BEAN1

protein-coding

brain expressed associated with NEDD4 1

Gene summary

The protein encoded by this gene is one of several proteins that interact with NEDD4, a member of a family of ubiquitin-protein ligases. These proteins have PY motifs in common that bind to the WW domains of NEDD4. NEDD4 is developmentally regulated, and is highly expressed in embryonic tissues. Mutations in this gene (i.e., intronic insertions of >100 copies of pentanucleotide repeats including a (TGGAA)n sequence) are associated with spinocerebellar ataxia type 31. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]

Previous symbols:

SCA31

MANE transcript

NM_001178020.3

Inheritance

ClinVar variants

U:61B:23

Top phenotype

Spinocerebellar ataxia 31

gnomAD constraint

pLI —, LoF o/e 0.97

Max pathogenic AF

—

Genomic locus

chr16:66,427,295-66,493,529

External References & Databases

Ensembl (ENSG00000166546)

Transcript & Mutation Effects

hg38 • Region Span ~66.2 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

spinocerebellar ataxia type 31LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0007296

Submitter: Ambry Genetics

spinocerebellar ataxia type 31STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007296

Submitter: Labcorp Genetics (formerly Invitae)

spinocerebellar ataxia type 31SUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007296

Submitter: Orphanet

Clinical Genomic Database (CGD)

Spinocerebellar ataxia 31AD

Manifestation: Audiologic/Otolaryngologic; Neurologic

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: 17611710; 19878914

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BEAN1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 80

not providedTotal: 14

BEAN1-related disorderTotal: 3

Spinocerebellar ataxia type 31Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001178020.3. 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				10 clinvar		10
missense			61 clinvar	11 clinvar	1 clinvar	73
nonsense				1 clinvar		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	61	22	1	84

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001178020.3	RefSeq	NP_001171491.1	4	MANE Select
ENST00000536005.7	Ensembl	ENSP00000442793.2	4	MANE Select
NM_001136106.5	RefSeq	NP_001129578.1	2	Standard
NM_001197224.4	RefSeq	NP_001184153.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000536005
Coding exons: 4
Length: 66233
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.10	124	164	0.757	0.0000111	1634
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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 (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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