SEC22C

SEC22 homolog C, vesicle trafficking protein, the group of SNAREs

Basic information

Region (hg38): 3:42547969-42601080

Previous symbols: [ "SEC22L3" ]

Links

ENSG00000093183 ∙ NCBI:9117 ∙ OMIM:604028 ∙ HGNC:16828 ∙ Uniprot:Q9BRL7 ∙ 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 SEC22C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC22C 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						0
missense			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in SEC22C

This is a list of pathogenic ClinVar variants found in the SEC22C region.

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

Position	Type	Phenotype	Significance	ClinVar
3-42553259-A-G		not specified	Uncertain significance (Dec 07, 2023)
3-42553267-T-G		not specified	Uncertain significance (Sep 06, 2022)
3-42553328-G-A		not specified	Uncertain significance (Mar 26, 2024)
3-42553359-G-T		not specified	Uncertain significance (May 23, 2023)
3-42553372-T-G		not specified	Uncertain significance (May 08, 2023)
3-42553424-G-A		not specified	Uncertain significance (May 08, 2023)
3-42555938-T-C		not specified	Uncertain significance (Apr 20, 2024)
3-42555958-A-G		not specified	Uncertain significance (May 05, 2023)
3-42557595-C-T		not specified	Uncertain significance (Aug 02, 2021)
3-42557633-A-G		not specified	Uncertain significance (Oct 21, 2024)
3-42557646-T-C		not specified	Likely benign (Dec 09, 2024)
3-42561134-G-A		not specified	Uncertain significance (Nov 11, 2024)
3-42561258-C-G		not specified	Uncertain significance (Oct 21, 2024)
3-42563531-A-G		not specified	Uncertain significance (Sep 26, 2024)
3-42563550-A-C		not specified	Uncertain significance (Aug 02, 2023)
3-42563576-T-C		not specified	Uncertain significance (Aug 02, 2023)
3-42563625-T-C		not specified	Uncertain significance (Nov 30, 2022)
3-42568881-A-G		not specified	Likely benign (May 26, 2024)
3-42568898-C-T		not specified	Uncertain significance (Oct 22, 2021)
3-42568931-C-T		not specified	Uncertain significance (Mar 06, 2023)
3-42568941-G-A		not specified	Uncertain significance (Jan 04, 2022)
3-42590917-C-T		not specified	Uncertain significance (Sep 24, 2024)
3-42590921-C-A		not specified	Uncertain significance (Nov 15, 2024)
3-42590932-G-C		not specified	Uncertain significance (Jan 17, 2024)
3-42591545-G-T		not specified	Uncertain significance (May 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEC22C	protein_coding	protein_coding	ENST00000264454	6	53112

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.86e-7	0.528	125645	0	103	125748	0.000410

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.837	137	167	0.818	0.00000858	1987
Missense in Polyphen		35	55.417	0.63157		688
Synonymous	0.502	58	63.1	0.920	0.00000338	596
Loss of Function	0.902	12	15.9	0.756	9.80e-7	153

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000507	0.000507
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000206	0.000202
Middle Eastern	0.000218	0.000217
South Asian	0.00191	0.00180
Other	0.000662	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in vesicle transport between the ER and the Golgi complex. {ECO:0000269|PubMed:9501016}.
• 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: 0.0825

Intolerance Scores

• loftool: 0.855
• rvis_EVS: -0.18
• rvis_percentile_EVS: 39.95

Haploinsufficiency Scores

• pHI: 0.379
• hipred: N
• hipred_score: 0.170
• ghis: 0.579

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.149

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sec22c

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;protein transport
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: protein binding