NBR1

NBR1 autophagy cargo receptor, the group of Zinc fingers ZZ-type

Basic information

Region (hg38): 17:43170480-43211689

Previous symbols: [ "M17S2" ]

Links

ENSG00000188554 ∙ NCBI:4077 ∙ OMIM:166945 ∙ HGNC:6746 ∙ Uniprot:Q14596 ∙ 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 NBR1 gene.

• Inborn genetic diseases (37 variants)
• not provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NBR1 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				1	3	4
missense			37	2	1	40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	37	3	4

Variants in NBR1

This is a list of pathogenic ClinVar variants found in the NBR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-43175821-A-C		not specified	Uncertain significance (Jan 26, 2023)
17-43186279-G-T		not specified	Uncertain significance (Dec 18, 2023)
17-43186282-G-C		not specified	Uncertain significance (Aug 17, 2022)
17-43186284-A-C		not specified	Uncertain significance (Dec 15, 2023)
17-43186301-C-T		not specified	Uncertain significance (Jun 01, 2023)
17-43186308-T-C		not specified	Uncertain significance (Sep 30, 2021)
17-43186311-A-G		not specified	Uncertain significance (Dec 02, 2022)
17-43186319-C-T		not specified	Uncertain significance (Jun 21, 2022)
17-43186323-C-G		not specified	Uncertain significance (Jan 24, 2024)
17-43186415-A-G		not specified	Uncertain significance (Aug 21, 2023)
17-43189043-C-T		not specified	Uncertain significance (Dec 21, 2022)
17-43189127-T-C			Likely benign (Jun 20, 2018)
17-43189609-G-A		not specified	Uncertain significance (Nov 07, 2022)
17-43189613-C-T		not specified	Uncertain significance (Jun 27, 2022)
17-43189619-A-G		not specified	Uncertain significance (Dec 15, 2022)
17-43189700-C-T		not specified	Uncertain significance (Sep 29, 2023)
17-43189722-T-G		not specified	Uncertain significance (Jul 20, 2021)
17-43189783-G-C		not specified	Uncertain significance (Dec 15, 2022)
17-43190636-A-C		not specified	Uncertain significance (Mar 04, 2024)
17-43190676-G-A		not specified	Uncertain significance (Jan 16, 2024)
17-43190692-G-A		not specified	Uncertain significance (Feb 27, 2024)
17-43190710-C-T		not specified	Uncertain significance (Dec 13, 2022)
17-43190720-G-A			Benign (Jan 12, 2018)
17-43191399-T-C			Benign (Feb 25, 2018)
17-43191407-C-T		not specified	Uncertain significance (Feb 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NBR1	protein_coding	protein_coding	ENST00000422280	20	41211

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.66e-9	1.00	124620	0	37	124657	0.000148

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.36	402	487	0.826	0.0000239	6290
Missense in Polyphen		113	173.01	0.65313		2197
Synonymous	2.40	138	179	0.771	0.00000881	1854
Loss of Function	3.50	22	48.2	0.456	0.00000247	599

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.0000994	0.0000993
East Asian	0.000502	0.000501
Finnish	0.000187	0.000186
European (Non-Finnish)	0.000120	0.000115
Middle Eastern	0.000502	0.000501
South Asian	0.000181	0.000163
Other	0.000330	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts probably as a receptor for selective autophagosomal degradation of ubiquitinated targets. {ECO:0000269|PubMed:19250911}.
• Pathway: Mitophagy - animal - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.796
• rvis_EVS: 0.87
• rvis_percentile_EVS: 88.82

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.602
• ghis: 0.508

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.981

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nbr1
• Phenotype: hematopoietic system phenotype; skeleton phenotype; immune system phenotype; limbs/digits/tail phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: macroautophagy;regulation of bone mineralization;regulation of stress-activated MAPK cascade;negative regulation of osteoblast differentiation;protein complex oligomerization
• Cellular component: phagophore assembly site;nucleoplasm;mitochondrion;lysosome;late endosome;autophagosome;cytosol;membrane;nuclear body;M band;intracellular membrane-bounded organelle
• Molecular function: protein binding;zinc ion binding;ubiquitin binding;mitogen-activated protein kinase binding