ZNF565

zinc finger protein 565, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:36182276-36246257

Links

ENSG00000196357 ∙ NCBI:147929 ∙ OMIM:614275 ∙ HGNC:26726 ∙ Uniprot:Q8N9K5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Schizophrenia	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	21743468

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF565 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF565 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			24	3		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	25	3	0

Variants in ZNF565

This is a list of pathogenic ClinVar variants found in the ZNF565 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-36182509-A-T		not specified	Uncertain significance (Mar 22, 2023)
19-36182554-C-T		not specified	Uncertain significance (Oct 12, 2021)
19-36182582-G-C		not specified	Uncertain significance (May 31, 2023)
19-36182677-C-T		not specified	Uncertain significance (Jul 19, 2023)
19-36182777-C-T		not specified	Uncertain significance (Mar 02, 2023)
19-36182791-T-G		not specified	Uncertain significance (Oct 29, 2024)
19-36182797-G-T		not specified	Uncertain significance (Jul 14, 2021)
19-36182960-C-T		not specified	Uncertain significance (Feb 28, 2024)
19-36182986-C-T		not specified	Uncertain significance (Aug 02, 2021)
19-36183097-C-T		not specified	Uncertain significance (Feb 14, 2023)
19-36183128-C-T		not specified	Uncertain significance (Dec 19, 2022)
19-36183140-C-T		not specified	Uncertain significance (Jun 22, 2021)
19-36183160-T-A		not specified	Uncertain significance (Sep 27, 2021)
19-36183265-C-T		not specified	Uncertain significance (Dec 05, 2022)
19-36183266-G-A		not specified	Uncertain significance (Aug 20, 2024)
19-36183313-G-A		not specified	Uncertain significance (Sep 10, 2024)
19-36183325-T-C		not specified	Uncertain significance (Aug 20, 2024)
19-36183376-C-A		not specified	Uncertain significance (May 03, 2023)
19-36183430-C-T		not specified	Uncertain significance (Feb 27, 2024)
19-36183488-T-C		not specified	Uncertain significance (Jan 23, 2024)
19-36183496-C-T		not specified	Likely benign (Oct 06, 2023)
19-36183511-G-A		not specified	Uncertain significance (Feb 27, 2023)
19-36183548-C-T		not specified	Likely benign (Nov 24, 2024)
19-36183553-A-G		not specified	Uncertain significance (May 11, 2022)
19-36183575-C-T		not specified	Uncertain significance (Oct 26, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF565	protein_coding	protein_coding	ENST00000392173	4	63972

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000102	0.987	125710	0	37	125747	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.45	213	281	0.757	0.0000157	3305
Missense in Polyphen		79	115.77	0.6824		1368
Synonymous	1.31	86	103	0.835	0.00000634	900
Loss of Function	2.24	12	23.8	0.505	0.00000135	269

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000394	0.000271
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000212	0.000211
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• loftool: 0.755
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.200
• hipred: N
• hipred_score: 0.257
• ghis: 0.517

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.771

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp84
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

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