GRCh37/hg19 13q12.2-12.3(chr13:28669064-31367407)x1 AND 13q12.2q12.3 deletion

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jan 11, 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:: RCV001579311.2

Allele description [Variation Report for GRCh37/hg19 13q12.2-12.3(chr13:28669064-31367407)x1]

GRCh37/hg19 13q12.2-12.3(chr13:28669064-31367407)x1

Genes:

ALOX5AP:arachidonate 5-lipoxygenase activating protein [Gene - OMIM - HGNC]
FLT1:fms related receptor tyrosine kinase 1 [Gene - OMIM - HGNC]
FLT3:fms related receptor tyrosine kinase 3 [Gene - OMIM - HGNC]
HMGB1:high mobility group box 1 [Gene - OMIM - HGNC]
KATNAL1:katanin catalytic subunit A1 like 1 [Gene - OMIM - HGNC]
LINC00427:long intergenic non-protein coding RNA 427 [Gene - HGNC]
MTUS2:microtubule associated scaffold protein 2 [Gene - OMIM - HGNC]
PAN3:poly(A) specific ribonuclease subunit PAN3 [Gene - OMIM - HGNC]
POMP:proteasome maturation protein [Gene - OMIM - HGNC]
SLC46A3:solute carrier family 46 member 3 [Gene - OMIM - HGNC]
SLC7A1:solute carrier family 7 member 1 [Gene - OMIM - HGNC]
UBL3:ubiquitin like 3 [Gene - OMIM - HGNC]
USPL1:ubiquitin specific peptidase like 1 [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

13q12.2-12.3

Genomic location:

Chr13: 28669064 - 31367407 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 13q12.2-12.3(chr13:28669064-31367407)x1

HGVS:

NC_000013.10:g.(?_28669064)_(31367407_?)del

Observations:

Condition(s)

Name:: 13q12.2q12.3 deletion
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001805854	Medicover Genetics GmbH, Medicover Humangenetik Berlin-Lichtenberg MVZ	no assertion criteria provided	Likely pathogenic (Jan 11, 2021)	unknown	clinical testing	PubMed (4) [See all records that cite these PMIDs] 24664804, 31690835, 33023587, 25506442

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001805854

Medicover Genetics GmbH, Medicover Humangenetik Berlin-Lichtenberg MVZ

no assertion criteria provided

Likely pathogenic
(Jan 11, 2021)

unknown

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A newly recognized 13q12.3 microdeletion syndrome characterized by intellectual disability, microcephaly, and eczema/atopic dermatitis encompassing the HMGB1 and KATNAL1 genes.

Bartholdi D, Stray-Pedersen A, Azzarello-Burri S, Kibaek M, Kirchhoff M, Oneda B, Rødningen O, Schmitt-Mechelke T, Rauch A, Kjaergaard S.

Am J Med Genet A. 2014 May;164A(5):1277-83. doi: 10.1002/ajmg.a.36439. Epub 2014 Mar 24.

PubMed [citation]

PMID:: 24664804

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

See all PubMed Citations (4)

Details of each submission

From Medicover Genetics GmbH, Medicover Humangenetik Berlin-Lichtenberg MVZ, SCV001805854.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1		1	not provided	not provided	clinical testing	PubMed (4)

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

Last Updated: Oct 14, 2023

ClinVar

Relating variation to medicine