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NC_000021.8:g.(?_32439271)_(39212984_?)dup AND Amyotrophic lateral sclerosis type 1

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 7, 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:
RCV001939883.11

Allele description [Variation Report for NC_000021.8:g.(?_32439271)_(39212984_?)dup]

NC_000021.8:g.(?_32439271)_(39212984_?)dup

Genes:
  • ATP5PO:ATP synthase peripheral stalk subunit OSCP [Gene - OMIM - HGNC]
  • DONSON:DNA replication fork stabilization factor DONSON [Gene - OMIM - HGNC]
  • DOP1B:DOP1 leucine zipper like protein B [Gene - OMIM - HGNC]
  • DNAJC28:DnaJ heat shock protein family (Hsp40) member C28 [Gene - HGNC]
  • MIS18A:MIS18 kinetochore protein A [Gene - OMIM - HGNC]
  • MORC3:MORC family CW-type zinc finger 3 [Gene - OMIM - HGNC]
  • PAXBP1:PAX3 and PAX7 binding protein 1 [Gene - OMIM - HGNC]
  • RUNX1:RUNX family transcription factor 1 [Gene - OMIM - HGNC]
  • SETD4:SET domain containing 4 [Gene - HGNC]
  • SIM2:SIM bHLH transcription factor 2 [Gene - OMIM - HGNC]
  • SON:SON DNA and RNA binding protein [Gene - OMIM - HGNC]
  • SCAF4:SR-related CTD associated factor 4 [Gene - OMIM - HGNC]
  • TIAM1:TIAM Rac1 associated GEF 1 [Gene - OMIM - HGNC]
  • URB1:URB1 ribosome biogenesis homolog [Gene - OMIM - HGNC]
  • VPS26C:VPS26 endosomal protein sorting factor C [Gene - OMIM - HGNC]
  • CBR1:carbonyl reductase 1 [Gene - OMIM - HGNC]
  • CBR3:carbonyl reductase 3 [Gene - OMIM - HGNC]
  • CLIC6:chloride intracellular channel 6 [Gene - OMIM - HGNC]
  • CHAF1B:chromatin assembly factor 1 subunit B [Gene - OMIM - HGNC]
  • CFAP298:cilia and flagella associated protein 298 [Gene - OMIM - HGNC]
  • CLDN14:claudin 14 [Gene - OMIM - HGNC]
  • CRYZL1:crystallin zeta like 1 [Gene - OMIM - HGNC]
  • DYRK1A:dual specificity tyrosine phosphorylation regulated kinase 1A [Gene - OMIM - HGNC]
  • EVA1C:eva-1 homolog C [Gene - HGNC]
  • EPCIP:exosomal polycystin 1 interacting protein [Gene - HGNC]
  • HLCS:holocarboxylase synthetase [Gene - OMIM - HGNC]
  • HUNK:hormonally up-regulated Neu-associated kinase [Gene - OMIM - HGNC]
  • IFNAR1:interferon alpha and beta receptor subunit 1 [Gene - OMIM - HGNC]
  • IFNAR2:interferon alpha and beta receptor subunit 2 [Gene - OMIM - HGNC]
  • IFNGR2:interferon gamma receptor 2 [Gene - OMIM - HGNC]
  • IL10RB:interleukin 10 receptor subunit beta [Gene - OMIM - HGNC]
  • ITSN1:intersectin 1 [Gene - OMIM - HGNC]
  • MRAP:melanocortin 2 receptor accessory protein [Gene - OMIM - HGNC]
  • MRPS6:mitochondrial ribosomal protein S6 [Gene - OMIM - HGNC]
  • OLIG1:oligodendrocyte transcription factor 1 [Gene - OMIM - HGNC]
  • OLIG2:oligodendrocyte transcription factor 2 [Gene - OMIM - HGNC]
  • PIGP:phosphatidylinositol glycan anchor biosynthesis class P [Gene - OMIM - HGNC]
  • GART:phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase [Gene - OMIM - HGNC]
  • KCNJ6:potassium inwardly rectifying channel subfamily J member 6 [Gene - OMIM - HGNC]
  • KCNE1:potassium voltage-gated channel subfamily E regulatory subunit 1 [Gene - OMIM - HGNC]
  • KCNE2:potassium voltage-gated channel subfamily E regulatory subunit 2 [Gene - OMIM - HGNC]
  • RCAN1:regulator of calcineurin 1 [Gene - OMIM - HGNC]
  • RIPPLY3:ripply transcriptional repressor 3 [Gene - OMIM - HGNC]
  • SMIM11:small integral membrane protein 11 [Gene - HGNC]
  • SLC5A3:solute carrier family 5 member 3 [Gene - OMIM - HGNC]
  • SOD1:superoxide dismutase 1 [Gene - OMIM - HGNC]
  • SYNJ1:synaptojanin 1 [Gene - OMIM - HGNC]
  • TCP10L:t-complex 10 like [Gene - OMIM - HGNC]
  • TTC3:tetratricopeptide repeat domain 3 [Gene - OMIM - HGNC]
  • TMEM50B:transmembrane protein 50B [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
21q22.11-22.13
Genomic location:
Chr21: 32439271 - 39212984 (on Assembly GRCh37)
Preferred name:
NC_000021.8:g.(?_32439271)_(39212984_?)dup
HGVS:
NC_000021.8:g.(?_32439271)_(39212984_?)dup

Condition(s)

Name:
Amyotrophic lateral sclerosis type 1 (ALS1)
Synonyms:
AMYOTROPHIC LATERAL SCLEROSIS 1, FAMILIAL
Identifiers:
MONDO: MONDO:0007103; MedGen: C1862939; Orphanet: 803; OMIM: 105400

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002186768Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Oct 7, 2022) 		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, SCV002186768.3

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

Description

A copy number gain of the genomic region encompassing the full coding sequence of the SOD1 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. A similar copy number variant has been observed in individual(s) with clinical features of amyotrophic lateral sclerosis (Invitae). 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 16, 2024