ZNF521

zinc finger protein 521, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 18:25061923-25352190

Links

ENSG00000198795 ∙ NCBI:25925 ∙ OMIM:610974 ∙ HGNC:24605 ∙ Uniprot:Q96K83 ∙ 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 ZNF521 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF521 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			61	1		62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	61	2	1

Variants in ZNF521

This is a list of pathogenic ClinVar variants found in the ZNF521 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-25062732-T-C		not specified	Uncertain significance (May 10, 2024)
18-25092005-T-C		not specified	Uncertain significance (Jun 06, 2022)
18-25195184-C-T		not specified	Uncertain significance (May 31, 2023)
18-25224377-T-C		not specified	Uncertain significance (Apr 19, 2023)
18-25224412-T-C		not specified	Uncertain significance (May 17, 2023)
18-25224496-G-C		not specified	Uncertain significance (Oct 20, 2021)
18-25224520-A-G		not specified	Likely benign (Jan 18, 2023)
18-25224526-C-T		not specified	Uncertain significance (Dec 09, 2023)
18-25224533-C-T		not specified	Uncertain significance (Aug 24, 2023)
18-25224611-C-T		not specified	Uncertain significance (Sep 12, 2023)
18-25224691-G-C		not specified	Uncertain significance (Jun 06, 2023)
18-25224791-T-C		not specified	Uncertain significance (Mar 20, 2023)
18-25224823-G-A		not specified	Uncertain significance (Aug 19, 2023)
18-25224857-G-A		not specified	Uncertain significance (Feb 02, 2022)
18-25224868-A-C		not specified	Uncertain significance (Jun 01, 2023)
18-25224931-G-A		not specified	Uncertain significance (Jul 19, 2023)
18-25225040-T-G		not specified	Uncertain significance (Apr 22, 2022)
18-25225081-C-T		not specified	Uncertain significance (Apr 25, 2022)
18-25225093-T-A		not specified	Uncertain significance (May 31, 2023)
18-25225105-G-T		not specified	Uncertain significance (Feb 26, 2024)
18-25225181-G-T		not specified	Uncertain significance (Apr 15, 2024)
18-25225259-C-T		not specified	Uncertain significance (May 04, 2022)
18-25225265-T-C		not specified	Uncertain significance (Aug 08, 2023)
18-25225282-A-G		not specified	Uncertain significance (Aug 17, 2022)
18-25225283-C-T		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF521	protein_coding	protein_coding	ENST00000361524	7	290265

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.23e-7	125729	0	3	125732	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.45	539	725	0.744	0.0000406	8842
Missense in Polyphen		184	301.29	0.61071		3881
Synonymous	-1.23	313	287	1.09	0.0000181	2373
Loss of Function	6.32	1	48.5	0.0206	0.00000283	583

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)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that can both act as an activator or a repressor depending on the context. Involved in BMP signaling and in the regulation of the immature compartment of the hematopoietic system. Associates with SMADs in response to BMP2 leading to activate transcription of BMP target genes. Acts as a transcriptional repressor via its interaction with EBF1, a transcription factor involved specification of B-cell lineage; this interaction preventing EBF1 to bind DNA and activate target genes. {ECO:0000269|PubMed:14630787}.
• Disease: DISEASE: Note=A chromosomal aberration involving ZNF521 is found in acute lymphoblastic leukemia. Translocation t(9;18)(p13;q11.2) with PAX5. The translocation generates the PAX5-ZNF521 oncogene consisting of the N-terminus part of PAX5 and the C-terminus part of ZNF521. {ECO:0000269|PubMed:17344859}.
• Pathway: RUNX2 regulates osteoblast differentiation;RUNX2 regulates bone development;Transcriptional regulation by RUNX2;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.00496
• rvis_EVS: -1.77
• rvis_percentile_EVS: 2.32

Haploinsufficiency Scores

• pHI: 0.717
• hipred: Y
• hipred_score: 0.786
• ghis: 0.597

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.927

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp521
• Phenotype: cellular phenotype; craniofacial phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; respiratory system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; renal/urinary system phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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)

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;neuron fate commitment
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein domain specific binding;metal ion binding