BET1

Bet1 golgi vesicular membrane trafficking protein, the group of SNAREs

Basic information

Region (hg38): 7:93962762-94004382

Links

ENSG00000105829

∙ NCBI:10282 ∙ OMIM:605456 ∙ HGNC:14562 ∙ Uniprot:O15155 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Muscular dystrophy, congenital, with rapid progression	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	Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	34779586

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BET1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BET1 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			5 clinvar			5
nonsense						0
start loss						0
frameshift			1 clinvar			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in BET1

This is a list of pathogenic ClinVar variants found in the BET1 region.

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

Position	Phenotype	Significance	ClinVar
7-93994306-G-T	not specified	Uncertain significance (Oct 30, 2023)	3133746
7-93994308-T-A	not specified	Uncertain significance (Jul 14, 2023)	2612002
7-93994385-C-G	Progressive muscle weakness;Seizure • Muscular dystrophy, congenital, with rapid progression	Uncertain significance (Feb 25, 2019)	619194
7-93996314-A-C	Muscular dystrophy, congenital, with rapid progression	Uncertain significance (Aug 28, 2020)	977650
7-93999179-AG-A	Progressive muscle weakness;Seizure • Muscular dystrophy, congenital, with rapid progression	Uncertain significance (Feb 25, 2019)	619186
7-93999198-A-C	not specified	Uncertain significance (Jun 12, 2023)	2559572

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BET1	protein_coding	protein_coding	ENST00000222547	4	41621

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00383	0.657	125714	0	33	125747	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.216	52	56.6	0.919	0.00000240	768
Missense in Polyphen		13	15.227	0.85376		218
Synonymous	1.68	11	20.7	0.531	8.91e-7	218
Loss of Function	0.570	4	5.43	0.736	2.26e-7	80

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000214
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000230	0.000229
Middle Eastern	0.00	0.00
South Asian	0.0000401	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Required for vesicular transport from the ER to the Golgi complex. Functions as a SNARE involved in the docking process of ER-derived vesicles with the cis-Golgi membrane (By similarity). {ECO:0000250}.;
Pathway: SNARE interactions in vesicular transport - Homo sapiens (human);miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPI-mediated anterograde transport;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport (Consensus)

Recessive Scores

pRec: 0.0904

Intolerance Scores

loftool: 0.698
rvis_EVS: -0.01
rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

pHI: 0.0625
hipred: Y
hipred_score: 0.513
ghis: 0.597

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.533

Mouse Genome Informatics

Gene name: Bet1
Phenotype

Gene ontology

Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;protein transport;COPII vesicle coating;vesicle fusion with Golgi apparatus
Cellular component: Golgi trans cisterna;Golgi membrane;endoplasmic reticulum membrane;membrane;transport vesicle;integral component of Golgi membrane;SNARE complex;endoplasmic reticulum-Golgi intermediate compartment membrane
Molecular function: SNAP receptor activity;protein binding