SEC23B

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

Basic information

Region (hg38): 20:18507520-18561415

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.

  • Congenital_dyserythropoietic_anemia,_type_II (541 variants)
  • Cowden_syndrome_7 (524 variants)
  • not_provided (159 variants)
  • Inborn_genetic_diseases (67 variants)
  • SEC23B-related_disorder (29 variants)
  • not_specified (27 variants)
  • See_cases (2 variants)
  • Susceptibility_to_severe_COVID-19 (1 variants)
  • Congenital_dyserythropoietic_anemia (1 variants)
  • Hereditary_ataxia (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. These statistics are base on transcript: NM_000006363.6. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
clinvar
188
clinvar
5
clinvar
195
missense
3
clinvar
22
clinvar
168
clinvar
16
clinvar
209
nonsense
21
clinvar
6
clinvar
27
start loss
1
1
frameshift
20
clinvar
13
clinvar
1
clinvar
34
splice donor/acceptor (+/-2bp)
5
clinvar
15
clinvar
1
clinvar
1
clinvar
22
Total 50 56 172 205 5

Highest pathogenic variant AF is 0.000265481

Loading clinvar variants...

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