SEC31B

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

Basic information

Region (hg38): 10:100486646-100519864

Previous symbols: [ "SEC31L2" ]

Links

ENSG00000075826 ∙ NCBI:25956 ∙ OMIM:610258 ∙ HGNC:23197 ∙ Uniprot:Q9NQW1 ∙ 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 SEC31B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC31B 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			76	7		83
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	76	7	0

Variants in SEC31B

This is a list of pathogenic ClinVar variants found in the SEC31B region.

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

Position	Type	Phenotype	Significance	ClinVar
10-100487635-G-A		not specified	Uncertain significance (Jan 03, 2024)
10-100487636-C-T		not specified	Uncertain significance (Mar 29, 2022)
10-100487639-T-C		not specified	Uncertain significance (Jun 29, 2022)
10-100487648-C-T		not specified	Uncertain significance (May 21, 2024)
10-100487660-T-G		not specified	Uncertain significance (Mar 30, 2024)
10-100487666-T-G		not specified	Uncertain significance (May 09, 2023)
10-100487681-C-T		not specified	Uncertain significance (Jul 27, 2021)
10-100487691-G-C		not specified	Uncertain significance (Oct 27, 2021)
10-100487745-A-C		not specified	Uncertain significance (Dec 07, 2023)
10-100487791-G-A		not specified	Uncertain significance (Sep 14, 2022)
10-100488056-A-G			Likely benign (Dec 01, 2022)
10-100488868-G-A		not specified	Uncertain significance (Jun 22, 2021)
10-100488932-G-A		not specified	Uncertain significance (Jan 26, 2022)
10-100489280-G-A		not specified	Uncertain significance (Apr 22, 2022)
10-100489280-G-C		not specified	Uncertain significance (Apr 04, 2023)
10-100489284-G-T		not specified	Uncertain significance (Apr 22, 2022)
10-100489326-T-A		not specified	Uncertain significance (Jul 27, 2021)
10-100489331-T-C		not specified	Likely benign (May 03, 2023)
10-100489379-G-A		not specified	Uncertain significance (Mar 14, 2023)
10-100489380-G-A		not specified	Uncertain significance (Oct 12, 2022)
10-100489718-G-T		not specified	Uncertain significance (Aug 12, 2021)
10-100490074-G-A		not specified	Uncertain significance (Dec 27, 2023)
10-100490095-T-C		not specified	Uncertain significance (Mar 14, 2023)
10-100490128-G-A		not specified	Uncertain significance (Aug 09, 2021)
10-100490139-A-G		not specified	Likely benign (Aug 25, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEC31B	protein_coding	protein_coding	ENST00000370345	25	43230

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.59e-29	0.00486	125392	1	355	125748	0.00142

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0619	618	622	0.993	0.0000314	7589
Missense in Polyphen		105	112.89	0.93014		1521
Synonymous	-0.0785	249	247	1.01	0.0000124	2434
Loss of Function	1.22	50	60.3	0.830	0.00000289	685

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00563	0.00563
Ashkenazi Jewish	0.00	0.00
East Asian	0.00370	0.00370
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.00110	0.00110
Middle Eastern	0.00370	0.00370
South Asian	0.000954	0.000948
Other	0.000815	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: As a component of the coat protein complex II (COPII), may function in vesicle budding and cargo export from the endoplasmic reticulum. {ECO:0000269|PubMed:16495487}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);Sterol Regulatory Element-Binding Proteins (SREBP) signalling (Consensus)

Recessive Scores

• pRec: 0.0776

Intolerance Scores

• loftool: 0.974
• rvis_EVS: 2.08
• rvis_percentile_EVS: 97.82

Haploinsufficiency Scores

• pHI: 0.0655
• hipred: N
• hipred_score: 0.248
• ghis: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0500

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Sec31b

Zebrafish Information Network

• Gene name: sec31b
• Affected structure: intestine
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;endoplasmic reticulum organization;COPII-coated vesicle cargo loading;COPII-coated vesicle budding
• Cellular component: Golgi membrane;endoplasmic reticulum membrane;vesicle coat;COPII vesicle coat;endoplasmic reticulum exit site
• Molecular function: structural molecule activity