protein [Gene - OMIM - HGNC]
  • TALDO1:transaldolase 1 [Gene - OMIM - HGNC]
  • TRPM5:transient receptor potential cation channel subfamily M member 5 [Gene - OMIM - HGNC]
  • TMEM80:transmembrane protein 80 [Gene - OMIM - HGNC]
  • TNNI2:troponin I2, fast skeletal type [Gene - OMIM - HGNC]
  • TNNT3:troponin T3, fast skeletal type [Gene - OMIM - HGNC]
  • TSSC4:tumor suppressing subtransferable candidate 4 [Gene - OMIM - HGNC]
  • TH:tyrosine hydroxylase [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
11p15.5-15.4
Genomic location:
Chr11: 532616 - 2906985 (on Assembly GRCh37)
Preferred name:
NC_000011.9:g.(?_532616)_(2906985_?)dup
HGVS:
NC_000011.9:g.(?_532616)_(2906985_?)dup

Condition(s)

Name:
Neuronal ceroid lipofuscinosis
Synonyms:
Ceroid storage disease
Identifiers:
MONDO: MONDO:0016295; MedGen: C0027877; Orphanet: 79263; OMIM: PS256730

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001195864Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jan 31, 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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001195864.1

#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 CTSD 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 CTSD-related conditions. 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: Oct 14, 2023