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GeneBe

SEC23B

SEC23 homolog B, COPII coat complex component, the group of COPII coat complex

Basic information

Region (hg38): 20:18507519-18561415

Previous symbols: [ "CDAN2" ]

Links

ENSG00000101310NCBI:10483OMIM:610512HGNC:10702Uniprot:Q15437AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • congenital dyserythropoietic anemia type 2 (Definitive), mode of inheritance: AR
  • congenital dyserythropoietic anemia (Limited), mode of inheritance: AR
  • congenital dyserythropoietic anemia type 2 (Strong), mode of inheritance: AR
  • Cowden disease (Supportive), mode of inheritance: AD
  • congenital dyserythropoietic anemia type 2 (Supportive), mode of inheritance: AR
  • Cowden syndrome 7 (Limited), mode of inheritance: AD
  • congenital dyserythropoietic anemia type 2 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Cowden syndrome 7; Anemia, dyserythropoietic congenital, type IIAD/ARGastrointestinal; Hematologic; OncologicIndividuals with Cowden syndrome have been described with cancer, and awareness may be beneficial to allow screening, prompt diagnosis, and management; Individuals with Anemia, dyserythropoietic congenital, type II may require RBC transfusions in the neonatal period; Splenectomy may be beneficial; Gallbladder complications are common, and early treatment may be beneficial; Iron overload is commonEndocrine; Gastrointestinal; Hematologic; Oncologic13884336; 5807784; 5807786; 4340898; 10753261; 11493480; 19621418; 19561605; 20381388; 20941788;21252497; 21378561; 21850656; 22208203; 22428539; 23065504; 23453696; 23940284; 23978024; 24196372; 26522472
Heterozygotes with variants related to Anemia, dyserythropoietic congenital, type II may have mild manifestations

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEC23B gene.

  • not provided (154 variants)
  • Congenital dyserythropoietic anemia, type II;Cowden syndrome 7 (101 variants)
  • Congenital dyserythropoietic anemia, type II (79 variants)
  • Cowden syndrome 7;Congenital dyserythropoietic anemia, type II (54 variants)
  • not specified (21 variants)
  • Inborn genetic diseases (20 variants)
  • Cowden syndrome 7 (16 variants)
  • Congenital dyserythropoietic anemia (14 variants)
  • SEC23B-related condition (4 variants)
  • SEC23B-Related Disorders (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC23B gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
4
clinvar
30
clinvar
4
clinvar
38
missense
4
clinvar
1
clinvar
101
clinvar
7
clinvar
2
clinvar
115
nonsense
8
clinvar
2
clinvar
10
start loss
0
frameshift
6
clinvar
6
clinvar
1
clinvar
13
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
1
clinvar
1
clinvar
1
clinvar
3
splice region
1
4
4
3
12
non coding
22
clinvar
27
clinvar
55
clinvar
104
Total 19 10 130 64 61

