ZNF18

protein-coding

zinc finger protein 18, the group of Zinc fingers C2H2-type|SCAN domain containing

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 transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001303281.2

Inheritance

ClinVar variants

U:51B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.46

Max pathogenic AF

—

Genomic locus

chr17:11,977,439-11,997,475

External References & Databases

Ensembl (ENSG00000154957)

Transcript & Mutation Effects

hg38 • Region Span ~20.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0700092

Submitter: PMGRC

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZNF18 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 53

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001303281.2. 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			49 clinvar	5 clinvar		54
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	51	5	0	56

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001303281.2	RefSeq	NP_001290210.1	6	MANE Select
ENST00000580306.7	Ensembl	ENSP00000463471.1	6	MANE Select
NM_001303282.2	RefSeq	NP_001290211.1	6	Standard
NM_144680.4	RefSeq	NP_653281.2	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription

Biological Process

regulation of transcription by RNA polymerase II

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000322748
Coding exons: 6
Length: 20072
Individuals with no LoFs: 125713
Homozygous LoFs: 1
Heterozygous LoFs: 34
Defined: 125748
p: 0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.01	239	287	0.833	0.0000143	3587
Missense (PolyPhen)		56	82.867	0.67578		1076
Synonymous	0.959	99	112	0.885	0.00000582	1031
Loss of Function	2.43	11	23.8	0.463	0.00000101	305

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00036	0.00032	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0.00043	0.00042	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.106

Intolerance Scores

RVIS EVS: -0.07
RVIS percentile EVS: 48.69

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0871

Gene Damage Prediction

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