GRCh37/hg19 22q13.31-13.33(chr22:45977448-51197838)x1 AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 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:: RCV002472642.1

Allele description [Variation Report for GRCh37/hg19 22q13.31-13.33(chr22:45977448-51197838)x1]

GRCh37/hg19 22q13.31-13.33(chr22:45977448-51197838)x1

Genes:

ALG12:ALG12 alpha-1,6-mannosyltransferase [Gene - OMIM - HGNC]
DENND6B:DENN domain containing 6B [Gene - HGNC]
GTSE1:G2 and S-phase expressed 1 [Gene - OMIM - HGNC]
GRAMD4:GRAM domain containing 4 [Gene - OMIM - HGNC]
MOV10L1:Mov10 like RISC complex RNA helicase 1 [Gene - OMIM - HGNC]
PRR34:PRR34 long non-coding RNA [Gene - HGNC]
PIM3:Pim-3 proto-oncogene, serine/threonine kinase [Gene - OMIM - HGNC]
SBF1:SET binding factor 1 [Gene - OMIM - HGNC]
SHANK3:SH3 and multiple ankyrin repeat domains 3 [Gene - OMIM - HGNC]
TAFA5:TAFA chemokine like family member 5 [Gene - OMIM - HGNC]
TBC1D22A:TBC1 domain family member 22A [Gene - OMIM - HGNC]
TRABD:TraB domain containing [Gene - HGNC]
WNT7B:Wnt family member 7B [Gene - OMIM - HGNC]
ACR:acrosin [Gene - OMIM - HGNC]
ADM2:adrenomedullin 2 [Gene - OMIM - HGNC]
ARSA:arylsulfatase A [Gene - OMIM - HGNC]
ATXN10:ataxin 10 [Gene - OMIM - HGNC]
BRD1:bromodomain containing 1 [Gene - OMIM - HGNC]
CELSR1:cadherin EGF LAG seven-pass G-type receptor 1 [Gene - OMIM - HGNC]
CPT1B:carnitine palmitoyltransferase 1B [Gene - OMIM - HGNC]
CERK:ceramide kinase [Gene - OMIM - HGNC]
CHKB:choline kinase beta [Gene - OMIM - HGNC]
CDPF1:cysteine rich DPF motif domain containing 1 [Gene - HGNC]
CRELD2:cysteine rich with EGF like domains 2 [Gene - OMIM - HGNC]
FBLN1:fibulin 1 [Gene - OMIM - HGNC]
HDAC10:histone deacetylase 10 [Gene - OMIM - HGNC]
IL17REL:interleukin 17 receptor E like [Gene - OMIM - HGNC]
KLHDC7B:kelch domain containing 7B [Gene - HGNC]
LMF2:lipase maturation factor 2 [Gene - HGNC]
MIRLET7A3:microRNA let-7a-3 [Gene - OMIM - HGNC]
MIRLET7B:microRNA let-7b [Gene - OMIM - HGNC]
MAPK11:mitogen-activated protein kinase 11 [Gene - OMIM - HGNC]
MAPK12:mitogen-activated protein kinase 12 [Gene - OMIM - HGNC]
MAPK8IP2:mitogen-activated protein kinase 8 interacting protein 2 [Gene - OMIM - HGNC]
MLC1:modulator of VRAC current 1 [Gene - OMIM - HGNC]
MIOX:myo-inositol oxygenase [Gene - OMIM - HGNC]
NCAPH2:non-SMC condensin II complex subunit H2 [Gene - OMIM - HGNC]
ODF3B:outer dense fiber of sperm tails 3B [Gene - HGNC]
PANX2:pannexin 2 [Gene - OMIM - HGNC]
PPARA:peroxisome proliferator activated receptor alpha [Gene - OMIM - HGNC]
PLXNB2:plexin B2 [Gene - OMIM - HGNC]
PKDREJ:polycystin family receptor for egg jelly [Gene - OMIM - HGNC]
PPP6R2:protein phosphatase 6 regulatory subunit 2 [Gene - OMIM - HGNC]
SELENOO:selenoprotein O [Gene - OMIM - HGNC]
SYCE3:synaptonemal complex central element protein 3 [Gene - OMIM - HGNC]
SCO2:synthesis of cytochrome C oxidase 2 [Gene - OMIM - HGNC]
TRMU:tRNA mitochondrial 2-thiouridylase [Gene - OMIM - HGNC]
TTC38:tetratricopeptide repeat domain 38 [Gene - HGNC]
TYMP:thymidine phosphorylase [Gene - OMIM - HGNC]
TUBGCP6:tubulin gamma complex associated protein 6 [Gene - OMIM - HGNC]
TTLL8:tubulin tyrosine ligase like 8 [Gene - OMIM - HGNC]
ZBED4:zinc finger BED-type containing 4 [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

22q13.31-13.33

Genomic location:

Chr22: 45977448 - 51197838 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 22q13.31-13.33(chr22:45977448-51197838)x1

HGVS:

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
SCV002772510	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Pathogenic (Dec 21, 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

SCV002772510

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Pathogenic
(Dec 21, 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, SCV002772510.1

#	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 of 22q13.31q13.33 includes multiple genes including SHANK3 (OMIM 606230). This deletion causes Phelan-McDermid syndrome (PMS; OMIM 606232), also called 22q13.3 deletion syndrome, which is a neurodevelopmental disorder characterized by global developmental delay, intellectual disability, severe speech delays, hypotonia, and autism spectrum disorder (ASD).

#	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: Mar 26, 2023

ClinVar

Relating variation to medicine