ZRANB1

zinc finger RANBP2-type containing 1, the group of OTU domain containing|Zinc fingers RANBP2-type

Basic information

Region (hg38): 10:124942122-124988189

Links

ENSG00000019995 ∙ NCBI:54764 ∙ OMIM:611749 ∙ HGNC:18224 ∙ Uniprot:Q9UGI0 ∙ 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 ZRANB1 gene.

• Inborn genetic diseases (17 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZRANB1 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	1
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	1

Variants in ZRANB1

This is a list of pathogenic ClinVar variants found in the ZRANB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-124942738-T-A		not specified	Uncertain significance (Jul 15, 2021)
10-124942765-A-G		not specified	Uncertain significance (Nov 05, 2021)
10-124942878-C-T		not specified	Uncertain significance (Dec 27, 2023)
10-124942982-G-C		not specified	Uncertain significance (Aug 08, 2022)
10-124943026-A-G		not specified	Uncertain significance (Jun 29, 2022)
10-124943035-A-G		not specified	Uncertain significance (Dec 03, 2021)
10-124943073-A-G		not specified	Uncertain significance (Jan 23, 2023)
10-124943152-C-T		not specified	Uncertain significance (Feb 26, 2024)
10-124943157-C-T		not specified	Uncertain significance (Dec 13, 2021)
10-124943158-G-A		not specified	Uncertain significance (Nov 09, 2023)
10-124943295-A-C		not specified	Uncertain significance (Mar 04, 2024)
10-124966668-G-A		not specified	Uncertain significance (Sep 20, 2023)
10-124966767-A-G		not specified	Uncertain significance (Nov 18, 2022)
10-124966768-T-C		not specified	Uncertain significance (Jan 26, 2023)
10-124972080-A-G		not specified	Uncertain significance (Jun 09, 2022)
10-124972084-T-G		not specified	Uncertain significance (Dec 21, 2022)
10-124973647-A-G		not specified	Uncertain significance (May 03, 2023)
10-124973666-C-G		not specified	Uncertain significance (Aug 20, 2023)
10-124983198-G-T			Benign (Jun 20, 2018)
10-124983576-A-G		not specified	Uncertain significance (Feb 22, 2023)
10-124984870-C-T		not specified	Uncertain significance (Oct 26, 2021)
10-124984873-C-T		not specified	Uncertain significance (Jun 30, 2022)
10-124984936-C-T		not specified	Uncertain significance (Jun 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZRANB1	protein_coding	protein_coding	ENST00000359653	9	46067

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00115	125735	0	6	125741	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.08	222	394	0.564	0.0000216	4637
Missense in Polyphen		41	120.18	0.34115		1416
Synonymous	-0.757	145	134	1.08	0.00000679	1345
Loss of Function	5.05	4	37.3	0.107	0.00000205	416

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000618	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Specifically hydrolyzes 'Lys-29'-linked and 'Lys-33'- linked diubiquitin. Also cleaves 'Lys-63'-linked chains, but with 40-fold less efficiency compared to 'Lys-29'-linked ones. Positive regulator of the Wnt signaling pathway that deubiquitinates APC protein, a negative regulator of Wnt-mediated transcription. Plays a role in the regulation of cell morphology and cytoskeletal organization. Required in the stress fiber dynamics and cell migration. May also modulate TNF-alpha signaling. {ECO:0000269|PubMed:18281465, ECO:0000269|PubMed:21834987, ECO:0000269|PubMed:22157957, ECO:0000269|PubMed:23827681}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Ovarian tumor domain proteases;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.131
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.99

Haploinsufficiency Scores

• pHI: 0.159
• hipred: Y
• hipred_score: 0.819
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.719

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zranb1
• Phenotype: homeostasis/metabolism phenotype; limbs/digits/tail phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; immune system phenotype

Zebrafish Information Network

• Gene name: zranb1b
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: curled

Gene ontology

• Biological process: cytoskeleton organization;Wnt signaling pathway;cell migration;protein deubiquitination;regulation of cell morphogenesis;positive regulation of Wnt signaling pathway;protein K29-linked deubiquitination;protein K63-linked deubiquitination;protein deubiquitination involved in ubiquitin-dependent protein catabolic process;protein K33-linked deubiquitination
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;intracellular membrane-bounded organelle
• Molecular function: thiol-dependent ubiquitin-specific protease activity;protein binding;thiol-dependent ubiquitinyl hydrolase activity;metal ion binding;K63-linked polyubiquitin modification-dependent protein binding