NC_000015.9:g.(?_75628431)_(76054677_?)del AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 15, 2017
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:: RCV003122680.3

Allele description [Variation Report for NC_000015.9:g.(?_75628431)_(76054677_?)del]

NC_000015.9:g.(?_75628431)_(76054677_?)del

Genes:

COMMD4:COMM domain containing 4 [Gene - OMIM - HGNC]
IMP3:IMP U3 small nucleolar ribonucleoprotein 3 [Gene - OMIM - HGNC]
SIN3A:SIN3 transcription regulator family member A [Gene - OMIM - HGNC]
CSPG4:chondroitin sulfate proteoglycan 4 [Gene - OMIM - HGNC]
CIMAP1C:ciliary microtubule associated protein 1C [Gene - HGNC]
MAN2C1:mannosidase alpha class 2C member 1 [Gene - OMIM - HGNC]
NEIL1:nei like DNA glycosylase 1 [Gene - OMIM - HGNC]
PTPN9:protein tyrosine phosphatase non-receptor type 9 [Gene - OMIM - HGNC]
SNUPN:snurportin 1 [Gene - OMIM - HGNC]
SNX33:sorting nexin 33 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

15q24.2

Genomic location:

Chr15: 75628431 - 76054677 (on Assembly GRCh37)

Preferred name:

NC_000015.9:g.(?_75628431)_(76054677_?)del

HGVS:

NC_000015.9:g.(?_75628431)_(76054677_?)del

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003793090	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 15, 2017)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 27399968, 28093361, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003793090

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 15, 2017)

germline

clinical testing

PubMed (3)
[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

Haploinsufficiency of MeCP2-interacting transcriptional co-repressor SIN3A causes mild intellectual disability by affecting the development of cortical integrity.

Witteveen JS, Willemsen MH, Dombroski TC, van Bakel NH, Nillesen WM, van Hulten JA, Jansen EJ, Verkaik D, Veenstra-Knol HE, van Ravenswaaij-Arts CM, Wassink-Ruiter JS, Vincent M, David A, Le Caignec C, Schieving J, Gilissen C, Foulds N, Rump P, Strom T, Cremer K, Zink AM, Engels H, et al.

Nat Genet. 2016 Aug;48(8):877-87. doi: 10.1038/ng.3619. Epub 2016 Jul 11.

PubMed [citation]

PMID:: 27399968

NEIL1 is a candidate gene associated with common variable immunodeficiency in a patient with a chromosome 15q24 deletion.

Romano R, Zaravinos A, Liadaki K, Caridha R, Lundin J, Carlsson G, Winiarski J, Pan-Hammarström Q, Hammarström L.

Clin Immunol. 2017 Mar;176:71-76. doi: 10.1016/j.clim.2017.01.006. Epub 2017 Jan 14.

PubMed [citation]

PMID:: 28093361

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003793090.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the NEIL1 gene has been identified. The boundaries of this event are unknown as the deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. Isolated whole-gene deletions of NEIL1 have not been reported in the literature. However, larger copy number events that include this gene have been reported (PMID: 27399968, 28093361). The current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in NEIL1 cause disease. 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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