ZNF90

protein-coding

zinc finger protein 90, the group of Zinc fingers C2H2-type

Gene summary

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of DNA-templated transcription. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_007138.2

Inheritance

—

ClinVar variants

U:122B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.81

Max pathogenic AF

—

Genomic locus

chr19:20,077,994-20,127,076

External References & Databases

Ensembl (ENSG00000213988)

Transcript & Mutation Effects

hg38 • Region Span ~49.1 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZNF90 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 127

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007138.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			122 clinvar	6 clinvar		128
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	122	6	1	129

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007138.2	RefSeq	NP_009069.1	4	MANE Select
ENST00000418063.3	Ensembl	ENSP00000410466.2	4	MANE Select
ENST00000469078.5	Ensembl	ENSP00000420111.1	4	Standard
ENST00000473524.5	Ensembl	ENSP00000418166.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
DNA-binding transcription factor activity
zinc ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000418063
Coding exons: 4
Length: 49083
Individuals with no LoFs: 125611
Homozygous LoFs: 0
Heterozygous LoFs: 58
Defined: 125669
p: 0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.04	356	305	1.17	0.0000148	3929
Missense (PolyPhen)		90	100.5	0.89551		1376
Synonymous	-0.188	107	105	1.02	0.00000468	1046
Loss of Function	0.395	4	4.95	0.808	2.09e-7	62

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000062	rare
Latino/Admixed American	0.000031	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0025	0.0024	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0.00027	0.00026	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation.;

Intolerance Scores

RVIS EVS: 1.22
RVIS percentile EVS: 93.14

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.200

Gene Damage Prediction

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