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GeneBe

SEC24B

SEC24 homolog B, COPII coat complex component, the group of COPII coat complex|MicroRNA protein coding host genes

Basic information

Region (hg38): 4:109433771-109540896

Links

ENSG00000138802NCBI:10427OMIM:607184HGNC:10704Uniprot:O95487AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEC24B gene.

  • Inborn genetic diseases (50 variants)
  • not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC24B 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
0
missense
48
clinvar
3
clinvar
51
nonsense
1
clinvar
1
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
0
Total 0 0 49 3 0

Variants in SEC24B

This is a list of pathogenic ClinVar variants found in the SEC24B region.

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

Position Type Phenotype Significance ClinVar
4-109433976-C-T not specified Uncertain significance (Feb 12, 2024)3159282
4-109433981-C-G not specified Uncertain significance (May 02, 2023)2512370
4-109433981-C-T not specified Uncertain significance (Jul 12, 2022)2384404
4-109462891-G-GCTTTT Benign (Jul 12, 2018)767969
4-109462921-C-G not specified Uncertain significance (May 11, 2022)2371370
4-109463050-T-A not specified Uncertain significance (Sep 20, 2023)3159291
4-109463081-A-G not specified Likely benign (Apr 12, 2022)2283115
4-109463099-C-G not specified Uncertain significance (Sep 16, 2021)3159292
4-109463189-C-T not specified Uncertain significance (Jul 26, 2022)2303366
4-109463252-C-T not specified Uncertain significance (Dec 28, 2022)3159299
4-109463321-T-C not specified Uncertain significance (May 03, 2023)2513250
4-109463341-G-A not specified Uncertain significance (Jun 06, 2023)2563500
4-109463417-C-T not specified Uncertain significance (Dec 22, 2023)3159301
4-109463447-T-C Likely benign (Feb 01, 2024)3025157
4-109463468-T-C not specified Uncertain significance (Sep 21, 2021)2393625
4-109463480-C-T not specified Likely benign (Oct 25, 2022)2366383
4-109463534-G-A not specified Uncertain significance (Jan 03, 2024)3159302
4-109463554-T-A not specified Uncertain significance (May 24, 2023)2510195
4-109463573-C-T not specified Uncertain significance (Sep 26, 2022)2408987
4-109463587-C-T not specified Uncertain significance (Dec 14, 2021)2267270
4-109463599-C-T not specified Uncertain significance (Nov 28, 2023)3159303
4-109473039-G-A not specified Uncertain significance (Dec 14, 2023)3159304
4-109473100-C-T not specified Uncertain significance (Oct 18, 2021)2374049
4-109481706-C-G not specified Uncertain significance (Mar 14, 2023)2495865
4-109491332-G-A not specified Uncertain significance (Dec 13, 2022)2334333

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SEC24Bprotein_codingprotein_codingENST00000265175 24107125
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.000004221248610191248800.0000761
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.235586460.8630.00003248140
Missense in Polyphen190276.870.686253375
Synonymous0.6952302440.9430.00001292597
Loss of Function6.53661.10.09820.00000313793

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004010.000400
Ashkenazi Jewish0.000.00
East Asian0.00005560.0000554
Finnish0.000.00
European (Non-Finnish)0.00004460.0000441
Middle Eastern0.00005560.0000554
South Asian0.0001040.0000980
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 (PubMed:17499046, PubMed:20427317, PubMed:18843296). Plays a central role in cargo selection within the COPII complex and together with SEC24A may have a different specificity compared to SEC24C and SEC24D. May package preferentially cargos with cytoplasmic DxE or LxxLE motifs and may also recognize conformational epitopes (PubMed:17499046, PubMed:18843296). {ECO:0000269|PubMed:17499046, ECO:0000269|PubMed:18843296, ECO:0000269|PubMed:20427317}.;
Pathway
Protein processing in endoplasmic reticulum - Homo sapiens (human);Sterol Regulatory Element-Binding Proteins (SREBP) signalling;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
0.109

Intolerance Scores

loftool
0.222
rvis_EVS
-1.3
rvis_percentile_EVS
4.92

Haploinsufficiency Scores

pHI
0.151
hipred
Y
hipred_score
0.653
ghis
0.626

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.609

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sec24b
Phenotype
vision/eye phenotype; hearing/vestibular/ear 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); respiratory system phenotype; embryo 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); growth/size/body region phenotype; 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);

Gene ontology

Biological process
neural tube closure;antigen processing and presentation of peptide antigen via MHC class I;outflow tract morphogenesis;intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;antigen processing and presentation of exogenous peptide antigen via MHC class II;cochlear nucleus development;aorta morphogenesis;COPII vesicle coating;auditory receptor cell stereocilium organization;lung lobe morphogenesis;coronary artery morphogenesis;pulmonary artery morphogenesis;COPII-coated vesicle cargo loading;regulation of establishment of planar polarity involved in neural tube closure;regulation of cargo loading into COPII-coated vesicle
Cellular component
Golgi membrane;endoplasmic reticulum membrane;cytosol;ER to Golgi transport vesicle membrane;COPII vesicle coat
Molecular function
protein binding;zinc ion binding