NM_006363.6(SEC23B):c.938G>A (p.Arg313His) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 28, 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:: RCV003783741.2

Allele description [Variation Report for NM_006363.6(SEC23B):c.938G>A (p.Arg313His)]

NM_006363.6(SEC23B):c.938G>A (p.Arg313His)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

20p11.23

Genomic location:

Preferred name:

NM_006363.6(SEC23B):c.938G>A (p.Arg313His)

HGVS:

NC_000020.11:g.18526476G>A
NG_016281.2:g.23995G>A
NM_001172745.3:c.938G>A
NM_001172746.3:c.884G>A
NM_006363.6:c.938G>AMANE SELECT
NM_032985.6:c.938G>A
NM_032986.5:c.938G>A
NP_001166216.1:p.Arg313His
NP_001166217.1:p.Arg295His
NP_006354.2:p.Arg313His
NP_116780.1:p.Arg313His
NP_116781.1:p.Arg313His
LRG_1134t1:c.938G>A
LRG_1134:g.23995G>A
LRG_1134p1:p.Arg313His
NC_000020.10:g.18507120G>A

Protein change:

R295H

Molecular consequence:

NM_001172745.3:c.938G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001172746.3:c.884G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_006363.6:c.938G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_032985.6:c.938G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_032986.5:c.938G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV004571418	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 28, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 19561605, 24196372, 25912935, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004571418

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 28, 2023)

germline

clinical testing

PubMed (4)
[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

Congenital dyserythropoietic anemia in China: a case report from two families and a review.

Ru Y, Liu G, Bai J, Dong S, Nie N, Zhang H, Zhao S, Zheng Y, Zhu X, Nie G, Zhang F, Eyden B.

Ann Hematol. 2014 May;93(5):773-7. doi: 10.1007/s00277-013-1933-8. Epub 2013 Nov 7. Review.

PubMed [citation]

PMID:: 24196372

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004571418.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt SEC23B protein function. This missense change has been observed in individuals with congenital dyserythropoietic anemia type II (PMID: 19561605, 24196372, 25912935). It has also been observed to segregate with disease in related individuals. This variant is present in population databases (no rsID available, gnomAD 0.003%). This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 313 of the SEC23B protein (p.Arg313His).

#	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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