SEC24B

protein-coding

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

Gene summary

The protein encoded by this gene is a member of the SEC24 subfamily of the SEC23/SEC24 family, which is involved in vesicle trafficking. The encoded protein is thought to be a cargo-binding component of the COPII vesicle, and is thought to be involved in the transport of secretory proteins from the endoplasmic reticulum to the Golgi apparatus. Mutations in this gene have been associated with neural tube defects, and are thought to be a result of a disruption in interactions with the protein encoded by the VANGL planar cell polarity protein 2 (VANGL2) gene. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]

MANE transcript

NM_006323.5

Inheritance

—

ClinVar variants

U:204B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chr4:109,433,772-109,540,896

External References & Databases

Ensembl (ENSG00000138802)

Transcript & Mutation Effects

hg38 • Region Span ~107.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SEC24B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 187

not providedTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006323.5. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	1 clinvar		5
missense			183 clinvar	13 clinvar		196
nonsense			5 clinvar			5
start loss			1 clinvar			1
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			9 clinvar			9
Total	0	0	204	14	0	218

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 78 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006323.5	RefSeq	NP_006314.2	24	MANE Select
ENST00000265175.5	Ensembl	ENSP00000265175.4	24	MANE Select
NM_001042734.4	RefSeq	NP_001036199.1	23	Standard
NM_001300813.3	RefSeq	NP_001287742.1	25	Standard

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
Vesicle-mediated transport
Membrane Trafficking
Post-translational protein modification

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

Molecular Function

protein binding
zinc ion binding

Cellular Component

Golgi membrane
endoplasmic reticulum membrane
cytosol
ER to Golgi transport vesicle membrane
COPII vesicle coat

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000265175
Coding exons: 24
Length: 107125
Individuals with no LoFs: 124861
Homozygous LoFs: 0
Heterozygous LoFs: 19
Defined: 124880
p: 0.0000761

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.23	558	646	0.863	0.0000324	8140
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00019	rare
Latino/Admixed American	0.00021	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000056	0.000055	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000045	0.000044	rare
South Asian	0.00010	0.000098	rare
Other	0	0.0	absent

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 (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}.;

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.222
RVIS EVS: -1.3
RVIS percentile EVS: 4.92

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.609

Gene Damage Prediction

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