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GRCh37/hg19 16q13-21(chr16:56950941-60203590)x1 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 21, 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:
RCV000683823.2

Allele description [Variation Report for GRCh37/hg19 16q13-21(chr16:56950941-60203590)x1]

GRCh37/hg19 16q13-21(chr16:56950941-60203590)x1

Genes:
  • ARL2BP:ADP ribosylation factor like GTPase 2 binding protein [Gene - OMIM - HGNC]
  • CCL17:C-C motif chemokine ligand 17 [Gene - OMIM - HGNC]
  • CCL22:C-C motif chemokine ligand 22 [Gene - OMIM - HGNC]
  • CX3CL1:C-X3-C motif chemokine ligand 1 [Gene - OMIM - HGNC]
  • CNOT1:CCR4-NOT transcription complex subunit 1 [Gene - OMIM - HGNC]
  • GINS3:GINS complex subunit 3 [Gene - OMIM - HGNC]
  • NDRG4:NDRG family member 4 [Gene - OMIM - HGNC]
  • NLRC5:NLR family CARD domain containing 5 [Gene - OMIM - HGNC]
  • POLR2C:RNA polymerase II subunit C [Gene - OMIM - HGNC]
  • SETD6:SET domain containing 6, protein lysine methyltransferase [Gene - OMIM - HGNC]
  • USB1:U6 snRNA biogenesis phosphodiesterase 1 [Gene - OMIM - HGNC]
  • ADGRG1:adhesion G protein-coupled receptor G1 [Gene - OMIM - HGNC]
  • ADGRG3:adhesion G protein-coupled receptor G3 [Gene - OMIM - HGNC]
  • ADGRG5:adhesion G protein-coupled receptor G5 [Gene - OMIM - HGNC]
  • CSNK2A2:casein kinase 2 alpha 2 [Gene - OMIM - HGNC]
  • CETP:cholesteryl ester transfer protein [Gene - OMIM - HGNC]
  • CFAP20:cilia and flagella associated protein 20 [Gene - OMIM - HGNC]
  • COQ9:coenzyme Q9 [Gene - OMIM - HGNC]
  • CCDC102A:coiled-coil domain containing 102A [Gene - HGNC]
  • CCDC113:coiled-coil domain containing 113 [Gene - OMIM - HGNC]
  • CPNE2:copine 2 [Gene - OMIM - HGNC]
  • CNGB1:cyclic nucleotide gated channel subunit beta 1 [Gene - OMIM - HGNC]
  • CIAPIN1:cytokine induced apoptosis inhibitor 1 [Gene - OMIM - HGNC]
  • DOK4:docking protein 4 [Gene - OMIM - HGNC]
  • DRC7:dynein regulatory complex subunit 7 [Gene - OMIM - HGNC]
  • GOT2:glutamic-oxaloacetic transaminase 2 [Gene - OMIM - HGNC]
  • HERPUD1:homocysteine inducible ER protein with ubiquitin like domain 1 [Gene - OMIM - HGNC]
  • KATNB1:katanin regulatory subunit B1 [Gene - OMIM - HGNC]
  • KIFC3:kinesin family member C3 [Gene - OMIM - HGNC]
  • MMP15:matrix metallopeptidase 15 [Gene - OMIM - HGNC]
  • PLLP:plasmolipin [Gene - OMIM - HGNC]
  • PSME3IP1:proteasome activator subunit 3 interacting protein 1 [Gene - OMIM - HGNC]
  • RSPRY1:ring finger and SPRY domain containing 1 [Gene - OMIM - HGNC]
  • PRSS54:serine protease 54 [Gene - HGNC]
  • SLC38A7:solute carrier family 38 member 7 [Gene - OMIM - HGNC]
  • TEPP:testis, prostate and placenta expressed [Gene - OMIM - HGNC]
  • ZNF319:zinc finger protein 319 [Gene - HGNC]
Variant type:
copy number loss
Cytogenetic location:
16q13-21
Genomic location:
Chr16: 56950941 - 60203590 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 16q13-21(chr16:56950941-60203590)x1
HGVS:
NC_000016.9:g.(?_56950941)_(60203590_?)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
SCV000811332Quest Diagnostics Nichols Institute San Juan Capistrano
criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)		Pathogenic
(Oct 21, 2021) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical 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. doi: 10.1038/s41436-021-01150-9.

PubMed [citation]
PMID:
31690835
PMCID:
PMC7313390

Details of each submission

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV000811332.2

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

Description

The copy number loss of 16q13q21 is expected to cause phenotypic and/or developmental abnormalities. It involves multiple protein coding genes that are associated with autosomal recessive disorders and autosomal dominant disorders, including CETP and CNOT1. Heterozygous sequence variants of CETP are associated with autosomal dominant hyperalphalipoproteinemia (OMIM 143470). Heterozygous sequence variants of CNOT1 are associated with autosomal dominant holoprosencephaly-12 with or without pancreatic agenesis (OMIM 618500) and Vissers-Bodmer syndrome (OMIM 619033). Further, larger overlapping deletions have been reported in patients with neurodevelopmental delays and bilateral frontoparietal polymicrogyria (Vissers 2020, Borgatti 2009). References Borgatti et al., Clin Genet. 2009 Dec;76(6):573-6. PMID: 19807741 Vissers et al., Am J Hum Genet. 2020 Jul 2;107(1):164-172. PMID: 32553196

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

Last Updated: Mar 26, 2023