BET1

protein-coding

Bet1 golgi vesicular membrane trafficking protein, the group of SNAREs

Gene summary

This gene encodes a golgi-associated membrane protein that participates in vesicular transport from the endoplasmic reticulum (ER) to the Golgi complex. The encoded protein functions as a soluble N-ethylaleimide-sensitive factor attachment protein receptor and may be involved in the docking of ER-derived vesicles with the cis-Golgi membrane. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

MANE transcript

NM_005868.6

Inheritance

ClinVar variants

P:1U:16

Top phenotype

Muscular dystrophy, congenital, with rapid progression

gnomAD constraint

pLI —, LoF o/e 0.74

Max pathogenic AF

—

Genomic locus

chr7:93,962,762-94,004,382

External References & Databases

Ensembl (ENSG00000105829)

Transcript & Mutation Effects

hg38 • Region Span ~41.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

muscular dystrophy, congenital, with rapid progressionMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0009682

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Muscular dystrophy, congenital, with rapid progressionAR

Manifestation: Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic

Intervention: General

Rationale: 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

Refs: 34779586

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BET1 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 10

Muscular dystrophy, congenital, with rapid progressionTotal: 4

Progressive muscle weaknessTotal: 2

SeizureTotal: 2

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005868.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			12 clinvar			12
nonsense						0
start loss						0
frameshift		1 clinvar	1 clinvar			2
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	1	16	0	0	17

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005868.6	RefSeq	NP_005859.1	4	MANE Select
ENST00000222547.8	Ensembl	ENSP00000222547.3	4	MANE Select
NM_001317739.2	RefSeq	NP_001304668.1	5	Standard
ENST00000357520.8	Ensembl	ENSP00000350125.4	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

endoplasmic reticulum to Golgi vesicle-mediated transport
protein transport
COPII vesicle coating
vesicle fusion with Golgi apparatus

Molecular Function

SNAP receptor activity
protein binding

Cellular Component

Golgi trans cisterna
Golgi membrane
endoplasmic reticulum membrane
membrane
transport vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000222547
Coding exons: 4
Length: 41621
Individuals with no LoFs: 125714
Homozygous LoFs: 0
Heterozygous LoFs: 33
Defined: 125747
p: 0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.216	52	56.6	0.919	0.00000240	768
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00023	0.00023	rare
South Asian	0.000040	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0904

Intolerance Scores

LoFtool: 0.698
RVIS EVS: -0.01
RVIS percentile EVS: 52.85

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.533