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NC_000021.8:g.(?_34540717)_(35013574_?)del AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 20, 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:
RCV001385476.6

Allele description

NC_000021.8:g.(?_34540717)_(35013574_?)del

Genes:
  • DONSON:DNA replication fork stabilization factor DONSON [Gene - OMIM - HGNC]
  • DNAJC28:DnaJ heat shock protein family (Hsp40) member C28 [Gene - HGNC]
  • SON:SON DNA and RNA binding protein [Gene - OMIM - HGNC]
  • CRYZL1:crystallin zeta like 1 [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]
  • GART:phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase [Gene - OMIM - HGNC]
  • TMEM50B:transmembrane protein 50B [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
21q22.11
Genomic location:
Chr21: 34540717 - 35013574 (on Assembly GRCh37)
Preferred name:
NC_000021.8:g.(?_34540717)_(35013574_?)del
HGVS:
NC_000021.8:g.(?_34540717)_(35013574_?)del

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001585340Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Aug 20, 2021) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

De Novo Truncating Variants in SON Cause Intellectual Disability, Congenital Malformations, and Failure to Thrive.

Tokita MJ, Braxton AA, Shao Y, Lewis AM, Vincent M, Küry S, Besnard T, Isidor B, Latypova X, Bézieau S, Liu P, Motter CS, Melver CW, Robin NH, Infante EM, McGuire M, El-Gharbawy A, Littlejohn RO, McLean SD, Bi W, Bacino CA, Lalani SR, et al.

Am J Hum Genet. 2016 Sep 1;99(3):720-727. doi: 10.1016/j.ajhg.2016.06.035. Epub 2016 Aug 18.

PubMed [citation]
PMID:
27545676
PMCID:
PMC5011061

De Novo Mutations in SON Disrupt RNA Splicing of Genes Essential for Brain Development and Metabolism, Causing an Intellectual-Disability Syndrome.

Kim JH, Shinde DN, Reijnders MRF, Hauser NS, Belmonte RL, Wilson GR, Bosch DGM, Bubulya PA, Shashi V, Petrovski S, Stone JK, Park EY, Veltman JA, Sinnema M, Stumpel CTRM, Draaisma JM, Nicolai J; University of Washington Center for Mendelian Genomics., Yntema HG, Lindstrom K, de Vries BBA, Jewett T, et al.

Am J Hum Genet. 2016 Sep 1;99(3):711-719. doi: 10.1016/j.ajhg.2016.06.029. Epub 2016 Aug 18.

PubMed [citation]
PMID:
27545680
PMCID:
PMC5011044
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001585340.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the SON gene has been identified. Loss-of-function variants in SON are known to be pathogenic (PMID: 27545676, 27545680). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. Isolated whole-gene deletions of SON have not been reported in the literature. However, larger copy number events that include this gene have been reported (PMID: 27545680). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 26, 2023