SEC22A

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

Basic information

Region (hg38): 3:123201927-123274136

Previous symbols: [ "SEC22L2" ]

Links

ENSG00000121542 ∙ NCBI:26984 ∙ OMIM:612442 ∙ HGNC:20260 ∙ Uniprot:Q96IW7 ∙ 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 SEC22A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC22A 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	0

Variants in SEC22A

This is a list of pathogenic ClinVar variants found in the SEC22A region.

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

Position	Type	Phenotype	Significance	ClinVar
3-123209281-A-G		not specified	Uncertain significance (Feb 22, 2024)
3-123209386-C-A		not specified	Uncertain significance (Jun 29, 2023)
3-123209395-A-G		not specified	Uncertain significance (Nov 24, 2024)
3-123223585-A-G		not specified	Uncertain significance (May 15, 2024)
3-123223623-G-T		not specified	Uncertain significance (Jan 29, 2025)
3-123223676-G-A		not specified	Uncertain significance (Aug 17, 2022)
3-123225104-T-A		not specified	Uncertain significance (Jul 12, 2022)
3-123225217-C-T		not specified	Uncertain significance (Jul 10, 2024)
3-123225219-A-G		not specified	Uncertain significance (Jan 30, 2025)
3-123225221-G-A		not specified	Uncertain significance (Oct 11, 2024)
3-123225264-G-T		not specified	Uncertain significance (May 16, 2024)
3-123225271-G-C		not specified	Uncertain significance (Dec 04, 2024)
3-123225290-T-G		not specified	Uncertain significance (Sep 01, 2021)
3-123271550-G-C		not specified	Uncertain significance (Aug 04, 2023)
3-123271553-G-A		not specified	Uncertain significance (Feb 26, 2024)
3-123271587-C-G		not specified	Uncertain significance (Oct 04, 2024)
3-123271619-G-A		not specified	Uncertain significance (Oct 20, 2024)
3-123271680-G-C		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEC22A	protein_coding	protein_coding	ENST00000309934	6	72204

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000139	0.630	125691	0	55	125746	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0768	161	164	0.983	0.00000812	2004
Missense in Polyphen		37	44.53	0.83089		506
Synonymous	0.523	55	60.2	0.914	0.00000305	596
Loss of Function	1.01	11	15.2	0.722	8.75e-7	175

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000590	0.000589
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00111	0.00111
European (Non-Finnish)	0.0000793	0.0000791
Middle Eastern	0.000109	0.000109
South Asian	0.0000676	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in vesicle transport between the ER and the Golgi complex. {ECO:0000250|UniProtKB:Q642F4}.
• Pathway: Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics;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: 0.108

Intolerance Scores

• loftool: 0.737
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.312
• hipred: Y
• hipred_score: 0.699
• ghis: 0.651

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.786

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sec22a

Gene ontology

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