GRCh37/hg19 16p11.2(chr16:28802397-29051191)x1 AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 11, 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:: RCV000683802.3

Allele description [Variation Report for GRCh37/hg19 16p11.2(chr16:28802397-29051191)x1]

GRCh37/hg19 16p11.2(chr16:28802397-29051191)x1

Genes:

ATP2A1:ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1 [Gene - OMIM - HGNC]
CD19:CD19 molecule [Gene - OMIM - HGNC]
SH2B1:SH2B adaptor protein 1 [Gene - OMIM - HGNC]
SPNS1:SPNS lysolipid transporter 1, lysophospholipid [Gene - OMIM - HGNC]
TUFM:Tu translation elongation factor, mitochondrial [Gene - OMIM - HGNC]
ATXN2L:ataxin 2 like [Gene - OMIM - HGNC]
LAT:linker for activation of T cells [Gene - OMIM - HGNC]
NFATC2IP:nuclear factor of activated T cells 2 interacting protein [Gene - OMIM - HGNC]
RABEP2:rabaptin, RAB GTPase binding effector protein 2 [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

16p11.2

Genomic location:

Chr16: 28802397 - 29051191 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 16p11.2(chr16:28802397-29051191)x1

HGVS:

NC_000016.9:g.(?_28802397)_(29051191_?)del

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000811311	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Pathogenic (Jun 11, 2021)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000811311

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Pathogenic
(Jun 11, 2021)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen).

Riggs ER, Andersen EF, Cherry AM, Kantarci S, Kearney H, Patel A, Raca G, Ritter DI, South ST, Thorland EC, Pineda-Alvarez D, Aradhya S, Martin CL.

Genet Med. 2020 Feb;22(2):245-257. doi: 10.1038/s41436-019-0686-8. Epub 2019 Nov 6. Erratum in: Genet Med. 2021 Nov;23(11):2230.

PubMed [citation]

PMID:: 31690835
PMCID:: PMC7313390

Details of each submission

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV000811311.3

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

Description

This copy number loss involves several genes including SH2B1 (OMIM 608937) and is associated with the distal (BP2-BP3) 16p11.2 microdeletion syndrome (OMIM 613444). Typical features include developmental delay and early-onset obesity (Bachmann-Gagescu, et al., Genet Med. 2010 Oct;12(10):641-7, PMID: 20808231; Walters, et al., Nature. 2010 Feb 4;463(7281):671-5, PMID: 20130649). Inheritance from a normal or mildly affected parent has been reported, suggesting incomplete penetrance and/or variable expressivity.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 31, 2022

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