GRCh37/hg19 3p26.3-25.3(chr3:61892-9769457)x1 AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 8, 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:: RCV002472587.1

Allele description [Variation Report for GRCh37/hg19 3p26.3-25.3(chr3:61892-9769457)x1]

GRCh37/hg19 3p26.3-25.3(chr3:61892-9769457)x1

Genes:

ARL8B:ADP ribosylation factor like GTPase 8B [Gene - OMIM - HGNC]
EDEM1:ER degradation enhancing alpha-mannosidase like protein 1 [Gene - OMIM - HGNC]
LHFPL4:LHFPL tetraspan subfamily member 4 [Gene - OMIM - HGNC]
LMCD1:LIM and cysteine rich domains 1 [Gene - OMIM - HGNC]
RAD18:RAD18 E3 ubiquitin protein ligase [Gene - OMIM - HGNC]
SETMAR:SET domain and mariner transposase fusion gene [Gene - OMIM - HGNC]
SETD5:SET domain containing 5 [Gene - OMIM - HGNC]
SRGAP3:SLIT-ROBO Rho GTPase activating protein 3 [Gene - OMIM - HGNC]
THUMPD3:THUMP domain containing 3 [Gene - HGNC]
BHLHE40:basic helix-loop-helix family member e40 [Gene - OMIM - HGNC]
CAV3:caveolin 3 [Gene - OMIM - HGNC]
CHL1:cell adhesion molecule L1 like [Gene - OMIM - HGNC]
CRBN:cereblon [Gene - OMIM - HGNC]
CNTN4:contactin 4 [Gene - OMIM - HGNC]
CNTN6:contactin 6 [Gene - OMIM - HGNC]
CPNE9:copine family member 9 [Gene - HGNC]
EGOT:eosinophil granule ontogeny transcript [Gene - OMIM - HGNC]
GRM7:glutamate metabotropic receptor 7 [Gene - OMIM - HGNC]
ITPR1:inositol 1,4,5-trisphosphate receptor type 1 [Gene - OMIM - HGNC]
IL5RA:interleukin 5 receptor subunit alpha [Gene - OMIM - HGNC]
LRRN1:leucine rich repeat neuronal 1 [Gene - OMIM - HGNC]
LINC00312:long intergenic non-protein coding RNA 312 [Gene - OMIM - HGNC]
MTMR14:myotubularin related protein 14 [Gene - OMIM - HGNC]
OXTR:oxytocin receptor [Gene - OMIM - HGNC]
SSUH2:ssu-2 homolog [Gene - OMIM - HGNC]
SUMF1:sulfatase modifying factor 1 [Gene - OMIM - HGNC]
TRNT1:tRNA nucleotidyl transferase 1 [Gene - OMIM - HGNC]

Variant type:

copy number loss

Cytogenetic location:

3p26.3-25.3

Genomic location:

Chr3: 61892 - 9769457 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 3p26.3-25.3(chr3:61892-9769457)x1

HGVS:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002772455	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Pathogenic (Oct 8, 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

SCV002772455

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Pathogenic
(Oct 8, 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	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. doi: 10.1038/s41436-021-01150-9.

PubMed [citation]

PMID:: 31690835
PMCID:: PMC7313390

Details of each submission

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV002772455.1

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

Description

This genomic loss is expected to cause phenotypic and/or developmental abnormalities and may be consistent with 3p- syndrome (OMIM 613792). Characteristic features of the distal 3p- syndrome include low birth weight, microcephaly, trigonocephaly, hypotonia, psychomotor and growth delay, ptosis, telecanthus, downslanting palpebral fissures, and micrognathia. Postaxial polydactyly, renal anomalies, cleft palate, congenital heart defects (especially atrioventricular septal defects), preauricular pits, sacral dimple, and gastrointestinal anomalies are variable features. CAV3 has been suggested as the gene responsible for those 3p- patients with heart defects (PMID 10386585). Heterozygous loss-of-function mutations and deletions affecting SETD5 have been identified in multiple unrelated patients with intellectual disability and similar facial features (PMID 25138099).

#	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: Dec 31, 2022

ClinVar

Relating variation to medicine