ZNF536

zinc finger protein 536, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:30224890-30713586

Links

ENSG00000198597 ∙ NCBI:9745 ∙ OMIM:618037 ∙ HGNC:29025 ∙ Uniprot:O15090 ∙ 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 ZNF536 gene.

• Inborn genetic diseases (47 variants)
• not provided (15 variants)
• not specified (1 variants)
• Neurodevelopmental disorder (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF536 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				5	4	9
missense			44	6	2	52
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	46	11	6

Variants in ZNF536

This is a list of pathogenic ClinVar variants found in the ZNF536 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-30443572-G-A		not specified	Uncertain significance (Dec 01, 2022)
19-30443576-G-A		not specified	Uncertain significance (Feb 27, 2023)
19-30443606-C-T		not specified	Uncertain significance (Jun 24, 2022)
19-30443762-A-G		not specified	Uncertain significance (Jun 07, 2023)
19-30443782-G-C		not specified	Uncertain significance (Oct 10, 2023)
19-30443815-G-A		not specified	Uncertain significance (Feb 15, 2023)
19-30443816-C-A		not specified	Uncertain significance (Feb 15, 2023)
19-30443835-G-C		not specified	Likely benign (Apr 07, 2023)
19-30443962-C-A		not specified	Uncertain significance (Oct 27, 2021)
19-30444152-G-C		not specified	Uncertain significance (Dec 03, 2021)
19-30444178-G-T		not specified	Uncertain significance (Jan 23, 2024)
19-30444337-A-G		not specified	Uncertain significance (Feb 14, 2024)
19-30444365-T-G		not specified	Uncertain significance (Apr 07, 2023)
19-30444560-G-A		not specified	Uncertain significance (Jul 14, 2023)
19-30444562-C-T		not specified	Uncertain significance (Jul 14, 2021)
19-30444572-G-T		not specified	Uncertain significance (Sep 20, 2023)
19-30444577-G-T		Neurodevelopmental disorder	Uncertain significance (Jan 31, 2022)
19-30444802-C-T		not specified	Uncertain significance (Dec 27, 2023)
19-30444860-G-T		not specified	Uncertain significance (Nov 22, 2021)
19-30444874-T-C		High myopia	Uncertain significance (Dec 17, 2018)
19-30444890-A-G		not specified	Uncertain significance (Apr 19, 2023)
19-30444952-G-A			Likely benign (Jul 13, 2018)
19-30445002-C-T			Benign (Jul 13, 2018)
19-30445004-C-T		not specified	Uncertain significance (Nov 01, 2022)
19-30445020-C-G		not specified	Uncertain significance (Oct 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF536	protein_coding	protein_coding	ENST00000355537	4	485249

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000417	125741	0	6	125747	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.40	630	824	0.764	0.0000550	8528
Missense in Polyphen		205	403.2	0.50844		4126
Synonymous	0.0400	382	383	0.997	0.0000297	2603
Loss of Function	5.06	3	35.6	0.0843	0.00000153	448

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000998	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000366	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation. Recognizes and binds 2 copies of the core DNA sequence 5'-CCCCCA- 3'.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.0816
• rvis_EVS: -1.57
• rvis_percentile_EVS: 3.2

Haploinsufficiency Scores

• pHI: 0.121
• hipred: Y
• hipred_score: 0.809
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.262

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp536
• Phenotype: homeostasis/metabolism 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; 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); respiratory system phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;negative regulation of neuron differentiation;negative regulation of retinoic acid receptor signaling pathway
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;retinoic acid-responsive element binding;metal ion binding