SEC16B

SEC16 homolog B, endoplasmic reticulum export factor

Basic information

Region (hg38): 1:177923956-177984303

Previous symbols: [ "LZTR2" ]

Links

ENSG00000120341 ∙ NCBI:89866 ∙ OMIM:612855 ∙ HGNC:30301 ∙ Uniprot:Q96JE7 ∙ 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 SEC16B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC16B 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				1		1
missense			67	11	4	82
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	67	12	4

Variants in SEC16B

This is a list of pathogenic ClinVar variants found in the SEC16B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-177929895-C-T		not specified	Uncertain significance (May 24, 2024)
1-177929905-G-A		not specified	Uncertain significance (Oct 05, 2022)
1-177929910-A-G		not specified	Uncertain significance (May 15, 2024)
1-177929920-C-T		not specified	Uncertain significance (Jul 26, 2024)
1-177930553-C-G		not specified	Uncertain significance (May 30, 2023)
1-177930562-G-T		not specified	Uncertain significance (Sep 27, 2024)
1-177930564-T-C			Benign (Jul 15, 2018)
1-177930595-G-A		not specified	Uncertain significance (Mar 15, 2024)
1-177930595-G-T		not specified	Uncertain significance (Nov 08, 2021)
1-177932495-G-A		not specified	Uncertain significance (Dec 03, 2024)
1-177932495-G-C		not specified	Uncertain significance (Oct 24, 2024)
1-177932506-C-A		not specified	Uncertain significance (Nov 15, 2021)
1-177932516-C-G		not specified	Uncertain significance (Dec 22, 2023)
1-177932524-G-A		not specified	Uncertain significance (Oct 04, 2024)
1-177932546-C-T		not specified	Likely benign (May 15, 2024)
1-177932554-C-T		not specified	Likely benign (Dec 21, 2022)
1-177932748-G-A		not specified	Uncertain significance (Apr 20, 2024)
1-177932764-G-A		not specified	Uncertain significance (Jun 25, 2024)
1-177932802-G-T		not specified	Uncertain significance (Jun 06, 2023)
1-177933233-G-A			Benign (Jul 15, 2018)
1-177933239-T-C		not specified	Uncertain significance (Dec 04, 2023)
1-177933242-T-C		not specified	Uncertain significance (Mar 01, 2024)
1-177933278-G-A		not specified	Uncertain significance (Aug 21, 2023)
1-177933521-T-C		not specified	Likely benign (Jan 16, 2024)
1-177933533-C-T		not specified	Likely benign (Feb 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEC16B	protein_coding	protein_coding	ENST00000308284	25	60348

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.09e-25	0.129	124559	0	103	124662	0.000413

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.352	546	570	0.959	0.0000311	6762
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000928	0.000914
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.000558	0.000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000365	0.000354
Middle Eastern	0.000558	0.000556
South Asian	0.000729	0.000719
Other	0.000832	0.000826

dbNSFP

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}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport (Consensus)

Recessive Scores

• pRec: 0.0945

Intolerance Scores

• loftool: 0.856
• rvis_EVS: 3.61
• rvis_percentile_EVS: 99.54

Haploinsufficiency Scores

• pHI: 0.433
• hipred: N
• hipred_score: 0.172

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.211

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sec16b
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;endoplasmic reticulum organization;Golgi organization;peroxisome organization;positive regulation of gene expression;protein transport;peroxisome fission;COPII vesicle coating;positive regulation of protein exit from endoplasmic reticulum;protein localization to endoplasmic reticulum exit site
• Cellular component: Golgi membrane;endoplasmic reticulum membrane;cytosol;ER to Golgi transport vesicle membrane;intracellular membrane-bounded organelle;endoplasmic reticulum exit site
• Molecular function: protein binding