NC_000005.9:g.(?_178413111)_(179263593_?)dup AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 9, 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:: RCV003107771.4

Allele description [Variation Report for NC_000005.9:g.(?_178413111)_(179263593_?)dup]

NC_000005.9:g.(?_178413111)_(179263593_?)dup

Genes:

ADAMTS2:ADAM metallopeptidase with thrombospondin type 1 motif 2 [Gene - OMIM - HGNC]
RUFY1:RUN and FYVE domain containing 1 [Gene - OMIM - HGNC]
SPATA31J1:SPATA31 subfamily J member 1 [Gene - HGNC]
MGAT4B:alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase B [Gene - OMIM - HGNC]
CANX:calnexin [Gene - OMIM - HGNC]
CBY3:chibby family member 3 [Gene - OMIM - HGNC]
GRM6:glutamate metabotropic receptor 6 [Gene - OMIM - HGNC]
HNRNPH1:heterogeneous nuclear ribonucleoprotein H1 [Gene - OMIM - HGNC]
LTC4S:leukotriene C4 synthase [Gene - OMIM - HGNC]
MAML1:mastermind like transcriptional coactivator 1 [Gene - OMIM - HGNC]
SQSTM1:sequestosome 1 [Gene - OMIM - HGNC]
ZNF354C:zinc finger protein 354C [Gene - OMIM - HGNC]
ZNF879:zinc finger protein 879 [Gene - HGNC]

Variant type:

Duplication

Cytogenetic location:

5q35.3

Genomic location:

Chr5: 178413111 - 179263593 (on Assembly GRCh37)

Preferred name:

NC_000005.9:g.(?_178413111)_(179263593_?)dup

HGVS:

NC_000005.9:g.(?_178413111)_(179263593_?)dup

Condition(s)

Name:: Frontotemporal dementia and/or amyotrophic lateral sclerosis 1 (FTDALS1)
Synonyms:: Frontotemporal dementia with motor neuron disease 1
Identifiers:: MONDO: MONDO:0007105; MedGen: C5779877; Orphanet: 275872; OMIM: 105550

Name:: Paget disease of bone 2, early-onset (PDB2)
Synonyms:: Paget disease of bone 2
Identifiers:: MONDO: MONDO:0011183; MedGen: C4085251; OMIM: 602080

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003792533	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 9, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 26925868, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003792533

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 9, 2022)

germline

clinical testing

PubMed (2)
[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

Analysis copy number variation of Chinese children in early-onset epileptic encephalopathies with unknown cause.

Ma Y, Chen C, Wang Y, Wu L, He F, Chen C, Zhang C, Deng X, Yang L, Chen Y, Wu L, Yin F, Peng J.

Clin Genet. 2016 Nov;90(5):428-436. doi: 10.1111/cge.12768. Epub 2016 Apr 26.

PubMed [citation]

PMID:: 26925868

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, SCV003792533.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

A copy number gain of the genomic region encompassing the full coding sequence of the SQSTM1 gene has been identified. 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. Isolated whole-gene copy number gains of SQSTM1 have not been reported in the literature. However, larger copy number events that include this gene have been reported (PMID: 26925868). 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: Sep 29, 2024

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