NBEAL1

neurobeachin like 1, the group of Armadillo like helical domain containing|BEACH domain containing |WD repeat domain containing

Basic information

Region (hg38): 2:203014608-203226378

Previous symbols: [ "ALS2CR17", "ALS2CR16" ]

Links

ENSG00000144426 ∙ NCBI:65065 ∙ OMIM:609816 ∙ HGNC:20681 ∙ Uniprot:Q6ZS30 ∙ 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 NBEAL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NBEAL1 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				7	3	10
missense			168	9	3	180
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1	1		2
splice region				1		1
non coding					2	2
Total	0	0	169	17	8

Variants in NBEAL1

This is a list of pathogenic ClinVar variants found in the NBEAL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-203041770-T-A		not specified	Uncertain significance (Nov 29, 2023)
2-203041811-G-A		not specified	Uncertain significance (Oct 12, 2024)
2-203041831-G-A		not specified	Uncertain significance (Nov 10, 2024)
2-203041843-A-G		not specified	Uncertain significance (Jun 11, 2021)
2-203049817-A-G			Likely benign (Sep 01, 2022)
2-203049827-C-T		not specified	Uncertain significance (Jun 22, 2022)
2-203049890-T-A		not specified	Uncertain significance (Jan 31, 2022)
2-203049905-G-T		not specified	Uncertain significance (Jan 03, 2024)
2-203049933-C-T		not specified	Uncertain significance (Jun 03, 2022)
2-203056468-T-C		not specified	Uncertain significance (Aug 10, 2024)
2-203056485-A-G		not specified	Uncertain significance (Dec 14, 2021)
2-203057352-A-G			Benign/Likely benign (Apr 01, 2023)
2-203057440-C-T		not specified	Uncertain significance (Jun 10, 2022)
2-203057446-A-G		not specified	Uncertain significance (May 16, 2023)
2-203068395-G-A		not specified	Uncertain significance (Jan 19, 2024)
2-203068468-C-G		not specified	Uncertain significance (Nov 21, 2023)
2-203077784-A-G		not specified	Uncertain significance (Nov 13, 2023)
2-203077786-T-G		not specified	Uncertain significance (Dec 27, 2023)
2-203077804-G-C		not specified	Uncertain significance (Oct 06, 2021)
2-203083237-A-G		not specified	Uncertain significance (Mar 20, 2024)
2-203083289-C-G		not specified	Uncertain significance (May 24, 2023)
2-203083297-G-A		not specified	Uncertain significance (May 17, 2023)
2-203083316-T-A		not specified	Uncertain significance (Jul 30, 2023)
2-203083316-T-C		not specified	Uncertain significance (Nov 25, 2024)
2-203083408-A-G		not specified	Uncertain significance (Nov 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NBEAL1	protein_coding	protein_coding	ENST00000449802	54	211500

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.11e-33	1.00	124466	0	326	124792	0.00131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.88	1068	1.26e+3	0.851	0.0000621	17636
Missense in Polyphen		321	443.09	0.72445		6222
Synonymous	1.82	392	441	0.890	0.0000222	4948
Loss of Function	5.07	77	142	0.541	0.00000815	1845

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00135	0.00134
Ashkenazi Jewish	0.000507	0.000497
East Asian	0.00247	0.00245
Finnish	0.00493	0.00493
European (Non-Finnish)	0.000704	0.000689
Middle Eastern	0.00247	0.00245
South Asian	0.00181	0.00173
Other	0.00135	0.00132

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0930

Intolerance Scores

• loftool: 0.967
• rvis_EVS: 1.19
• rvis_percentile_EVS: 92.85

Haploinsufficiency Scores

• pHI: 0.415
• hipred: N
• hipred_score: 0.414
• ghis: 0.493

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.144

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nbeal1