NEBL

nebulette, the group of LIM domain containing

Basic information

Region (hg38): 10:20779972-21293011

Previous symbols: [ "C10orf113" ]

Links

ENSG00000078114 ∙ NCBI:10529 ∙ OMIM:605491 ∙ HGNC:16932 ∙ Uniprot:O76041 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• dilated cardiomyopathy (Limited), mode of inheritance: AD

ClinVar

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

• Primary dilated cardiomyopathy (685 variants)
• Inborn genetic diseases (288 variants)
• not provided (222 variants)
• not specified (159 variants)
• Cardiovascular phenotype (13 variants)
• Primary familial hypertrophic cardiomyopathy (3 variants)
• Hypertrophic cardiomyopathy (3 variants)
• NEBL-related condition (2 variants)
• Hypertrophic cardiomyopathy;Sudden unexplained death;Long QT syndrome (1 variants)
• Cardiomyopathy (1 variants)
• NEBL-related Cardiomyopathy (1 variants)
• Sudden cardiac death (1 variants)
• Sudden unexplained death (1 variants)
• Hypertrophic cardiomyopathy;Aborted sudden cardiac death (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEBL 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			3	166	3	172
missense			407	22		429
nonsense			16	1		17
start loss			1			1
frameshift		1	21			22
inframe indel			9			9
splice donor/acceptor (+/-2bp)			20		1	21
splice region			30	34	11	75
non coding			5	144	79	228
Total	0	1	482	333	83

Variants in NEBL

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

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

Position	Type	Phenotype	Significance	ClinVar
10-20785526-T-C			Benign (Jun 15, 2018)
10-20785743-A-T		not specified	Benign (Aug 24, 2015)
10-20785749-A-G		Primary dilated cardiomyopathy	Uncertain significance (Sep 09, 2021)
10-20785756-A-C		not specified	Uncertain significance (Apr 03, 2023)
10-20785756-A-G		Primary dilated cardiomyopathy	Likely benign (May 05, 2022)
10-20785761-C-T		Primary dilated cardiomyopathy • not specified	Uncertain significance (Jul 17, 2023)
10-20785764-T-C		Primary dilated cardiomyopathy	Uncertain significance (Jun 06, 2020)
10-20785771-C-T		Primary dilated cardiomyopathy • not specified	Benign/Likely benign (Jun 05, 2023)
10-20785772-G-T		not specified	Uncertain significance (Oct 14, 2022)
10-20785779-G-A		Primary dilated cardiomyopathy	Uncertain significance (Jan 11, 2024)
10-20785795-T-C		not specified • Primary dilated cardiomyopathy	Benign/Likely benign (Feb 01, 2024)
10-20785807-T-C		Primary dilated cardiomyopathy • not specified	Likely benign (Oct 18, 2022)
10-20785807-T-G		not specified	Likely benign (Sep 28, 2019)
10-20785813-G-A		Primary dilated cardiomyopathy • not specified	Likely benign (Jul 17, 2023)
10-20785826-T-C		Primary dilated cardiomyopathy • not specified	Uncertain significance (Nov 04, 2022)
10-20785827-C-T		Primary dilated cardiomyopathy	Uncertain significance (Mar 23, 2022)
10-20785828-G-A		Primary dilated cardiomyopathy • not specified	Likely benign (Nov 15, 2023)
10-20785833-T-C		Primary dilated cardiomyopathy	Uncertain significance (Nov 28, 2022)
10-20785834-A-T		not specified	Likely benign (Feb 06, 2024)
10-20785836-G-A		not specified	Uncertain significance (Dec 29, 2023)
10-20785837-C-A		Primary dilated cardiomyopathy	Uncertain significance (Apr 02, 2020)
10-20785843-G-A		Primary dilated cardiomyopathy • not specified	Likely benign (Mar 18, 2023)
10-20785845-T-C		Primary dilated cardiomyopathy	Uncertain significance (Mar 06, 2020)
10-20785847-A-G		not specified	Uncertain significance (Nov 01, 2023)
10-20785848-C-T		not specified	Uncertain significance (Apr 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEBL	protein_coding	protein_coding	ENST00000377122	28	394215

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.77e-36	0.0000554	125044	2	702	125748	0.00280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.940	606	544	1.11	0.0000282	6803
Missense in Polyphen		169	176.01	0.96019		2197
Synonymous	-1.28	211	189	1.12	0.0000114	1690
Loss of Function	0.627	58	63.4	0.915	0.00000355	773

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00370	0.00370
Ashkenazi Jewish	0.00109	0.00109
East Asian	0.000871	0.000816
Finnish	0.00363	0.00356
European (Non-Finnish)	0.00399	0.00395
Middle Eastern	0.000871	0.000816
South Asian	0.00122	0.00118
Other	0.00279	0.00277

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to actin and plays an important role in the assembly of the Z-disk. May functionally link sarcomeric actin to the desmin intermediate filaments in the heart muscle sarcomeres (PubMed:27733623). Isoform 2 might play a role in the assembly of focal adhesion (PubMed:15004028). {ECO:0000269|PubMed:15004028, ECO:0000269|PubMed:27733623}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.970
• rvis_EVS: 0.57
• rvis_percentile_EVS: 81.75

Haploinsufficiency Scores

• pHI: 0.569
• hipred: N
• hipred_score: 0.170
• ghis: 0.533

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.425

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nebl

Gene ontology

• Biological process: muscle fiber development;cardiac muscle thin filament assembly
• Cellular component: stress fiber;Z disc;I band;extracellular exosome
• Molecular function: protein binding;tropomyosin binding;cytoskeletal protein binding;structural constituent of muscle;filamin binding;actin filament binding