NM_004766.3(COPB2):c.247dup (p.Val83fs) AND Osteoporosis, childhood- or juvenile-onset, with developmental delay

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 24, 2022
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:: RCV002248441.1

Allele description [Variation Report for NM_004766.3(COPB2):c.247dup (p.Val83fs)]

NM_004766.3(COPB2):c.247dup (p.Val83fs)

Gene:

COPB2:COPI coat complex subunit beta 2 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

3q23

Genomic location:

Preferred name:

NM_004766.3(COPB2):c.247dup (p.Val83fs)

HGVS:

NC_000003.12:g.139379155dup
NM_004766.3:c.247dupMANE SELECT
NP_004757.1:p.Val83fs
NC_000003.11:g.139097997dup
NM_004766.2:c.247dup
NM_004766.2:c.247dupG
NR_023350.1:n.456dup

Protein change:

V83fs

Links:

OMIM: 606990.0005; dbSNP: rs2107807701

NCBI 1000 Genomes Browser:

rs2107807701

Molecular consequence:

NM_004766.3:c.247dup - frameshift variant - [Sequence Ontology: SO:0001589]
NR_023350.1:n.456dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Osteoporosis, childhood- or juvenile-onset, with developmental delay
Identifiers:: MONDO: MONDO:0859253; MedGen: C5676992; OMIM: 619884

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002520543	OMIM	no assertion criteria provided	Pathogenic (May 24, 2022)	germline	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002520543

OMIM

no assertion criteria provided

Pathogenic
(May 24, 2022)

germline

literature only

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	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

COPB2 loss of function causes a coatopathy with osteoporosis and developmental delay.

Marom R, Burrage LC, Venditti R, Clément A, Blanco-Sánchez B, Jain M, Scott DA, Rosenfeld JA, Sutton VR, Shinawi M, Mirzaa G, DeVile C, Roberts R, Calder AD, Allgrove J, Grafe I, Lanza DG, Li X, Joeng KS, Lee YC, Song IW, Sliepka JM, et al.

Am J Hum Genet. 2021 Sep 2;108(9):1710-1724. doi: 10.1016/j.ajhg.2021.08.002. Epub 2021 Aug 26.

PubMed [citation]

PMID:: 34450031
PMCID:: PMC8456174

Details of each submission

From OMIM, SCV002520543.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In a 3-year-old Asian girl (patient 4) with global developmental delay, microcephaly, and abnormal muscle tone (OPDD; 619884), Marom et al. (2021) identified heterozygosity for a de novo 1-bp duplication (c.247dupG, NM_004766.2) in exon 4 of the COPB2 gene, causing a frameshift predicted to result in a premature termination codon (Val83GlyfsTer14). The variant was not found in the gnomAD database. Bone mineral density assessment had not been performed in the proband.

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

Last Updated: Dec 24, 2023

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