GRCh37/hg19 22q11.21(chr22:18912870-21431174) AND DiGeorge syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 1, 2018
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:: RCV000767633.1

Allele description [Variation Report for GRCh37/hg19 22q11.21(chr22:18912870-21431174)]

GRCh37/hg19 22q11.21(chr22:18912870-21431174)

Genes:

ARVCF:ARVCF delta catenin family member [Gene - OMIM - HGNC]
CRKL:CRK like proto-oncogene, adaptor protein [Gene - OMIM - HGNC]
DGCR8:DGCR8 microprocessor complex subunit [Gene - OMIM - HGNC]
DGCR2:DiGeorge syndrome critical region gene 2 [Gene - OMIM - HGNC]
DGCR6L:DiGeorge syndrome critical region gene 6 like [Gene - OMIM - HGNC]
GNB1L:G protein subunit beta 1 like [Gene - OMIM - HGNC]
RANBP1:RAN binding protein 1 [Gene - OMIM - HGNC]
RIMBP3:RIMS binding protein 3 [Gene - OMIM - HGNC]
TBX1:T-box transcription factor 1 [Gene - OMIM - HGNC]
THAP7:THAP domain containing 7 [Gene - OMIM - HGNC]
AIFM3:apoptosis inducing factor mitochondria associated 3 [Gene - OMIM - HGNC]
COMT:catechol-O-methyltransferase [Gene - OMIM - HGNC]
CDC45:cell division cycle 45 [Gene - OMIM - HGNC]
C22orf39:chromosome 22 open reading frame 39 [Gene - HGNC]
CLTCL1:clathrin heavy chain like 1 [Gene - OMIM - HGNC]
CLDN5:claudin 5 [Gene - OMIM - HGNC]
ESS2:ess-2 splicing factor homolog [Gene - OMIM - HGNC]
FAM230A:family with sequence similarity 230 member A [Gene - HGNC]
GGTLC3:gamma-glutamyltransferase light chain family member 3 [Gene - OMIM - HGNC]
GP1BB:glycoprotein Ib platelet subunit beta [Gene - OMIM - HGNC]
GSC2:goosecoid homeobox 2 [Gene - OMIM - HGNC]
HIRA:histone cell cycle regulator [Gene - OMIM - HGNC]
KLHL22:kelch like family member 22 [Gene - OMIM - HGNC]
LZTR1:leucine zipper like post translational regulator 1 [Gene - OMIM - HGNC]
MED15:mediator complex subunit 15 [Gene - OMIM - HGNC]
MRPL40:mitochondrial ribosomal protein L40 [Gene - OMIM - HGNC]
PI4KA:phosphatidylinositol 4-kinase alpha [Gene - OMIM - HGNC]
PRODH:proline dehydrogenase 1 [Gene - OMIM - HGNC]
P2RX6:purinergic receptor P2X 6 [Gene - OMIM - HGNC]
RTN4R:reticulon 4 receptor [Gene - OMIM - HGNC]
RTL10:retrotransposon Gag like 10 [Gene - HGNC]
SCARF2:scavenger receptor class F member 2 [Gene - OMIM - HGNC]
SEPTIN5:septin 5 [Gene - OMIM - HGNC]
SERPIND1:serpin family D member 1 [Gene - OMIM - HGNC]
SLC25A1:solute carrier family 25 member 1 [Gene - OMIM - HGNC]
SLC7A4:solute carrier family 7 member 4 [Gene - OMIM - HGNC]
SNAP29:synaptosome associated protein 29 [Gene - OMIM - HGNC]
TRMT2A:tRNA methyltransferase 2 homolog A [Gene - OMIM - HGNC]
TSSK2:testis specific serine kinase 2 [Gene - OMIM - HGNC]
TXNRD2:thioredoxin reductase 2 [Gene - OMIM - HGNC]
TMEM191B:transmembrane protein 191B [Gene - HGNC]
TANGO2:transport and golgi organization 2 homolog [Gene - OMIM - HGNC]
UFD1:ubiquitin recognition factor in ER associated degradation 1 [Gene - OMIM - HGNC]
USP41:ubiquitin specific peptidase 41 [Gene - HGNC]
ZDHHC8:zinc finger DHHC-type palmitoyltransferase 8 [Gene - OMIM - HGNC]
ZNF74:zinc finger protein 74 [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

22q11.21

Genomic location:

Chr22: 18912870 - 21431174 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 22q11.21(chr22:18912870-21431174)

HGVS:

NC_000022.10:g.(?_18912870)_(21431174_?)del

Observations:

Condition(s)

Name:: DiGeorge syndrome
Synonyms:: Hypoplasia of thymus and parathyroid; Third and fourth pharyngeal pouch syndrome; DiGeorge anomaly; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008564; MedGen: C0012236; Orphanet: 567; OMIM: 188400

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000898255	Baylor Genetics	criteria provided, single submitter (ACMG CNV Guidelines, 2011)	Pathogenic (Nov 1, 2018)	germline	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

SCV000898255

Baylor Genetics

criteria provided, single submitter

(ACMG CNV Guidelines, 2011)

Pathogenic
(Nov 1, 2018)

germline

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	germline	yes	1	1	not provided	not provided	not provided	clinical testing

Citations

PubMed

American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants.

Kearney HM, Thorland EC, Brown KK, Quintero-Rivera F, South ST; Working Group of the American College of Medical Genetics Laboratory Quality Assurance Committee.

Genet Med. 2011 Jul;13(7):680-5. doi: 10.1097/GIM.0b013e3182217a3a.

PubMed [citation]

PMID:: 21681106

Details of each submission

From Baylor Genetics, SCV000898255.1

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

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

Last Updated: Mar 26, 2023

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