NBL1

NBL1, DAN family BMP antagonist, the group of DAN family

Basic information

Region (hg38): 1:19596979-19658456

Links

ENSG00000158747 ∙ NCBI:4681 ∙ OMIM:600613 ∙ HGNC:7650 ∙ Uniprot:P41271 ∙ 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 NBL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NBL1 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						0
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in NBL1

This is a list of pathogenic ClinVar variants found in the NBL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-19597052-G-A		not specified	Uncertain significance (Jun 26, 2023)
1-19597059-A-C		not specified	Uncertain significance (Feb 28, 2024)
1-19597089-C-T		not specified	Uncertain significance (May 04, 2022)
1-19597092-A-G		not specified	Uncertain significance (Apr 25, 2022)
1-19597107-T-C		not specified	Uncertain significance (Nov 16, 2021)
1-19600964-C-A		not specified	Uncertain significance (Jun 10, 2024)
1-19622103-C-G		not specified	Uncertain significance (Dec 28, 2022)
1-19623581-A-C		not specified	Uncertain significance (Jul 14, 2023)
1-19625551-C-A		not specified	Uncertain significance (Oct 04, 2022)
1-19643366-C-T		not specified	Uncertain significance (Sep 17, 2021)
1-19655338-A-G		not specified	Uncertain significance (Feb 14, 2023)
1-19656882-C-T		not specified	Uncertain significance (Jul 19, 2022)
1-19656900-C-A		not specified	Uncertain significance (Jun 12, 2023)
1-19656947-G-A		not specified	Uncertain significance (Aug 21, 2023)
1-19656948-C-A		not specified	Uncertain significance (Aug 21, 2023)
1-19656973-G-C		not specified	Uncertain significance (Jun 10, 2022)
1-19656983-G-C		not specified	Uncertain significance (Jul 20, 2021)
1-19656990-T-C		not specified	Uncertain significance (Aug 15, 2023)
1-19657022-G-A		not specified	Uncertain significance (Apr 18, 2023)
1-19657061-G-A		not specified	Uncertain significance (Apr 05, 2023)
1-19657070-C-T		not specified	Uncertain significance (Oct 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NBL1	protein_coding	protein_coding	ENST00000289749	4	17898

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0590	0.875	125701	0	8	125709	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.52	78	126	0.619	0.00000689	1407
Missense in Polyphen		17	45.248	0.37571		510
Synonymous	0.678	48	54.4	0.883	0.00000366	424
Loss of Function	1.54	3	7.57	0.396	3.22e-7	86

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000886	0.0000886
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000368	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possible candidate as a tumor suppressor gene of neuroblastoma. May play an important role in preventing cells from entering the final stage (G1/S) of the transformation process.
• Pathway: TGF-beta signaling pathway - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.232

Intolerance Scores

• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

• pHI: 0.331
• hipred: N
• hipred_score: 0.461
• ghis: 0.556

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.749

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Nbl1
• Phenotype: normal phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: nbl1
• Affected structure: pars superior ear
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: nervous system development;regulation of signaling receptor activity;negative regulation of BMP signaling pathway;sequestering of BMP in extracellular matrix;sequestering of BMP from receptor via BMP binding;positive regulation of neuron differentiation;determination of dorsal identity;neuron projection morphogenesis;negative regulation of monocyte chemotaxis
• Cellular component: extracellular space
• Molecular function: protein binding;morphogen activity;BMP binding;protein homodimerization activity