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

ENSG00000138802 ∙ NCBI:10427 ∙ OMIM:607184 ∙ HGNC:10704 ∙ Uniprot:O95487 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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			66	4		70
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	67	4	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)
4-109433981-C-G		not specified	Uncertain significance (May 02, 2023)
4-109433981-C-T		not specified	Uncertain significance (Jul 12, 2022)
4-109462891-G-GCTTTT			Benign (Jul 12, 2018)
4-109462921-C-G		not specified	Uncertain significance (May 11, 2022)
4-109463050-T-A		not specified	Uncertain significance (Sep 20, 2023)
4-109463081-A-G		not specified	Likely benign (Apr 12, 2022)
4-109463099-C-G		not specified	Uncertain significance (Sep 16, 2021)
4-109463189-C-T		not specified	Uncertain significance (Jul 26, 2022)
4-109463252-C-T		not specified	Uncertain significance (Dec 28, 2022)
4-109463321-T-C		not specified	Uncertain significance (May 03, 2023)
4-109463341-G-A		not specified	Uncertain significance (Jun 06, 2023)
4-109463417-C-T		not specified	Uncertain significance (Dec 22, 2023)
4-109463447-T-C			Likely benign (Feb 01, 2024)
4-109463468-T-C		not specified	Uncertain significance (Sep 21, 2021)
4-109463480-C-T		not specified	Likely benign (Oct 25, 2022)
4-109463534-G-A		not specified	Uncertain significance (Jan 03, 2024)
4-109463554-T-A		not specified	Uncertain significance (May 24, 2023)
4-109463573-C-T		not specified	Uncertain significance (Sep 26, 2022)
4-109463587-C-T		not specified	Uncertain significance (Dec 14, 2021)
4-109463599-C-T		not specified	Uncertain significance (Nov 28, 2023)
4-109473039-G-A		not specified	Uncertain significance (Dec 14, 2023)
4-109473100-C-T		not specified	Uncertain significance (Oct 18, 2021)
4-109481706-C-G		not specified	Uncertain significance (Mar 14, 2023)
4-109491332-G-A		not specified	Uncertain significance (Dec 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEC24B	protein_coding	protein_coding	ENST00000265175	24	107125

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000422	124861	0	19	124880	0.0000761

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.23	558	646	0.863	0.0000324	8140
Missense in Polyphen		190	276.87	0.68625		3375
Synonymous	0.695	230	244	0.943	0.0000129	2597
Loss of Function	6.53	6	61.1	0.0982	0.00000313	793

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000401	0.000400
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000554
Finnish	0.00	0.00
European (Non-Finnish)	0.0000446	0.0000441
Middle Eastern	0.0000556	0.0000554
South Asian	0.000104	0.0000980
Other	0.00	0.00

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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