ZRANB2

zinc finger RANBP2-type containing 2, the group of MicroRNA protein coding host genes|Zinc fingers RANBP2-type

Basic information

Region (hg38): 1:71063291-71081289

Previous symbols: [ "ZNF265" ]

Links

ENSG00000132485 ∙ NCBI:9406 ∙ OMIM:604347 ∙ HGNC:13058 ∙ Uniprot:O95218 ∙ 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 ZRANB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZRANB2 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in ZRANB2

This is a list of pathogenic ClinVar variants found in the ZRANB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-71065091-T-A		not specified	Uncertain significance (Oct 24, 2024)
1-71065108-T-A		not specified	Uncertain significance (May 10, 2023)
1-71065109-G-T		not specified	Uncertain significance (Jul 02, 2024)
1-71065136-G-A		not specified	Uncertain significance (Jul 14, 2024)
1-71066813-G-A		not specified	Uncertain significance (Mar 22, 2023)
1-71066833-C-A		not specified	Uncertain significance (Jan 25, 2023)
1-71066839-C-T		not specified	Uncertain significance (Mar 24, 2023)
1-71069303-C-A		not specified	Uncertain significance (Dec 07, 2024)
1-71069336-G-A		not specified	Uncertain significance (Jul 16, 2024)
1-71070863-C-T		not specified	Uncertain significance (Sep 11, 2024)
1-71070864-G-A		not specified	Uncertain significance (Jun 11, 2024)
1-71070881-T-C		not specified	Uncertain significance (Jan 04, 2022)
1-71070890-C-T		not specified	Uncertain significance (Dec 06, 2023)
1-71070902-C-T		not specified	Uncertain significance (May 16, 2023)
1-71072192-C-T		not specified	Uncertain significance (Aug 27, 2024)
1-71078479-C-T		not specified	Uncertain significance (Aug 17, 2022)
1-71078658-C-T		not specified	Uncertain significance (Aug 11, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZRANB2	protein_coding	protein_coding	ENST00000370920	10	18007

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000512	125589	0	2	125591	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.68	122	186	0.655	0.0000110	2101
Missense in Polyphen		6	35.116	0.17086		465
Synonymous	-1.55	76	60.6	1.25	0.00000301	618
Loss of Function	4.56	1	26.2	0.0381	0.00000182	294

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000884	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Splice factor required for alternative splicing of TRA2B/SFRS10 transcripts. May interfere with constitutive 5'- splice site selection. {ECO:0000269|PubMed:11448987}.

Recessive Scores

• pRec: 0.212

Intolerance Scores

• loftool: 0.274
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

• pHI: 0.302
• hipred: Y
• hipred_score: 0.673
• ghis: 0.633

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.810

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zranb2
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of transcription, DNA-templated;mRNA processing;RNA splicing
• Cellular component: nucleus;nucleoplasm
• Molecular function: DNA-binding transcription factor activity;RNA binding;protein binding;metal ion binding