NC_000011.9:g.(?_46880534)_(47470516_?)del AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 30, 2021
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:: RCV001982909.5

Allele description [Variation Report for NC_000011.9:g.(?_46880534)_(47470516_?)del]

NC_000011.9:g.(?_46880534)_(47470516_?)del

Genes:

ARFGAP2:ARF GTPase activating protein 2 [Gene - OMIM - HGNC]
LRP4:LDL receptor related protein 4 [Gene - OMIM - HGNC]
MADD-AS1:MADD antisense RNA 1 [Gene - HGNC]
MADD:MAP kinase activating death domain [Gene - OMIM - HGNC]
SPI1:Spi-1 proto-oncogene [Gene - OMIM - HGNC]
ACP2:acid phosphatase 2, lysosomal [Gene - OMIM - HGNC]
CSTPP1:centriolar satellite-associated tubulin polyglutamylase complex regulator 1 [Gene - OMIM - HGNC]
DDB2:damage specific DNA binding protein 2 [Gene - OMIM - HGNC]
MYBPC3:myosin binding protein C3 [Gene - OMIM - HGNC]
NR1H3:nuclear receptor subfamily 1 group H member 3 [Gene - OMIM - HGNC]
PSMC3:proteasome 26S subunit, ATPase 3 [Gene - OMIM - HGNC]
PACSIN3:protein kinase C and casein kinase substrate in neurons 3 [Gene - OMIM - HGNC]
RAPSN:receptor associated protein of the synapse [Gene - OMIM - HGNC]
SLC39A13:solute carrier family 39 member 13 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

11p11.2

Genomic location:

Chr11: 46880534 - 47470516 (on Assembly GRCh37)

Preferred name:

NC_000011.9:g.(?_46880534)_(47470516_?)del

HGVS:

NC_000011.9:g.(?_46880534)_(47470516_?)del

Condition(s)

Name:: Fetal akinesia deformation sequence 1 (FADS1)
Synonyms:: Pena Shokeir syndrome, type 1; Lethal Pena-Shokeir 1 syndrome; Pena-Shokeir syndrome type I; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0100101; MedGen: C1276035; Orphanet: 994; OMIM: 208150; Human Phenotype Ontology: HP:0001989

Name:: Congenital myasthenic syndrome 11
Synonyms:: MYASTHENIC SYNDROME, CONGENITAL, Ie; Myasthenic syndrome, congenital, 11, associated with acetylcholine receptor deficiency
Identifiers:: MONDO: MONDO:0014588; MedGen: C4225367; Orphanet: 590; OMIM: 616326

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002243726	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 30, 2021)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 17686188, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002243726

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 30, 2021)

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

Congenital myasthenic syndromes: spotlight on genetic defects of neuromuscular transmission.

Müller JS, Mihaylova V, Abicht A, Lochmüller H.

Expert Rev Mol Med. 2007 Aug 9;9(22):1-20. Review.

PubMed [citation]

PMID:: 17686188

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, SCV002243726.3

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

Description

A gross deletion of the genomic region encompassing the full coding sequence of the RAPSN gene has been identified. Loss-of-function variants in RAPSN are known to be pathogenic (PMID: 17686188). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with RAPSN-related conditions. For these reasons, this variant has been classified as Pathogenic.

#	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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