SEC13

SEC13 homolog, nuclear pore and COPII coat complex component, the group of GATOR2 subcomplex|WD repeat domain containing|Nucleoporins|COPII coat complex

Basic information

Region (hg38): 3:10293130-10321112

Previous symbols: [ "D3S1231E", "SEC13L1" ]

Links

ENSG00000157020 ∙ NCBI:6396 ∙ OMIM:600152 ∙ HGNC:10697 ∙ Uniprot:P55735 ∙ 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 SEC13 gene.

• Inborn genetic diseases (26 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC13 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			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	0

Variants in SEC13

This is a list of pathogenic ClinVar variants found in the SEC13 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-10301302-C-T		not specified	Uncertain significance (Sep 17, 2021)
3-10301303-G-A			Likely benign (Apr 01, 2023)
3-10301323-C-T		not specified	Uncertain significance (Aug 02, 2022)
3-10301335-A-C		not specified	Uncertain significance (Nov 07, 2022)
3-10301346-C-T		not specified	Uncertain significance (Dec 13, 2022)
3-10301353-C-A		not specified	Uncertain significance (Jan 23, 2024)
3-10304087-A-G		not specified	Uncertain significance (Jan 03, 2024)
3-10304106-G-C		not specified	Uncertain significance (Jul 26, 2022)
3-10304126-G-A		not specified	Uncertain significance (Sep 27, 2022)
3-10304158-G-C		not specified	Uncertain significance (Aug 04, 2021)
3-10304165-C-G		not specified	Uncertain significance (Jun 24, 2022)
3-10305047-C-T		not specified	Uncertain significance (Sep 16, 2021)
3-10305052-G-C		not specified	Uncertain significance (Nov 08, 2022)
3-10305094-C-T		not specified	Uncertain significance (Feb 28, 2023)
3-10305108-G-T		not specified	Uncertain significance (Oct 03, 2023)
3-10305110-G-A		not specified	Uncertain significance (Apr 25, 2022)
3-10305575-G-A		not specified	Uncertain significance (Jul 26, 2022)
3-10305596-C-T		not specified	Uncertain significance (May 16, 2023)
3-10305604-T-C		not specified	Uncertain significance (Jul 21, 2022)
3-10305607-A-C		not specified	Uncertain significance (Dec 15, 2023)
3-10305616-G-T		not specified	Uncertain significance (Feb 15, 2023)
3-10305662-C-T		not specified	Uncertain significance (Jul 25, 2023)
3-10305682-T-C		not specified	Uncertain significance (Dec 02, 2022)
3-10312080-G-A		not specified	Uncertain significance (Jun 17, 2022)
3-10312588-C-T		not specified	Uncertain significance (Feb 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEC13	protein_coding	protein_coding	ENST00000350697	9	28048

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0179	0.981	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.621	172	196	0.875	0.0000112	2116
Missense in Polyphen		49	62.875	0.77933		707
Synonymous	1.18	70	83.7	0.837	0.00000569	599
Loss of Function	2.93	7	21.7	0.322	0.00000109	217

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000704	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000673	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a component of the nuclear pore complex (NPC) and the COPII coat. At the endoplasmic reticulum, SEC13 is involved in the biogenesis of COPII-coated vesicles. {ECO:0000269|PubMed:8972206}.
• Pathway: mTOR signaling pathway - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);RNA transport - Homo sapiens (human);Sterol Regulatory Element-Binding Proteins (SREBP) signalling;Signal Transduction;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;MHC class II antigen presentation;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;Immune System;Adaptive Immune System;RHO GTPases Activate Formins;Class I MHC mediated antigen processing & presentation;RHO GTPase Effectors;Signaling by Rho GTPases;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport;Antigen Presentation: Folding, assembly and peptide loading of class I MHC;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.177

Intolerance Scores

• loftool: 0.493
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.37

Haploinsufficiency Scores

• pHI: 0.310
• hipred: Y
• hipred_score: 0.714
• ghis: 0.605

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.745

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sec13

Zebrafish Information Network

• Gene name: sec13
• Affected structure: retinal ganglion cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: antigen processing and presentation of peptide antigen via MHC class I;intracellular protein transport;antigen processing and presentation of exogenous peptide antigen via MHC class II;positive regulation of TOR signaling;protein exit from endoplasmic reticulum;COPII vesicle coating;mRNA transport;COPII-coated vesicle cargo loading;COPII-coated vesicle budding
• Cellular component: Golgi membrane;kinetochore;nuclear envelope;nucleoplasm;lysosomal membrane;endoplasmic reticulum membrane;cytosol;ER to Golgi transport vesicle membrane;COPII vesicle coat;nuclear pore outer ring;intracellular membrane-bounded organelle;GATOR2 complex;extracellular exosome
• Molecular function: protein binding;identical protein binding