GRCh37/hg19 22q13.31-13.33(chr22:48223839-51197725)x1 AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 26, 2023
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:: RCV001007506.2

Allele description [Variation Report for GRCh37/hg19 22q13.31-13.33(chr22:48223839-51197725)x1]

GRCh37/hg19 22q13.31-13.33(chr22:48223839-51197725)x1

Genes:

ALG12:ALG12 alpha-1,6-mannosyltransferase [Gene - OMIM - HGNC]
DENND6B:DENN domain containing 6B [Gene - OMIM - HGNC]
MOV10L1:Mov10 like RNA helicase 1 [Gene - OMIM - 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]
TRABD:TraB domain containing [Gene - HGNC]
ACR:acrosin [Gene - OMIM - HGNC]
ADM2:adrenomedullin 2 [Gene - OMIM - HGNC]
ARSA:arylsulfatase A [Gene - OMIM - HGNC]
BRD1:bromodomain containing 1 [Gene - OMIM - HGNC]
CPT1B:carnitine palmitoyltransferase 1B [Gene - OMIM - HGNC]
CHKB:choline kinase beta [Gene - OMIM - HGNC]
CIMAP1B:ciliary microtubule associated protein 1B [Gene - HGNC]
CRELD2:cysteine rich with EGF like domains 2 [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 - OMIM - HGNC]
LMF2:lipase maturation factor 2 [Gene - 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]
PANX2:pannexin 2 [Gene - OMIM - HGNC]
PLXNB2:plexin B2 [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]
TYMP:thymidine phosphorylase [Gene - OMIM - HGNC]
TUBGCP6:tubulin gamma complex component 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: 48223839 - 51197725 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 22q13.31-13.33(chr22:48223839-51197725)x1

HGVS:

NC_000022.10:g.(?_48223839)_(51197725_?)del

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Nucleotide Links for Protein (Select 7524365) (3)
Nucleotide
neuronal cell adhesion molecule isoform X20 [Mus musculus]
neuronal cell adhesion molecule isoform X20 [Mus musculus]
gi|1907088039|ref|XP_036013371.1|

Protein
Oard1 O-acyl-ADP-ribose deacylase 1 [Mus musculus]
Oard1 O-acyl-ADP-ribose deacylase 1 [Mus musculus]
Gene ID:106821

Gene
Gene Links for Protein (Select 1276317637) (1)
Gene
Nucleotide Links for Protein (Select 1093953512) (2)
Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001167128	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Pathogenic (May 26, 2023)	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

SCV001167128

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Pathogenic
(May 26, 2023)

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.

PubMed [citation]

PMID:: 31690835
PMCID:: PMC7313390

Details of each submission

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV001167128.2

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

Description

Deletions of chromosome 22q13.3, including SHANK3 (OMIM 606230), are associated with Phelan-McDermid syndrome (PHMDS; 22q13.3 deletion syndrome; OMIM 606232). The SHANK3 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://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 4, 2024

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