NM_006363.6(SEC23B):c.983dup (p.Ala329fs) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 19, 2023
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:: RCV003803590.2

Allele description [Variation Report for NM_006363.6(SEC23B):c.983dup (p.Ala329fs)]

NM_006363.6(SEC23B):c.983dup (p.Ala329fs)

Gene:

SEC23B:SEC23 homolog B, COPII coat complex component [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

20p11.23

Genomic location:

Preferred name:

NM_006363.6(SEC23B):c.983dup (p.Ala329fs)

HGVS:

NC_000020.11:g.18526521dup
NG_016281.2:g.24040dup
NM_001172745.3:c.983dup
NM_001172746.3:c.929dup
NM_006363.6:c.983dupMANE SELECT
NM_032985.6:c.983dup
NM_032986.5:c.983dup
NP_001166216.1:p.Ala329fs
NP_001166217.1:p.Ala311fs
NP_006354.2:p.Ala329fs
NP_116780.1:p.Ala329fs
NP_116781.1:p.Ala329fs
LRG_1134t1:c.983dup
LRG_1134:g.24040dup
LRG_1134p1:p.Ala329fs
NC_000020.10:g.18507160_18507161insA
NC_000020.10:g.18507165dup

Protein change:

A311fs

Molecular consequence:

NM_001172745.3:c.983dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001172746.3:c.929dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_006363.6:c.983dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_032985.6:c.983dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_032986.5:c.983dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Congenital dyserythropoietic anemia, type II (CDAN2)
Synonyms:: Dyserythropoietic anemia, congenital type 2; CDA 2; HEMPAS anemia; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009134; MedGen: C1306589; Orphanet: 98873; OMIM: 224100

Name:: Cowden syndrome 7 (CWS7)
Identifiers:: MONDO: MONDO:0014802; MedGen: C4225179; Orphanet: 201; OMIM: 616858

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004593782	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 19, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 19561605, 25044164, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004593782

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 19, 2023)

germline

clinical testing

PubMed (3)
[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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutations affecting the secretory COPII coat component SEC23B cause congenital dyserythropoietic anemia type II.

Schwarz K, Iolascon A, Verissimo F, Trede NS, Horsley W, Chen W, Paw BH, Hopfner KP, Holzmann K, Russo R, Esposito MR, Spano D, De Falco L, Heinrich K, Joggerst B, Rojewski MT, Perrotta S, Denecke J, Pannicke U, Delaunay J, Pepperkok R, Heimpel H.

Nat Genet. 2009 Aug;41(8):936-40. doi: 10.1038/ng.405. Epub 2009 Jun 28.

PubMed [citation]

PMID:: 19561605

Retrospective cohort study of 205 cases with congenital dyserythropoietic anemia type II: definition of clinical and molecular spectrum and identification of new diagnostic scores.

Russo R, Gambale A, Langella C, Andolfo I, Unal S, Iolascon A.

Am J Hematol. 2014 Oct;89(10):E169-75. doi: 10.1002/ajh.23800. Epub 2014 Jul 22.

PubMed [citation]

PMID:: 25044164

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004593782.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Ala329Glyfs*6) in the SEC23B gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SEC23B are known to be pathogenic (PMID: 19561605, 25044164). This variant has not been reported in the literature in individuals affected with SEC23B-related conditions. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024

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