NM_004766.3(COPB2):c.1237_1238del (p.Lys413fs) AND COPB2-related disorder

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 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:: RCV001788996.3

Allele description [Variation Report for NM_004766.3(COPB2):c.1237_1238del (p.Lys413fs)]

NM_004766.3(COPB2):c.1237_1238del (p.Lys413fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

3q23

Genomic location:

Preferred name:

NM_004766.3(COPB2):c.1237_1238del (p.Lys413fs)

Other names:

p.K413NfsTer3

HGVS:

NC_000003.12:g.139369513_139369514del
NM_004766.3:c.1237_1238delMANE SELECT
NP_004757.1:p.Lys413fs
NC_000003.11:g.139088355_139088356del
NM_004766.2:c.1237_1238delAA
NR_023350.1:n.1446_1447del

Protein change:

K413fs

Links:

OMIM: 606990.0002; dbSNP: rs2107801839

Molecular consequence:

NM_004766.3:c.1237_1238del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_023350.1:n.1446_1447del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Name:: COPB2-related disorder
Synonyms:: COPB2-related condition
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002030293	Undiagnosed Diseases Network, NIH - Undiagnosed Diseases Network (NIH), UDN	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Nov 30, 2021)	de novo	clinical testing	PubMed (2) [See all records that cite these PMIDs] 34450031, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002030293

Undiagnosed Diseases Network, NIH - Undiagnosed Diseases Network (NIH), UDN

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Nov 30, 2021)

de novo

clinical testing

PubMed (2)
[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	de novo	yes	1	1	not provided	not provided	not provided	clinical testing

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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Undiagnosed Diseases Network, NIH - Undiagnosed Diseases Network (NIH), UDN, SCV002030293.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (2)

Description

This individual has been published in PMID: 34450031.

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

Last Updated: Apr 13, 2025

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