GRCh37/hg19 12q14.3-15(chr12:66045645-68872343)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:: RCV001832934.1

Allele description [Variation Report for GRCh37/hg19 12q14.3-15(chr12:66045645-68872343)x1]

GRCh37/hg19 12q14.3-15(chr12:66045645-68872343)x1

Genes:

HELB:DNA helicase B [Gene - OMIM - HGNC]
LLPH:LLP homolog, long-term synaptic facilitation factor [Gene - OMIM - HGNC]
MDM1:Mdm1 nuclear protein [Gene - OMIM - HGNC]
CAND1:cullin associated and neddylation dissociated 1 [Gene - OMIM - HGNC]
DYRK2:dual specificity tyrosine phosphorylation regulated kinase 2 [Gene - OMIM - HGNC]
GRIP1:glutamate receptor interacting protein 1 [Gene - OMIM - HGNC]
HMGA2:high mobility group AT-hook 2 [Gene - OMIM - HGNC]
IFNG:interferon gamma [Gene - OMIM - HGNC]
IRAK3:interleukin 1 receptor associated kinase 3 [Gene - OMIM - HGNC]
IL22:interleukin 22 [Gene - OMIM - HGNC]
IL26:interleukin 26 [Gene - OMIM - HGNC]
TMBIM4:transmembrane BAX inhibitor motif containing 4 [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

12q14.3-15

Genomic location:

Chr12: 66045645 - 68872343 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 12q14.3-15(chr12:66045645-68872343)x1

HGVS:

NC_000012.11:g.(?_66045645)_(68872343_?)del

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

Recent activity

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Caenorhabditis elegans Sodium/potassium-transporting ATPase subunit beta-1 (nkb-...
Caenorhabditis elegans Sodium/potassium-transporting ATPase subunit beta-1 (nkb-1), mRNA
gi|1972231985|ref|NM_060105.8|

Nucleotide
Translocating chain-associated membrane protein [Caenorhabditis elegans]
Translocating chain-associated membrane protein [Caenorhabditis elegans]
gi|17538748|ref|NP_501868.1|

Protein
Homo sapiens G protein beta 5 subunit mRNA, complete cds
Homo sapiens G protein beta 5 subunit mRNA, complete cds
gi|2570403|gb|AF017656.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002096040	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

SCV002096040

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, SCV002096040.1

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

Description

The copy number loss of 12q14.3q15 involves multiple coding genes, including HMGA2 (OMIM 600698), and is expected to cause phenotypic and/or developmental abnormalities. Deletions over this region of variable sizes affecting HMGA2 have been reported in the literature in patients with Silver-Russell syndrome-5 (OMIM 618908), a genetic disorder characterized by variable developmental disorders, intrauterine growth retardation with feeding difficulties in early childhood and postnatal growth failure, and dysmorphic features (Mercadante et al., Ital J Pediatr. 2020 Jul 28;46(1):108. PMID: 32723361). HMGA2 deletion is implicated for its role in growth regulation. Patients with focal deletions of HMGA2 have similar phenotypic features that include pre- and postnatal growth failure and underweight (Crescenzo et al., J Hum Genet. 2015 Jun;60(6):287-93. PMID: 25809938; Hubner et al., J Clin Endocrinol Metab. 2020 Jul 1;105(7):dgaa273. PMID: 32421827).

#	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: May 11, 2022

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