Highest pathogenic variant AF is 0.000243

Variants in SEC23B

This is a list of pathogenic ClinVar variants found in the SEC23B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
20-18507593-A-C Congenital dyserythropoietic anemia Uncertain significance (Jun 14, 2016)337778
20-18507686-G-A Congenital dyserythropoietic anemia Uncertain significance (Jun 14, 2016)337779
20-18507704-C-T Congenital dyserythropoietic anemia Uncertain significance (Jun 14, 2016)337780
20-18507755-C-G Congenital dyserythropoietic anemia Benign (Jul 27, 2018)337781
20-18507801-G-T Congenital dyserythropoietic anemia Uncertain significance (Jun 14, 2016)337782
20-18507893-C-G Congenital dyserythropoietic anemia Uncertain significance (Jun 14, 2016)337783
20-18507907-G-A Congenital dyserythropoietic anemia Uncertain significance (Jun 14, 2016)337784
20-18507911-G-C Congenital dyserythropoietic anemia Uncertain significance (Jun 14, 2016)337785
20-18507930-G-C Congenital dyserythropoietic anemia Likely benign (Jun 14, 2016)337786
20-18507935-T-G Congenital dyserythropoietic anemia Uncertain significance (Jun 14, 2016)337787
20-18507963-C-T Congenital dyserythropoietic anemia, type II Benign (Jan 13, 2018)337788
20-18508031-G-A Uncertain significance (Dec 01, 2020)1163639
20-18508110-G-C Benign (Jul 27, 2018)1281680
20-18508193-G-C Likely benign (Jun 17, 2019)1192948
20-18510821-G-A Congenital dyserythropoietic anemia, type II Uncertain significance (Dec 16, 2019)1030101
20-18510828-T-C Congenital dyserythropoietic anemia, type II Uncertain significance (Jan 13, 2018)337789
20-18510840-C-T Congenital dyserythropoietic anemia, type II;Cowden syndrome 7 Uncertain significance (Apr 11, 2022)2041736
20-18510841-G-A Congenital dyserythropoietic anemia, type II;Cowden syndrome 7 Likely benign (Dec 11, 2023)1895564
20-18510844-A-G Congenital dyserythropoietic anemia, type II;Cowden syndrome 7 Likely benign (Dec 18, 2023)2937249
20-18510859-C-A Cowden syndrome 7;Congenital dyserythropoietic anemia, type II Likely benign (Mar 08, 2023)2944611
20-18510859-C-T Cowden syndrome 7;Congenital dyserythropoietic anemia, type II Likely benign (Oct 15, 2023)2948326
20-18510875-C-T Congenital dyserythropoietic anemia, type II • Cowden syndrome 7;Congenital dyserythropoietic anemia, type II Pathogenic/Likely pathogenic (Mar 26, 2024)1223
20-18510888-G-A Congenital dyserythropoietic anemia, type II;Cowden syndrome 7 • not specified Conflicting classifications of pathogenicity (Mar 22, 2024)1701418
20-18510899-A-G Uncertain significance (Jul 01, 2022)1701419
20-18510901-C-T Congenital dyserythropoietic anemia, type II;Cowden syndrome 7 • SEC23B-related condition Benign/Likely benign (Jan 29, 2024)532196

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SEC23Bprotein_codingprotein_codingENST00000336714 1953923
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
6.10e-200.28212557401741257480.000692
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4733904170.9350.00002345029
Missense in Polyphen105128.730.815681496
Synonymous0.2911451500.9700.000008261510
Loss of Function1.683749.80.7430.00000329486

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0008300.000828
Ashkenazi Jewish0.000.00
East Asian0.0005440.000544
Finnish0.0004160.000416
European (Non-Finnish)0.0009510.000932
Middle Eastern0.0005440.000544
South Asian0.0007190.000719
Other0.0006550.000652

dbNSFP

Source: dbNSFP

Function
FUNCTION: Component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). The coat has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules for their transport to the Golgi complex. {ECO:0000250|UniProtKB:Q15436}.;
Disease
DISEASE: Anemia, congenital dyserythropoietic, 2 (CDAN2) [MIM:224100]: An autosomal recessive blood disorder characterized by morphological abnormalities of erythroblasts, ineffective erythropoiesis, normocytic anemia, iron overload, jaundice, and variable splenomegaly. Ultrastructural features include bi- or multinucleated erythroblasts in bone marrow, karyorrhexis, and the presence of Gaucher-like bone marrow histiocytes. The main biochemical feature of the disease is defective glycosylation of some red blood cells membrane proteins. {ECO:0000269|PubMed:19561605, ECO:0000269|PubMed:19621418}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Protein processing in endoplasmic reticulum - Homo sapiens (human);Sterol Regulatory Element-Binding Proteins (SREBP) signalling (Consensus)

Recessive Scores

pRec
0.152

Intolerance Scores

loftool
0.120
rvis_EVS
0.49
rvis_percentile_EVS
79.61

Haploinsufficiency Scores

pHI
0.104
hipred
N
hipred_score
0.333
ghis
0.554

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.738

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sec23b
Phenotype
cellular phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; immune system phenotype; digestive/alimentary phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Zebrafish Information Network

Gene name
sec23b
Affected structure
nucleate erythrocyte
Phenotype tag
abnormal
Phenotype quality
immature

Gene ontology

Biological process
intracellular protein transport;positive regulation of GTPase activity;COPII-coated vesicle cargo loading
Cellular component
Golgi membrane;endoplasmic reticulum;endoplasmic reticulum membrane;cytosol;endomembrane system;COPII vesicle coat;endoplasmic reticulum exit site
Molecular function
GTPase activator activity;protein binding