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GeneBe

SEC23A

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

Basic information

Region (hg38): 14:39031918-39109646

Links

ENSG00000100934NCBI:10484OMIM:610511HGNC:10701Uniprot:Q15436AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • craniolenticulosutural dysplasia (Limited), mode of inheritance: AR
  • craniolenticulosutural dysplasia (Supportive), mode of inheritance: AR
  • craniolenticulosutural dysplasia (Limited), mode of inheritance: AR
  • craniolenticulosutural dysplasia (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Craniolenticulosutural dysplasiaAD/ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Musculoskeletal; Ophthalmologic12677423; 16980979; 21039434; 34580982

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEC23A gene.

  • not provided (73 variants)
  • Craniolenticulosutural dysplasia (72 variants)
  • Inborn genetic diseases (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC23A 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
20
clinvar
3
clinvar
23
missense
1
clinvar
46
clinvar
1
clinvar
48
nonsense
2
clinvar
2
start loss
0
frameshift
2
clinvar
2
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
1
5
2
8
non coding
12
clinvar
52
clinvar
64
Total 0 2 51 32 56

Highest pathogenic variant AF is 0.0000131

Variants in SEC23A

This is a list of pathogenic ClinVar variants found in the SEC23A region.

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

Position Type Phenotype Significance ClinVar
14-39033275-AT-A Craniolenticulosutural dysplasia Uncertain significance (Nov 07, 2022)2802989
14-39033335-G-GA Craniolenticulosutural dysplasia Benign (Jan 31, 2024)683759
14-39033422-A-AAATAGAAC Benign (Jul 27, 2018)1283041
14-39033426-G-GAA Benign (May 23, 2021)1280265
14-39033427-C-CAATAA Benign (May 23, 2021)1252741
14-39038863-G-T Benign (Sep 05, 2018)1289736
14-39039011-G-A Craniolenticulosutural dysplasia Likely benign (Feb 24, 2022)2100035
14-39039025-A-T Craniolenticulosutural dysplasia Uncertain significance (Jan 23, 2023)576528
14-39039048-T-C not specified Uncertain significance (Dec 08, 2023)3159247
14-39039073-G-A Craniolenticulosutural dysplasia • SEC23A-related condition Likely benign (Sep 01, 2022)715781
14-39039085-G-A Craniolenticulosutural dysplasia Likely benign (Feb 03, 2022)725508
14-39039093-G-A Uncertain significance (Apr 22, 2021)1212127
14-39039403-C-T Benign (Jul 27, 2018)1181688
14-39040727-C-CTT Craniolenticulosutural dysplasia Likely benign (Aug 04, 2023)788183
14-39040770-T-C Craniolenticulosutural dysplasia Uncertain significance (Jul 26, 2023)39521
14-39040813-G-T SEC23A-related condition Likely benign (Sep 28, 2020)3054234
14-39040823-A-C Uncertain significance (Oct 22, 2019)1309243
14-39040830-G-A not specified Uncertain significance (Mar 29, 2023)2518339
14-39040836-T-C Craniolenticulosutural dysplasia • not specified Uncertain significance (Dec 05, 2022)1346764
14-39040902-A-G Craniolenticulosutural dysplasia Likely benign (Jun 20, 2023)2958231
14-39040969-T-C Benign (Jul 27, 2018)1291639
14-39042748-CT-C Benign (Sep 05, 2018)1242001
14-39042866-G-A Craniolenticulosutural dysplasia • not specified Conflicting classifications of pathogenicity (Feb 09, 2023)732301
14-39042878-G-A Craniolenticulosutural dysplasia Likely benign (Sep 28, 2023)2715411
14-39042882-A-G Craniolenticulosutural dysplasia Benign (Jan 18, 2024)791748

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SEC23Aprotein_codingprotein_codingENST00000307712 1977728
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.07e-110.9991256920561257480.000223
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.783194220.7560.00002165009
Missense in Polyphen77124.950.616261500
Synonymous0.5071231300.9440.000006021476
Loss of Function3.012648.70.5340.00000270527

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004370.000437
Ashkenazi Jewish0.00009920.0000992
East Asian0.0005990.000598
Finnish0.00004620.0000462
European (Non-Finnish)0.0001940.000193
Middle Eastern0.0005990.000598
South Asian0.0002290.000229
Other0.000.00

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:0000269|PubMed:16980979, ECO:0000269|PubMed:17499046, ECO:0000269|PubMed:18843296, ECO:0000269|PubMed:27551091, ECO:0000269|PubMed:8898360}.;
Disease
DISEASE: Craniolenticulosutural dysplasia (CLSD) [MIM:607812]: Autosomal recessive syndrome characterized by late-closing fontanels, sutural cataracts, facial dysmorphisms and skeletal defects. {ECO:0000269|PubMed:16980979}. 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;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;MHC class II antigen presentation;Immune System;Adaptive Immune System;Class I MHC mediated antigen processing & presentation;Cargo concentration in the ER;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport;Antigen Presentation: Folding, assembly and peptide loading of class I MHC (Consensus)

Recessive Scores

pRec
0.168

Intolerance Scores

loftool
0.500
rvis_EVS
-0.78
rvis_percentile_EVS
12.88

Haploinsufficiency Scores

pHI
0.689
hipred
Y
hipred_score
0.589
ghis
0.657

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.970

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sec23a
Phenotype
growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Zebrafish Information Network

Gene name
sec23a
Affected structure
pharyngeal arch cartilage
Phenotype tag
abnormal
Phenotype quality
decreased size

Gene ontology

Biological process
antigen processing and presentation of peptide antigen via MHC class I;intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;antigen processing and presentation of exogenous peptide antigen via MHC class II;positive regulation of GTPase activity;COPII vesicle coating;protein localization to plasma membrane;COPII-coated vesicle cargo loading
Cellular component
endoplasmic reticulum membrane;cytosol;ER to Golgi transport vesicle membrane;extrinsic component of membrane;COPII vesicle coat;endoplasmic reticulum exit site
Molecular function
GTPase activator activity;protein binding;zinc ion binding