BEAN1

brain expressed associated with NEDD4 1

Basic information

Region (hg38): 16:66427295-66493529

Previous symbols: [ "SCA31" ]

Links

ENSG00000166546 ∙ NCBI:146227 ∙ OMIM:612051 ∙ HGNC:24160 ∙ Uniprot:Q3B7T3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spinocerebellar ataxia type 31 (Strong), mode of inheritance: AD
• spinocerebellar ataxia type 31 (Supportive), mode of inheritance: AD
• spinocerebellar ataxia type 31 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spinocerebellar ataxia 31	AD	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; Neurologic	17611710; 19878914

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BEAN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BEAN1 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				2		2
missense			29	3	1	33
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4	1	2	7
Total	0	0	33	6	4

Variants in BEAN1

This is a list of pathogenic ClinVar variants found in the BEAN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-66437655-G-A			Likely benign (Jul 01, 2022)
16-66437945-G-A			Benign (Oct 01, 2022)
16-66447543-C-T			Benign (Dec 01, 2022)
16-66469666-T-G		Spinocerebellar ataxia type 31	Benign (-)
16-66469703-A-G		not specified	Uncertain significance (May 23, 2024)
16-66469754-C-T		not specified	Uncertain significance (Dec 12, 2023)
16-66469764-G-T		not specified	Uncertain significance (Sep 27, 2021)
16-66469766-C-G		not specified	Uncertain significance (Aug 12, 2024)
16-66469773-G-A			Likely benign (Aug 01, 2022)
16-66469782-G-A		not specified	Uncertain significance (Jul 14, 2024)
16-66469787-C-A		not specified	Uncertain significance (Apr 28, 2023)
16-66469787-C-T			Uncertain significance (Apr 01, 2022)
16-66469788-G-A		not specified	Uncertain significance (Sep 16, 2021)
16-66469788-GCCACCGCCA-G		BEAN1-related disorder	Benign (May 01, 2024)
16-66469793-C-T		not specified	Uncertain significance (Jan 12, 2024)
16-66469802-C-A			Benign (Jan 01, 2024)
16-66469812-A-G		not specified	Uncertain significance (Jul 17, 2024)
16-66469830-G-A		not specified	Uncertain significance (Aug 09, 2021)
16-66469835-C-T		not specified	Uncertain significance (Jan 26, 2022)
16-66469836-G-A		not specified	Uncertain significance (Feb 27, 2024)
16-66469845-G-A		not specified	Uncertain significance (Jun 26, 2024)
16-66469875-C-T		BEAN1-related disorder	Benign (Sep 10, 2019)
16-66477584-G-A		not specified	Uncertain significance (Mar 29, 2023)
16-66477593-G-A		not specified	Likely benign (Dec 15, 2023)
16-66477601-C-T		not specified	Uncertain significance (May 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BEAN1	protein_coding	protein_coding	ENST00000536005	4	66233

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000676	0.292	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	124	164	0.757	0.0000111	1634
Missense in Polyphen		32	49.873	0.64163		558
Synonymous	1.79	48	66.6	0.721	0.00000450	556
Loss of Function	0.0927	8	8.29	0.965	5.32e-7	85

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Spinocerebellar ataxia 31 (SCA31) [MIM:117210]: A form of spinocerebellar ataxia, a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCA31 belongs to the autosomal dominant cerebellar ataxias type III (ADCA III) which are characterized by pure cerebellar ataxia without additional signs. {ECO:0000269|PubMed:19878914}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bean1
• Phenotype: normal phenotype

Gene ontology

• Cellular component: integral component of membrane