GRCh37/hg19 22q13.2-13.33(chr22:42955616-51183840)x1 AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 1, 2021
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV000684529.2

Allele description [Variation Report for GRCh37/hg19 22q13.2-13.33(chr22:42955616-51183840)x1]

GRCh37/hg19 22q13.2-13.33(chr22:42955616-51183840)x1

Genes:

ARFGAP3:ADP ribosylation factor GTPase activating protein 3 [Gene - OMIM - HGNC]
ALG12:ALG12 alpha-1,6-mannosyltransferase [Gene - OMIM - HGNC]
ATP5MGL:ATP synthase membrane subunit g like [Gene - HGNC]
BIK:BCL2 interacting killer [Gene - OMIM - HGNC]
DENND6B:DENN domain containing 6B [Gene - HGNC]
POLDIP3:DNA polymerase delta interacting protein 3 [Gene - OMIM - HGNC]
EFCAB6:EF-hand calcium binding domain 6 [Gene - OMIM - HGNC]
GTSE1:G2 and S-phase expressed 1 [Gene - OMIM - HGNC]
GRAMD4:GRAM domain containing 4 [Gene - OMIM - HGNC]
KIAA0930:KIAA0930 [Gene - OMIM - HGNC]
MOV10L1:Mov10 like RISC complex RNA helicase 1 [Gene - OMIM - HGNC]
PHF21B:PHD finger protein 21B [Gene - OMIM - HGNC]
PRR34:PRR34 long non-coding RNA [Gene - HGNC]
PRR5-ARHGAP8:PRR5-ARHGAP8 readthrough [Gene - HGNC]
PIM3:Pim-3 proto-oncogene, serine/threonine kinase [Gene - OMIM - HGNC]
RIBC2:RIB43A domain with coiled-coils 2 [Gene - HGNC]
ARHGAP8:Rho GTPase activating protein 8 [Gene - OMIM - HGNC]
SAMM50:SAMM50 sorting and assembly machinery component [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]
TTLL1:TTL family tubulin polyglutamylase complex subunit L1 [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]
A4GALT:alpha 1,4-galactosyltransferase (P blood group) [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]
CYB5R3:cytochrome b5 reductase 3 [Gene - OMIM - HGNC]
FAM118A:family with sequence similarity 118 member A [Gene - 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]
MCAT:malonyl-CoA-acyl carrier protein transacylase [Gene - OMIM - HGNC]
MPPED1:metallophosphoesterase domain containing 1 [Gene - OMIM - 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]
NUP50:nucleoporin 50 [Gene - OMIM - HGNC]
ODF3B:outer dense fiber of sperm tails 3B [Gene - HGNC]
PANX2:pannexin 2 [Gene - OMIM - HGNC]
PARVB:parvin beta [Gene - OMIM - HGNC]
PARVG:parvin gamma [Gene - OMIM - HGNC]
PNPLA3:patatin like phospholipase domain containing 3 [Gene - OMIM - HGNC]
PNPLA5:patatin like phospholipase domain containing 5 [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]
PRR5:proline rich 5 [Gene - OMIM - HGNC]
PACSIN2:protein kinase C and casein kinase substrate in neurons 2 [Gene - OMIM - HGNC]
PPP6R2:protein phosphatase 6 regulatory subunit 2 [Gene - OMIM - HGNC]
RTL6:retrotransposon Gag like 6 [Gene - HGNC]
SELENOO:selenoprotein O [Gene - OMIM - HGNC]
SERHL2:serine hydrolase like 2 [Gene - OMIM - HGNC]
SHISAL1:shisa like 1 [Gene - OMIM - HGNC]
SCUBE1:signal peptide, CUB domain and EGF like domain containing 1 [Gene - OMIM - HGNC]
SMC1B:structural maintenance of chromosomes 1B [Gene - OMIM - HGNC]
SULT4A1:sulfotransferase family 4A member 1 [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]
TSPO:translocator protein [Gene - OMIM - HGNC]
TUBGCP6:tubulin gamma complex associated protein 6 [Gene - OMIM - HGNC]
TTLL12:tubulin tyrosine ligase like 12 [Gene - OMIM - HGNC]
TTLL8:tubulin tyrosine ligase like 8 [Gene - OMIM - HGNC]
UPK3A:uroplakin 3A [Gene - OMIM - HGNC]
ZBED4:zinc finger BED-type containing 4 [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

22q13.2-13.33

Genomic location:

Chr22: 42955616 - 51183840 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 22q13.2-13.33(chr22:42955616-51183840)x1

HGVS:

NC_000022.10:g.(?_42955616)_(51183840_?)del

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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claudin-14 isoform X1 [Homo sapiens]
claudin-14 isoform X1 [Homo sapiens]
gi|2217337492|ref|XP_047296692.1|

Protein
NCTC_3000
NCTC_3000
NCTC_3000

BioProject
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000812052	Quest Diagnostics Nichols Institute San Juan Capistrano	no assertion criteria provided	Pathogenic (Mar 1, 2021)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000812052

Quest Diagnostics Nichols Institute San Juan Capistrano

no assertion criteria provided

Pathogenic
(Mar 1, 2021)

germline

clinical testing

Help

Summary from all submissions

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

Details of each submission

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV000812052.2

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

Description

Deletions of chromosome 22q13.3, including SHANK3, are associated with Phelan-McDermid syndrome (PHMDS; 22q13.3 deletion syndrome) (OMIM #606232). The common clinical features include neonatal hypotonia, global developmental delay, absent or severely delayed speech, moderate to profound intellectual disability, autism spectrum disorder, normal to accelerated growth, and minor facial dysmorphism. Deletion sizes of chromosome 22q13.3 are highly variable ranging from 0.22 to 9 Mb with no common breakpoints. The SHANK3 (SH3 and multiple ankyrin repeat domains protein 3; previously known as PROSAP2) gene has been deleted in all reported cases with Phelan-McDermid syndrome (Phelan K, Rogers RC. Phelan-McDermid Syndrome. 2005 May 11 [GeneReviews [Internet]. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1198/.; Phelan K and McDermid HE. The 22q13.3 Deletion Syndrome (Phelan-McDermid Syndrome). Mol Syndromol. 2012;2(3-5):186-201).

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

Last Updated: Mar 26, 2023

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