ZRANB3

zinc finger RANBP2-type containing 3, the group of Zinc fingers RANBP2-type

Basic information

Region (hg38): 2:135136915-135531218

Links

ENSG00000121988 ∙ NCBI:84083 ∙ OMIM:615655 ∙ HGNC:25249 ∙ Uniprot:Q5FWF4 ∙ 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 ZRANB3 gene.

• Inborn genetic diseases (33 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZRANB3 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	2
missense			29	1	1	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding			3			3
Total	0	0	32	2	3

Variants in ZRANB3

This is a list of pathogenic ClinVar variants found in the ZRANB3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-135150276-T-C			Likely benign (Jun 14, 2018)
2-135150353-C-G			Likely benign (Aug 24, 2023)
2-135150366-C-T		Warburg micro syndrome 1	Uncertain significance (Apr 30, 2022)
2-135150371-A-G		RAB3GAP1-related disorder	Likely benign (Sep 18, 2023)
2-135150372-C-T			Uncertain significance (May 30, 2022)
2-135150374-A-G			Likely benign (Aug 15, 2022)
2-135150381-A-G			Uncertain significance (May 16, 2022)
2-135150434-A-G			Uncertain significance (Dec 06, 2023)
2-135150437-G-A		not specified • Warburg micro syndrome 1 • RAB3GAP1-related disorder	Benign (Jan 23, 2024)
2-135150450-C-T			Uncertain significance (Aug 01, 2022)
2-135150452-C-A		Warburg micro syndrome 1	Uncertain significance (Nov 15, 2022)
2-135150456-C-T		Warburg micro syndrome 1	Pathogenic (Jan 01, 2007)
2-135150462-C-T			Uncertain significance (Nov 27, 2023)
2-135150469-A-G			Uncertain significance (Jan 01, 2022)
2-135150477-T-TGTCTGCTCTCAGATATGGA		Warburg micro syndrome 1	Pathogenic (May 01, 2013)
2-135150524-A-G			Likely benign (Dec 02, 2022)
2-135153629-A-T			Likely benign (May 22, 2023)
2-135153635-T-G			Likely benign (Feb 23, 2023)
2-135153637-G-A			Likely benign (Aug 17, 2022)
2-135153658-C-A		Inborn genetic diseases	Uncertain significance (Jun 24, 2022)
2-135153685-A-C		Warburg micro syndrome 1	Uncertain significance (Jan 12, 2018)
2-135153690-G-A			Pathogenic (Sep 22, 2023)
2-135153690-G-T		Inborn genetic diseases	Uncertain significance (Jun 05, 2023)
2-135153708-T-G			Likely pathogenic (Nov 10, 2022)
2-135153718-G-A			Uncertain significance (Jul 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZRANB3	protein_coding	protein_coding	ENST00000264159	20	394321

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.23e-21	0.391	122467	80	2092	124639	0.00875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.489	502	534	0.940	0.0000265	7075
Missense in Polyphen		158	179.58	0.87983		2503
Synonymous	0.563	179	189	0.948	0.00000983	1966
Loss of Function	1.87	40	55.0	0.727	0.00000289	698

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.114	0.113
Ashkenazi Jewish	0.00404	0.00368
East Asian	0.000673	0.000668
Finnish	0.000515	0.000511
European (Non-Finnish)	0.00155	0.00151
Middle Eastern	0.000673	0.000668
South Asian	0.00463	0.00432
Other	0.00610	0.00580

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DNA annealing helicase and endonuclease required to maintain genome stability at stalled or collapsed replication forks by facilitating fork restart and limiting inappropriate recombination that could occur during template switching events (PubMed:21078962, PubMed:22704558, PubMed:22705370, PubMed:22759634, PubMed:26884333). Recruited to the sites of stalled DNA replication by polyubiquitinated PCNA and acts as a structure-specific endonuclease that cleaves the replication fork D-loop intermediate, generating an accessible 3'-OH group in the template of the leading strand, which is amenable to extension by DNA polymerase (PubMed:22759634). In addition to endonuclease activity, also catalyzes the fork regression via annealing helicase activity in order to prevent disintegration of the replication fork and the formation of double-strand breaks (PubMed:22705370, PubMed:22704558). {ECO:0000269|PubMed:21078962, ECO:0000269|PubMed:22704558, ECO:0000269|PubMed:22705370, ECO:0000269|PubMed:22759634, ECO:0000269|PubMed:26884333}.

Intolerance Scores

• rvis_EVS: 1.27
• rvis_percentile_EVS: 93.67

Haploinsufficiency Scores

• pHI: 0.0479
• hipred: N
• hipred_score: 0.204

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.414

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zranb3

Gene ontology

• Biological process: DNA strand renaturation;DNA repair;cellular response to DNA damage stimulus;response to UV;replication fork processing;DNA duplex unwinding;DNA rewinding;negative regulation of DNA recombination;replication fork protection;nucleic acid phosphodiester bond hydrolysis
• Cellular component: nucleus;nuclear replication fork
• Molecular function: DNA helicase activity;endodeoxyribonuclease activity;protein binding;ATP binding;annealing helicase activity;metal ion binding;K63-linked polyubiquitin modification-dependent protein binding