GRCh37/hg19 2q37.2-37.3(chr2:235942616-242783384)x1 AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 7, 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:: RCV002472625.1

Allele description [Variation Report for GRCh37/hg19 2q37.2-37.3(chr2:235942616-242783384)x1]

GRCh37/hg19 2q37.2-37.3(chr2:235942616-242783384)x1

Genes:

AGAP1:ArfGAP with GTPase domain, ankyrin repeat and PH domain 1 [Gene - OMIM - HGNC]
BOK:BCL2 family apoptosis regulator BOK [Gene - OMIM - HGNC]
COPS8:COP9 signalosome subunit 8 [Gene - OMIM - HGNC]
COPS9:COP9 signalosome subunit 9 [Gene - OMIM - HGNC]
D2HGDH:D-2-hydroxyglutarate dehydrogenase [Gene - OMIM - HGNC]
FARP2:FERM, ARH/RhoGEF and pleckstrin domain protein 2 [Gene - OMIM - HGNC]
GPR35:G protein-coupled receptor 35 [Gene - OMIM - HGNC]
ILKAP:ILK associated serine/threonine phosphatase [Gene - OMIM - HGNC]
IQCA1:IQ motif containing with AAA domain 1 [Gene - HGNC]
LRRFIP1:LRR binding FLII interacting protein 1 [Gene - OMIM - HGNC]
NDUFA10:NADH:ubiquinone oxidoreductase subunit A10 [Gene - OMIM - HGNC]
PASK:PAS domain containing serine/threonine kinase [Gene - OMIM - HGNC]
RAB17:RAB17, member RAS oncogene family [Gene - OMIM - HGNC]
RBM44:RNA binding motif protein 44 [Gene - OMIM - HGNC]
SH3BP4:SH3 domain binding protein 4 [Gene - OMIM - HGNC]
THAP4:THAP domain containing 4 [Gene - OMIM - HGNC]
TRAF3IP1:TRAF3 interacting protein 1 [Gene - OMIM - HGNC]
AGXT:alanine--glyoxylate aminotransferase [Gene - OMIM - HGNC]
ANKMY1:ankyrin repeat and MYND domain containing 1 [Gene - OMIM - HGNC]
ASB18:ankyrin repeat and SOCS box containing 18 [Gene - HGNC]
ASB1:ankyrin repeat and SOCS box containing 1 [Gene - OMIM - HGNC]
ANO7:anoctamin 7 [Gene - OMIM - HGNC]
AQP12A:aquaporin 12A [Gene - OMIM - HGNC]
AQP12B:aquaporin 12B [Gene - HGNC]
RNPEPL1:arginyl aminopeptidase like 1 [Gene - OMIM - HGNC]
ACKR3:atypical chemokine receptor 3 [Gene - OMIM - HGNC]
ATG4B:autophagy related 4B cysteine peptidase [Gene - OMIM - HGNC]
CAPN10:calpain 10 [Gene - OMIM - HGNC]
COL6A3:collagen type VI alpha 3 chain [Gene - OMIM - HGNC]
DTYMK:deoxythymidylate kinase [Gene - OMIM - HGNC]
DUSP28:dual specificity phosphatase 28 [Gene - HGNC]
ERFE:erythroferrone [Gene - OMIM - HGNC]
ESPNL:espin like [Gene - OMIM - HGNC]
GAL3ST2:galactose-3-O-sulfotransferase 2 [Gene - OMIM - HGNC]
GBX2:gastrulation brain homeobox 2 [Gene - OMIM - HGNC]
GPC1:glypican 1 [Gene - OMIM - HGNC]
HES6:hes family bHLH transcription factor 6 [Gene - OMIM - HGNC]
HDLBP:high density lipoprotein binding protein [Gene - OMIM - HGNC]
HDAC4:histone deacetylase 4 [Gene - OMIM - HGNC]
ING5:inhibitor of growth family member 5 [Gene - OMIM - HGNC]
KLHL30:kelch like family member 30 [Gene - HGNC]
KIF1A:kinesin family member 1A [Gene - OMIM - HGNC]
MAB21L4:mab-21 like 4 [Gene - HGNC]
MLPH:melanophilin [Gene - OMIM - HGNC]
MIR149:microRNA 149 [Gene - OMIM - HGNC]
MTERF4:mitochondrial transcription termination factor 4 [Gene - OMIM - HGNC]
NEU4:neuraminidase 4 [Gene - OMIM - HGNC]
OR6B2:olfactory receptor family 6 subfamily B member 2 [Gene - HGNC]
OR6B3:olfactory receptor family 6 subfamily B member 3 [Gene - HGNC]
OTOS:otospiralin [Gene - OMIM - HGNC]
PER2:period circadian regulator 2 [Gene - OMIM - HGNC]
PRLH:prolactin releasing hormone [Gene - OMIM - HGNC]
PRR21:proline rich 21 [Gene - HGNC]
PPP1R7:protein phosphatase 1 regulatory subunit 7 [Gene - OMIM - HGNC]
RAMP1:receptor activity modifying protein 1 [Gene - OMIM - HGNC]
SCLY:selenocysteine lyase [Gene - OMIM - HGNC]
SEPTIN2:septin 2 [Gene - OMIM - HGNC]
STK25:serine/threonine kinase 25 [Gene - OMIM - HGNC]
SNED1:sushi, nidogen and EGF like domains 1 [Gene - OMIM - HGNC]
TWIST2:twist family bHLH transcription factor 2 [Gene - OMIM - HGNC]
UBE2F:ubiquitin conjugating enzyme E2 F (putative) [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

2q37.2-37.3

Genomic location:

Chr2: 235942616 - 242783384 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 2q37.2-37.3(chr2:235942616-242783384)x1

HGVS:

Condition(s)

Synonyms:: none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002772493	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Pathogenic (Dec 7, 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

SCV002772493

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Pathogenic
(Dec 7, 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. 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, SCV002772493.1

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

Description

The terminal deletion is associated with chromosome 2q37 deletion syndrome (OMIM 600430). Patients with chromosome 2q37 deletion syndrome show highly variable clinical manifestations likely resulting from different deletion sizes and gene contents. The common clinical features include Albright hereditary osteodystrophy (AHO)-like metacarpal/metatarsal shortening (brachymetaphalangism), a variable degree of intellectual disability, facial dysmorphism, epilepsy, eczema, Wilm's tumor, and urogenital anomalies (Aldred et al 2004 J. Med. Genet. 41: 433-439. PMID: 15173228; Williams et al. Am J Hum Genet. 2010. Aug 13;87(2):219-28 PMID: 20691407; Fisch et al. Am J Med Genet A. 2016 Sep; 170(9):2282-91. PMID: 27282419; Doherty and Lacbawan. GeneReviews: 2q37 Microdeletion Syndrome (http://www.ncbi.nlm.nih.gov/books/NBK1158/)).

#	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: Jan 26, 2025

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