GRCh37/hg19 12q24.31-24.32(chr12:123878845-126829341) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 15, 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:: RCV001352637.1

Allele description [Variation Report for GRCh37/hg19 12q24.31-24.32(chr12:123878845-126829341)]

GRCh37/hg19 12q24.31-24.32(chr12:123878845-126829341)

Genes:

ATP6V0A2:ATPase H+ transporting V0 subunit a2 [Gene - OMIM - HGNC]
BRI3BP:BRI3 binding protein [Gene - OMIM - HGNC]
DDX55:DEAD-box helicase 55 [Gene - OMIM - HGNC]
DHX37:DEAH-box helicase 37 [Gene - OMIM - HGNC]
RILPL1:Rab interacting lysosomal protein like 1 [Gene - OMIM - HGNC]
RILPL2:Rab interacting lysosomal protein like 2 [Gene - OMIM - HGNC]
AACS:acetoacetyl-CoA synthetase [Gene - OMIM - HGNC]
CCDC92:coiled-coil domain containing 92 [Gene - HGNC]
DNAH10:dynein axonemal heavy chain 10 [Gene - OMIM - HGNC]
EIF2B1:eukaryotic translation initiation factor 2B subunit alpha [Gene - OMIM - HGNC]
GTF2H3:general transcription factor IIH subunit 3 [Gene - OMIM - HGNC]
KMT5A:lysine methyltransferase 5A [Gene - OMIM - HGNC]
NCOR2:nuclear receptor corepressor 2 [Gene - OMIM - HGNC]
RFLNA:refilin A [Gene - OMIM - HGNC]
SCARB1:scavenger receptor class B member 1 [Gene - OMIM - HGNC]
SNRNP35:small nuclear ribonucleoprotein U11/U12 subunit 35 [Gene - OMIM - HGNC]
TCTN2:tectonic family member 2 [Gene - OMIM - HGNC]
TMED2:transmembrane p24 trafficking protein 2 [Gene - OMIM - HGNC]
TMEM132B:transmembrane protein 132B [Gene - OMIM - HGNC]
UBC:ubiquitin C [Gene - OMIM - HGNC]
ZNF664:zinc finger protein 664 [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

12q24.31-24.32

Genomic location:

Chr12: 123878845 - 126829341 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 12q24.31-24.32(chr12:123878845-126829341)

HGVS:

NC_000012.11:g.(?_123878845)_(126829341_?)del

Condition(s)

Name:: Severe short stature
Synonyms:: Dwarfism
Identifiers:: MedGen: C0013336; Human Phenotype Ontology: HP:0003510

Name:: Abnormal facial shape
Synonyms:: Dysmorphic facies; Dysmorphic facial features
Identifiers:: MedGen: C0424503; Human Phenotype Ontology: HP:0001999

Name:: Neurodevelopmental delay
Identifiers:: MedGen: C4022738; Human Phenotype Ontology: HP:0012758

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001547205	Medical Genetics Laboratory, CHRU Nancy	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Pathogenic (Mar 15, 2021)	de novo	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

SCV001547205

Medical Genetics Laboratory, CHRU Nancy

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Pathogenic
(Mar 15, 2021)

de novo

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	de novo	yes	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 Medical Genetics Laboratory, CHRU Nancy, SCV001547205.1

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

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

Last Updated: Oct 8, 2024

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