ZSCAN18

protein-coding

zinc finger and SCAN domain containing 18, the group of SCAN domain containing|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 transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

ZNF447

MANE transcript

NM_001145543.2

Inheritance

—

ClinVar variants

U:84B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.32

Max pathogenic AF

—

Genomic locus

chr19:58,083,838-58,118,427

External References & Databases

Ensembl (ENSG00000121413)

Transcript & Mutation Effects

hg38 • Region Span ~34.6 kb

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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 ZSCAN18 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 87

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001145543.2. 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			83 clinvar	6 clinvar		89
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	84	6	0	90

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 68 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001145543.2	RefSeq	NP_001139015.1	6	MANE Select
ENST00000601144.6	Ensembl	ENSP00000468934.1	6	MANE Select
NM_001145542.1	RefSeq	NP_001139014.1	7	Standard
NM_001145544.2	RefSeq	NP_001139016.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription, DNA-templated

Molecular Function

DNA binding
DNA-binding transcription factor activity
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000600404
Coding exons: 7
Length: 34590
Individuals with no LoFs: 125726
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125732
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.427	326	348	0.936	0.0000229	3564
Missense (PolyPhen)		36	61.577	0.58463		745
Synonymous	-0.0766	169	168	1.01	0.0000130	1179
Loss of Function	2.49	5	15.6	0.321	6.94e-7	174

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.0924

Intolerance Scores

LoFtool: 0.385
RVIS EVS: 0.44
RVIS percentile EVS: 77.91

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.987

Gene Damage Prediction

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