ZFP90

ZFP90 zinc finger protein, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 16:68530090-68576072

Links

ENSG00000184939 ∙ NCBI:146198 ∙ OMIM:609451 ∙ HGNC:23329 ∙ Uniprot:Q8TF47 ∙ 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 ZFP90 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZFP90 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			45			45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	0	0

Variants in ZFP90

This is a list of pathogenic ClinVar variants found in the ZFP90 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-68558035-C-T		not specified	Uncertain significance (Jul 22, 2024)
16-68558525-G-C		not specified	Uncertain significance (Dec 27, 2023)
16-68558532-A-G		not specified	Uncertain significance (Aug 11, 2022)
16-68563077-A-G		not specified	Uncertain significance (Jan 04, 2024)
16-68563134-C-G		not specified	Uncertain significance (May 27, 2022)
16-68563159-C-A		not specified	Uncertain significance (Sep 16, 2021)
16-68563181-G-A		not specified	Uncertain significance (Dec 13, 2022)
16-68563236-C-T		not specified	Uncertain significance (Jan 10, 2023)
16-68563250-T-C		not specified	Uncertain significance (Sep 28, 2021)
16-68563277-T-A		not specified	Uncertain significance (Aug 30, 2021)
16-68563293-A-T		not specified	Uncertain significance (Apr 18, 2024)
16-68563395-A-C		not specified	Uncertain significance (Jul 15, 2021)
16-68563404-C-T		not specified	Uncertain significance (Aug 12, 2021)
16-68563409-A-G		not specified	Uncertain significance (Aug 12, 2022)
16-68563440-A-G		not specified	Uncertain significance (Nov 20, 2024)
16-68563457-T-C		not specified	Uncertain significance (Aug 17, 2021)
16-68563487-A-G		not specified	Uncertain significance (Jun 01, 2023)
16-68563559-G-A		not specified	Uncertain significance (Jan 23, 2023)
16-68563562-T-C		not specified	Uncertain significance (Jul 12, 2022)
16-68563572-C-A		not specified	Uncertain significance (Dec 16, 2023)
16-68563640-A-T		not specified	Uncertain significance (Dec 05, 2022)
16-68563703-G-A		not specified	Uncertain significance (May 24, 2023)
16-68563738-A-C		not specified	Uncertain significance (Jan 18, 2023)
16-68563749-G-A		not specified	Uncertain significance (Oct 29, 2024)
16-68563761-T-C		not specified	Uncertain significance (Mar 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZFP90	protein_coding	protein_coding	ENST00000570495	4	45983

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0317	0.968	125401	0	28	125429	0.000112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.946	284	333	0.854	0.0000157	4246
Missense in Polyphen		70	129.3	0.54137		1694
Synonymous	-0.896	132	120	1.10	0.00000583	1130
Loss of Function	3.47	8	27.7	0.289	0.00000164	335

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000180	0.000179
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.000219	0.000218
Finnish	0.00	0.00
European (Non-Finnish)	0.000160	0.000114
Middle Eastern	0.000219	0.000218
South Asian	0.0000980	0.0000980
Other	0.000166	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits the transcriptional repressor activity of REST by inhibiting its binding to DNA, thereby derepressing transcription of REST target genes. {ECO:0000269|PubMed:21284946}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• loftool: 0.388
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.6

Haploinsufficiency Scores

• pHI: 0.166
• hipred: N
• hipred_score: 0.346
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0298

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp90

Gene ontology

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