GRCh37/hg19 8p23.3-23.1(chr8:10501-7214947)x1 AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 30, 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:: RCV001801195.2

Allele description [Variation Report for GRCh37/hg19 8p23.3-23.1(chr8:10501-7214947)x1]

GRCh37/hg19 8p23.3-23.1(chr8:10501-7214947)x1

Genes:

AGPAT5:1-acylglycerol-3-phosphate O-acyltransferase 5 [Gene - OMIM - HGNC]
CLN8:CLN8 transmembrane ER and ERGIC protein [Gene - OMIM - HGNC]
CSMD1:CUB and Sushi multiple domains 1 [Gene - OMIM - HGNC]
DLGAP2:DLG associated protein 2 [Gene - OMIM - HGNC]
FBXO25:F-box protein 25 [Gene - OMIM - HGNC]
ARHGEF10:Rho guanine nucleotide exchange factor 10 [Gene - OMIM - HGNC]
XKR5:XK related 5 [Gene - HGNC]
ANGPT2:angiopoietin 2 [Gene - OMIM - HGNC]
DEFA1:defensin alpha 1 [Gene - OMIM - HGNC]
DEFA1B:defensin alpha 1B [Gene - HGNC]
DEFA3:defensin alpha 3 [Gene - OMIM - HGNC]
DEFA4:defensin alpha 4 [Gene - OMIM - HGNC]
DEFA5:defensin alpha 5 [Gene - OMIM - HGNC]
DEFA6:defensin alpha 6 [Gene - OMIM - HGNC]
DEFB1:defensin beta 1 [Gene - OMIM - HGNC]
ERICH1:glutamate rich 1 [Gene - HGNC]
KBTBD11:kelch repeat and BTB domain containing 11 [Gene - OMIM - HGNC]
MCPH1:microcephalin 1 [Gene - OMIM - HGNC]
MYOM2:myomesin 2 [Gene - OMIM - HGNC]
OR4F21:olfactory receptor family 4 subfamily F member 21 [Gene - HGNC]
TDRP:testis development related protein [Gene - OMIM - HGNC]
USP17L1:ubiquitin specific peptidase 17 like family member 1 [Gene - HGNC]
USP17L4:ubiquitin specific peptidase 17 like family member 4 [Gene - HGNC]
ZNF596:zinc finger protein 596 [Gene - HGNC]

Variant type:

copy number loss

Cytogenetic location:

8p23.3-23.1

Genomic location:

Chr8: 10501 - 7214947 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 8p23.3-23.1(chr8:10501-7214947)x1

HGVS:

NC_000008.10:g.(?_10501)_(7214947_?)del

Condition(s)

Name:: Obesity
Synonyms:: Obesity disorder
Identifiers:: MONDO: MONDO:0011122; MeSH: D009765; MedGen: C0028754; Orphanet: 71529; Human Phenotype Ontology: HP:0001513

Name:: Brachycephaly
Identifiers:: MedGen: C0221356; Human Phenotype Ontology: HP:0000248

Name:: Single transverse palmar crease
Identifiers:: MedGen: C0424731; Human Phenotype Ontology: HP:0000954

Name:: Large for gestational age
Identifiers:: MedGen: C1848395; Human Phenotype Ontology: HP:0001520

Name:: Short foot
Identifiers:: MedGen: C1848673; Human Phenotype Ontology: HP:0001773

Name:: Mild global developmental delay
Identifiers:: MedGen: C4012968; Human Phenotype Ontology: HP:0011342

Name:: Small hand
Synonyms:: Small hands
Identifiers:: MedGen: C0575802; Human Phenotype Ontology: HP:0200055

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mesendo_derived_outgroup_ATACseq_rep2
mesendo_derived_outgroup_ATACseq_rep2

biosample
ATP-binding protein [Ralstonia syzygii]
ATP-binding protein [Ralstonia syzygii]
gi|2815699809|ref|WP_377420869.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002047407	Institute of Human Genetics, University of Leipzig Medical Center	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Pathogenic (Aug 30, 2021)	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

SCV002047407

Institute of Human Genetics, University of Leipzig Medical Center

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Pathogenic
(Aug 30, 2021)

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	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 Institute of Human Genetics, University of Leipzig Medical Center, SCV002047407.1

#	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	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 9, 2024

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