GeneBe

SEC23A

protein-coding

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

Gene summary

The protein encoded by this gene is a member of the SEC23 subfamily of the SEC23/SEC24 family. It is part of a protein complex and found in the ribosome-free transitional face of the endoplasmic reticulum (ER) and associated vesicles. This protein has similarity to yeast Sec23p component of COPII. COPII is the coat protein complex responsible for vesicle budding from the ER. The encoded protein is suggested to play a role in the ER-Golgi protein trafficking. [provided by RefSeq, Jul 2008]

MANE transcript

NM_006364.4

Inheritance

AR, AD

ClinVar variants

P:4U:135B:29

Top phenotype

Craniolenticulosutural dysplasia

gnomAD constraint

pLI —, LoF o/e 0.53

Max pathogenic AF

—

Genomic locus

chr14:39,031,919-39,109,646

External References & Databases

Ensembl (ENSG00000100934)NCBI Gene (10484)OMIM (610511)HGNC:10701GenCCUniProt (Q15436)AlphaFoldClinVar (SEC23A)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~77.7 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

craniolenticulosutural dysplasiaMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0011911

Submitter: PanelApp Australia

craniolenticulosutural dysplasiaLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0011911

Submitter: Labcorp Genetics (formerly Invitae)

craniolenticulosutural dysplasiaLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0011911

Submitter: Labcorp Genetics (formerly Invitae)

craniolenticulosutural dysplasiaSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0011911

Submitter: Orphanet

craniolenticulosutural dysplasiaLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0011911

Submitter: G2P

Clinical Genomic Database (CGD)

Craniolenticulosutural dysplasiaAD/AR

Manifestation: Craniofacial; Musculoskeletal; Ophthalmologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 12677423; 16980979; 21039434; 34580982Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SEC23A variants in ClinVar

4 Conditions Cataloged
Craniolenticulosutural dysplasiaTotal: 120
not specifiedTotal: 72
not providedTotal: 19
SEC23A-related disorderTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006364.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
26
clinvar
1
clinvar
 28
missense
1
clinvar
2
clinvar
121
clinvar
2
clinvar
 126
nonsense
6
clinvar
 6
start loss
0
frameshift
4
clinvar
 4
splice donor/acceptor (+/-2bp)
1
clinvar
3
clinvar
 4
Total13135281168

Highest pathogenic variant AF is 0.00047081796

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_006364.4RefSeqNP_006355.219MANE Select
ENST00000307712.11EnsemblENSP00000306881.619MANE Select
ENST00000537403.5EnsemblENSP00000444193.115Standard
ENST00000537403.6EnsemblENSP00000444193.115Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
sec23aDanio rerio

Structure: pharyngeal arch cartilage

Quality: decreased size

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • 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

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

Molecular Function

  • GTPase activator activity
  • protein binding
  • zinc ion binding

Cellular Component

  • endoplasmic reticulum membrane
  • cytosol
  • ER to Golgi transport vesicle membrane
  • extrinsic component of membrane
  • COPII vesicle coat

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000307712
Coding exons
19
Length
77728
Individuals with no LoFs
125692
Homozygous LoFs
0
Heterozygous LoFs
56
Defined
125748
p
0.000223
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.783194220.7560.00002165009
Missense (PolyPhen)77124.950.616261500
Synonymous0.5071231300.9440.000006021476
Loss of Function3.012648.70.5340.00000270527

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.000380.00038rare
Ashkenazi Jewish0.0000990.000099rare
East Asian0.000600.00060rare
Finnish0.0000460.000046rare
European (Non-Finnish)0.000190.00019rare
South Asian0.000230.00023rare
Other00.0absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec
0.168

Intolerance Scores

LoFtool
0.500
RVIS EVS
-0.78
RVIS percentile EVS
12.88

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
S
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.970

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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