SEC16B

protein-coding

SEC16 homolog B, endoplasmic reticulum export factor

Gene summary

SEC16B is a mammalian homolog of S. cerevisiae Sec16 that is required for organization of transitional endoplasmic reticulum (ER) sites and protein export (Bhattacharyya and Glick, 2007 [PubMed 17192411]).[supplied by OMIM, Jun 2009]

Previous symbols:

LZTR2

MANE transcript

NM_033127.4

Inheritance

ClinVar variants

U:181B:27

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.75

Max pathogenic AF

—

Genomic locus

chr1:177,923,956-177,984,303

External References & Databases

Ensembl (ENSG00000120341)

Transcript & Mutation Effects

hg38 • Region Span ~60.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

autosomal dominant polycystic liver diseaseMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0000447

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SEC16B variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 182

not providedTotal: 11

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033127.4. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	2 clinvar		7
missense			169 clinvar	20 clinvar	5 clinvar	194
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	181	22	5	208

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 60 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033127.4	RefSeq	NP_149118.2	25	MANE Select
ENST00000308284.11	Ensembl	ENSP00000308339.6	25	MANE Select
NM_001356499.2	RefSeq	NP_001343428.1	13	Standard
NM_001390833.1	RefSeq	NP_001377762.1	25	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vesicle-mediated transport
Membrane Trafficking
Post-translational protein modification
Metabolism of proteins
Transport to the Golgi and subsequent modification

Biological Process

endoplasmic reticulum to Golgi vesicle-mediated transport
endoplasmic reticulum organization
Golgi organization
peroxisome organization
positive regulation of gene expression

Molecular Function

protein binding

Cellular Component

Golgi membrane
endoplasmic reticulum membrane
cytosol
ER to Golgi transport vesicle membrane
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000308284
Coding exons: 25
Length: 60348
Individuals with no LoFs: 124559
Homozygous LoFs: 0
Heterozygous LoFs: 103
Defined: 124662
p: 0.000413

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.352	546	570	0.959	0.0000311	6762
Missense (PolyPhen)		133	160.78	0.82722		1985
Synonymous	1.21	197	220	0.896	0.0000124	2080
Loss of Function	1.80	47	62.3	0.754	0.00000325	691

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00040	0.00039	rare
Latino/Admixed American	0.00053	0.00052	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00056	0.00056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00036	0.00035	rare
South Asian	0.00073	0.00072	rare
Other	0.00083	0.00083	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required for secretory cargo traffic from the endoplasmic reticulum to the Golgi apparatus and for normal transitional endoplasmic reticulum (tER) organization. {ECO:0000269|PubMed:17192411}.;

Recessive Scores

pRec: 0.0945

Intolerance Scores

LoFtool: 0.856
RVIS EVS: 3.61
RVIS percentile EVS: 99.54

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.211

Gene Damage Prediction

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