BET1L

Bet1 golgi vesicular membrane trafficking protein like, the group of SNAREs

Basic information

Region (hg38): 11:167783-207399

Links

ENSG00000177951 ∙ NCBI:51272 ∙ OMIM:615417 ∙ HGNC:19348 ∙ Uniprot:Q9NYM9 ∙ 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 BET1L gene.

• Inborn genetic diseases (4 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BET1L 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				1		1
missense			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	4	1	1

Variants in BET1L

This is a list of pathogenic ClinVar variants found in the BET1L region.

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

Position	Type	Phenotype	Significance	ClinVar
11-193112-C-T			Benign (Aug 29, 2018)
11-193722-A-G			Benign (Aug 29, 2018)
11-193863-T-C			Likely benign (Dec 31, 2019)
11-197345-G-A		not specified	Uncertain significance (Dec 30, 2023)
11-197353-G-C		not specified	Uncertain significance (Dec 01, 2022)
11-197395-C-G		not specified	Uncertain significance (Apr 22, 2022)
11-197640-C-A		not specified	Uncertain significance (Mar 21, 2023)
11-197681-T-G		not specified	Uncertain significance (Aug 08, 2022)
11-197704-C-T		not specified	Uncertain significance (Jan 04, 2024)
11-198236-C-G		not specified	Uncertain significance (Mar 06, 2023)
11-198237-G-A		not specified	Uncertain significance (Nov 21, 2023)
11-198291-A-G		not specified	Uncertain significance (Dec 21, 2021)
11-198297-C-A		not specified	Uncertain significance (Oct 05, 2023)
11-198546-C-G			Likely benign (Nov 01, 2022)
11-198552-C-G		not specified	Uncertain significance (Jul 25, 2023)
11-198571-G-A		not specified	Uncertain significance (Dec 15, 2022)
11-198582-C-G		not specified	Uncertain significance (Apr 25, 2022)
11-199405-C-T		not specified	Uncertain significance (Jan 31, 2024)
11-199983-G-A		not specified	Uncertain significance (Sep 17, 2021)
11-199999-A-G		not specified	Uncertain significance (Mar 16, 2022)
11-200020-T-C		not specified	Uncertain significance (Aug 10, 2021)
11-200029-A-G		not specified	Uncertain significance (Jul 25, 2023)
11-205316-T-C		not specified	Uncertain significance (Aug 09, 2021)
11-205361-C-T		not specified	Uncertain significance (Feb 23, 2023)
11-205409-T-C		not specified	Uncertain significance (Oct 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BET1L	protein_coding	protein_coding	ENST00000382762	4	39645

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00442	0.687	125740	0	6	125746	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.143	70	73.4	0.953	0.00000473	725
Missense in Polyphen		17	18.664	0.91085		198
Synonymous	0.387	26	28.6	0.908	0.00000183	222
Loss of Function	0.658	4	5.69	0.703	3.27e-7	56

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Vesicle SNARE required for targeting and fusion of retrograde transport vesicles with the Golgi complex. Required for the integrity of the Golgi complex (By similarity). {ECO:0000250|UniProtKB:O35152}.
• Pathway: SNARE interactions in vesicular transport - Homo sapiens (human);Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Intra-Golgi traffic;COPI-mediated anterograde transport;ER to Golgi Anterograde Transport;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Intolerance Scores

• loftool: 0.197
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.42

Haploinsufficiency Scores

• pHI: 0.124
• hipred: N
• hipred_score: 0.393
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bet1l

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;protein transport;retrograde transport, endosome to Golgi;membrane fusion;regulation of retrograde vesicle-mediated transport, Golgi to ER
• Cellular component: Golgi trans cisterna;Golgi membrane;endosome;Golgi apparatus;cytosol;membrane;integral component of Golgi membrane;SNARE complex
• Molecular function: SNAP receptor activity