ZNF93

zinc finger protein 93, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:19900913-19963464

Previous symbols: [ "ZNF505" ]

Links

ENSG00000184635 ∙ NCBI:81931 ∙ OMIM:603975 ∙ HGNC:13169 ∙ Uniprot:P35789 ∙ 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 ZNF93 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF93 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			54	2	1	57
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	54	3	3

Variants in ZNF93

This is a list of pathogenic ClinVar variants found in the ZNF93 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-19915290-A-G		not specified	Uncertain significance (Dec 13, 2021)
19-19915301-G-A		not specified	Uncertain significance (Feb 06, 2023)
19-19915331-C-T		not specified	Uncertain significance (Mar 28, 2024)
19-19915337-C-G		not specified	Uncertain significance (Nov 08, 2021)
19-19915365-G-A		not specified	Likely benign (Apr 06, 2022)
19-19915386-A-G		not specified	Uncertain significance (Sep 16, 2021)
19-19915397-G-A		not specified	Uncertain significance (Aug 25, 2024)
19-19915403-C-T		not specified	Uncertain significance (Sep 25, 2023)
19-19933186-A-G		not specified	Likely benign (Nov 26, 2024)
19-19933265-G-C		not specified	Uncertain significance (Dec 01, 2022)
19-19933283-A-C		not specified	Uncertain significance (Dec 07, 2023)
19-19933335-C-T		not specified	Uncertain significance (Jan 04, 2022)
19-19933361-T-C		not specified	Uncertain significance (Mar 14, 2025)
19-19933368-C-T		not specified	Uncertain significance (Dec 16, 2023)
19-19933385-G-A		not specified	Uncertain significance (Jul 20, 2021)
19-19933439-A-G		not specified	Uncertain significance (Jan 02, 2025)
19-19933535-A-G		not specified	Uncertain significance (Apr 08, 2022)
19-19933559-A-T		not specified	Uncertain significance (Jul 10, 2024)
19-19933572-G-A		not specified	Uncertain significance (Dec 25, 2024)
19-19933590-A-G		not specified	Uncertain significance (Dec 10, 2024)
19-19933608-C-T		not specified	Uncertain significance (Apr 18, 2023)
19-19933609-A-T			Benign (Mar 29, 2018)
19-19933617-G-C		not specified	Uncertain significance (Jan 06, 2023)
19-19933641-A-G		not specified	Uncertain significance (Jul 27, 2021)
19-19933654-A-T		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF93	protein_coding	protein_coding	ENST00000343769	4	34663

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000390	0.413	125700	0	47	125747	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0441	312	310	1.01	0.0000140	4077
Missense in Polyphen		70	74.166	0.94383		1093
Synonymous	-0.418	114	108	1.05	0.00000503	1074
Loss of Function	-0.00829	5	4.98	1.00	2.11e-7	58

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000481	0.000481
Ashkenazi Jewish	0.00109	0.00109
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.00	0.00
South Asian	0.000229	0.000229
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor specifically required to repress long interspersed nuclear element 1 (L1) retrotransposons: recognizes and binds L1 sequences and repress their expression by recruiting a repressive complex containing TRIM28/KAP1 (PubMed:25274305). Not able to repress expression of all subtypes of L1 elements. Binds to the 5' end of L1PA4, L1PA5 and L1PA6 subtypes, and some L1PA3 subtypes. Does not bind to L1PA7 or older subtypes nor at the most recently evolved L1PA2 and L1Hs. 50% of L1PA3 elements have lost the ZNF93-binding site, explaining why ZNF93 is not able to repress their expression (PubMed:25274305). {ECO:0000269|PubMed:25274305}.

Intolerance Scores

• loftool: 0.769
• rvis_EVS: 1.04
• rvis_percentile_EVS: 91.29

Haploinsufficiency Scores

• pHI: 0.617
• hipred: N
• hipred_score: 0.112
• ghis: 0.450

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp457

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;negative regulation of transcription, DNA-templated;negative regulation of transposon integration
• Cellular component: nucleus
• Molecular function: transcription regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;zinc ion binding