SEC16A

SEC16 homolog A, endoplasmic reticulum export factor

Basic information

Region (hg38): 9:136440096-136483759

Previous symbols: [ "KIAA0310" ]

Links

ENSG00000148396 ∙ NCBI:9919 ∙ OMIM:612854 ∙ HGNC:29006 ∙ Uniprot:O15027 ∙ 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 SEC16A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC16A 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				12	6	18
missense			132	18	9	159
nonsense						0
start loss			1			1
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)			1			1
splice region				1	3	4
non coding				1		1
Total	0	0	134	32	15

Variants in SEC16A

This is a list of pathogenic ClinVar variants found in the SEC16A region.

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

Position	Type	Phenotype	Significance	ClinVar
9-136440101-G-C			Likely benign (Jul 09, 2018)
9-136441762-A-G		not specified	Uncertain significance (Apr 11, 2023)
9-136441788-C-G		not specified	Uncertain significance (Mar 25, 2024)
9-136441804-C-T		not specified	Uncertain significance (Oct 22, 2021)
9-136441809-G-A			Benign (Jul 19, 2018)
9-136443851-G-C		not specified	Uncertain significance (Dec 01, 2022)
9-136443891-C-T		not specified	Uncertain significance (Jan 29, 2024)
9-136445068-C-G		not specified	Uncertain significance (Aug 22, 2023)
9-136445069-T-A		not specified	Uncertain significance (Apr 18, 2023)
9-136445077-C-T		not specified	Uncertain significance (Apr 12, 2024)
9-136445078-G-C		not specified	Uncertain significance (Mar 16, 2022)
9-136445105-G-A		not specified	Uncertain significance (Feb 16, 2023)
9-136445107-G-A		not specified	Uncertain significance (Jun 24, 2022)
9-136446907-C-T		not specified	Uncertain significance (Nov 17, 2023)
9-136447248-T-C			Benign (Nov 13, 2018)
9-136447268-G-C		not specified	Uncertain significance (Jun 02, 2023)
9-136447269-C-T		not specified	Uncertain significance (Feb 14, 2024)
9-136447279-G-A			Likely benign (May 03, 2018)
9-136447296-C-T		not specified	Uncertain significance (May 17, 2023)
9-136447595-G-A		not specified	Uncertain significance (Jul 14, 2021)
9-136447625-G-A		not specified	Uncertain significance (Nov 05, 2021)
9-136447631-G-A		not specified	Uncertain significance (Apr 05, 2023)
9-136447631-G-C		not specified	Uncertain significance (Feb 03, 2022)
9-136447675-T-A		not specified	Uncertain significance (Jun 19, 2024)
9-136451271-C-T			Likely benign (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEC16A	protein_coding	protein_coding	ENST00000313050	30	37593

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.360	0.640	124574	0	75	124649	0.000301

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.472	1458	1.41e+3	1.04	0.0000872	15157
Missense in Polyphen		434	473.1	0.91736		5336
Synonymous	-3.06	701	605	1.16	0.0000448	4899
Loss of Function	7.06	22	97.0	0.227	0.00000479	1110

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000982	0.000953
Ashkenazi Jewish	0.000424	0.000398
East Asian	0.000343	0.000334
Finnish	0.000285	0.000278
European (Non-Finnish)	0.000263	0.000257
Middle Eastern	0.000343	0.000334
South Asian	0.000132	0.000131
Other	0.000335	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Defines endoplasmic reticulum exit sites (ERES) and is required for secretory cargo traffic from the endoplasmic reticulum to the Golgi apparatus. SAR1A-GTP-dependent assembly of SEC16A on the ER membrane forms an organized scaffold defining an ERES. Required for normal transitional endoplasmic reticulum (tER) organization. {ECO:0000269|PubMed:17005010, 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;TNFalpha;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.999
• rvis_EVS: -2.29
• rvis_percentile_EVS: 1.23

Haploinsufficiency Scores

• pHI: 0.191
• hipred: N
• hipred_score: 0.314
• ghis: 0.522

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.743

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sec16a

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;endoplasmic reticulum organization;Golgi organization;substantia nigra development;protein exit from endoplasmic reticulum;response to endoplasmic reticulum stress;Golgi to plasma membrane CFTR protein transport;COPII vesicle coating;protein stabilization;positive regulation of protein exit from endoplasmic reticulum;protein localization to endoplasmic reticulum exit site;protein localization to plasma membrane
• Cellular component: Golgi membrane;endoplasmic reticulum;endoplasmic reticulum membrane;Golgi apparatus;cytosol;ER to Golgi transport vesicle membrane;organelle membrane;perinuclear region of cytoplasm;endoplasmic reticulum exit site
• Molecular function: protein binding