SEC31A

SEC31 homolog A, COPII coat complex component, the group of COPII coat complex|WD repeat domain containing

Basic information

Region (hg38): 4:82818509-82901166

Previous symbols: [ "SEC31L1" ]

Links

ENSG00000138674 ∙ NCBI:22872 ∙ OMIM:610257 ∙ HGNC:17052 ∙ Uniprot:O94979 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with spastic quadriplegia, optic atrophy, seizures, and structural brain anomalies (Limited), mode of inheritance: AR
• neurodevelopmental disorder with spastic quadriplegia, optic atrophy, seizures, and structural brain anomalies (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Halperin-Birk syndrome	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	30464055

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEC31A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC31A 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				7	3	10
missense			60	3	3	66
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region				2	1	3
non coding					3	3
Total	0	0	61	11	9

Variants in SEC31A

This is a list of pathogenic ClinVar variants found in the SEC31A region.

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

Position	Type	Phenotype	Significance	ClinVar
4-82819090-T-C		not specified	Uncertain significance (Feb 28, 2023)
4-82819214-T-C		not specified	Uncertain significance (Sep 02, 2024)
4-82819235-T-C		not specified	Uncertain significance (Dec 01, 2023)
4-82824576-G-C		not specified	Uncertain significance (Nov 06, 2023)
4-82824590-G-C		not specified	Uncertain significance (Nov 15, 2021)
4-82824637-T-G		not specified	Uncertain significance (Jun 29, 2023)
4-82824655-G-A		not specified	Uncertain significance (Jun 30, 2022)
4-82824658-G-A		not specified	Uncertain significance (Sep 16, 2021)
4-82827405-T-G		not specified	Uncertain significance (Jul 25, 2023)
4-82827414-G-A			Likely benign (Jul 26, 2018)
4-82827464-C-T			Likely benign (May 01, 2024)
4-82827532-G-A		not specified	Uncertain significance (Jan 30, 2024)
4-82827568-G-A			Benign (Dec 31, 2019)
4-82827568-G-C		not specified	Uncertain significance (Jul 09, 2024)
4-82827632-T-C		not specified	Uncertain significance (Dec 09, 2023)
4-82829002-T-C		not specified	Uncertain significance (Sep 08, 2024)
4-82842139-C-A		SEC31A-related disorder	Likely benign (Feb 01, 2022)
4-82842191-T-C		not specified	Uncertain significance (Jul 14, 2021)
4-82842197-G-T		not specified	Uncertain significance (Nov 12, 2024)
4-82842199-G-C		not specified	Uncertain significance (Nov 10, 2022)
4-82842234-T-C			Likely benign (May 01, 2022)
4-82842240-G-A			Likely benign (Nov 01, 2023)
4-82842275-G-A		not specified	Uncertain significance (Jun 28, 2024)
4-82842330-G-GTA		Neurodevelopmental disorder with spastic quadriplegia, optic atrophy, seizures, and structural brain anomalies	Pathogenic (Nov 16, 2021)
4-82842452-C-T		not specified	Uncertain significance (Aug 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEC31A	protein_coding	protein_coding	ENST00000395310	26	82506

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000788	1.00	125528	1	218	125747	0.000871

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.23	559	647	0.864	0.0000320	7945
Missense in Polyphen		127	177.4	0.71591		2240
Synonymous	-0.614	240	228	1.05	0.0000118	2390
Loss of Function	5.35	21	68.9	0.305	0.00000363	775

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00955	0.00927
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000333	0.000308
Middle Eastern	0.00	0.00
South Asian	0.0000329	0.0000327
Other	0.00219	0.00179

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER) (PubMed:10788476). The coat has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules (By similarity). {ECO:0000250|UniProtKB:Q9Z2Q1, ECO:0000269|PubMed:10788476}.
• Disease: DISEASE: Note=A chromosomal aberration involving SEC31A is associated with inflammatory myofibroblastic tumors (IMTs). Translocation t(2;4)(p23;q21) with ALK.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);Sterol Regulatory Element-Binding Proteins (SREBP) signalling;XBP1(S) activates chaperone genes;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;MHC class II antigen presentation;Immune System;Adaptive Immune System;Class I MHC mediated antigen processing & presentation;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport;Antigen Presentation: Folding, assembly and peptide loading of class I MHC (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.787
• rvis_EVS: -0.99
• rvis_percentile_EVS: 8.63

Haploinsufficiency Scores

• pHI: 0.390
• hipred: N
• hipred_score: 0.476
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.913

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sec31a

Zebrafish Information Network

• Gene name: sec31a
• Affected structure: endodermal 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;endoplasmic reticulum to Golgi vesicle-mediated transport;endoplasmic reticulum organization;antigen processing and presentation of exogenous peptide antigen via MHC class II;IRE1-mediated unfolded protein response;COPII vesicle coating;response to calcium ion;COPII-coated vesicle cargo loading;COPII-coated vesicle budding
• Cellular component: Golgi membrane;cytoplasm;endoplasmic reticulum;endoplasmic reticulum membrane;cytosol;ER to Golgi transport vesicle membrane;vesicle coat;COPII vesicle coat;COPII-coated ER to Golgi transport vesicle;intracellular membrane-bounded organelle;perinuclear region of cytoplasm;endoplasmic reticulum exit site
• Molecular function: structural molecule activity;protein binding;calcium-dependent protein binding