ZSCAN30

protein-coding

zinc finger and SCAN domain containing 30, 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 nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ZNF397OS

MANE transcript

NM_001112734.4

Inheritance

—

ClinVar variants

U:69B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.97

Max pathogenic AF

—

Genomic locus

chr18:35,251,058-35,290,245

External References & Databases

Ensembl (ENSG00000186814)

NCBI Gene (100101467)

Transcript & Mutation Effects

hg38 • Region Span ~39.2 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 ZSCAN30 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 74

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001112734.4. 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						0
missense			69 clinvar	5 clinvar		74
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	69	5	0	74

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 42 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001112734.4	RefSeq	NP_001106205.1	3	MANE Select
ENST00000333206.10	Ensembl	ENSP00000329738.4	3	MANE Select
NM_001166012.3	RefSeq	NP_001159484.1	3	Standard
NM_001288711.2	RefSeq	NP_001275640.1	1	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
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000420878
Coding exons: 3
Length: 39165
Individuals with no LoFs: 125613
Homozygous LoFs: 0
Heterozygous LoFs: 135
Defined: 125748
p: 0.000537

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0736	256	259	0.987	0.0000128	3265
Missense (PolyPhen)		60	72.7	0.82531		896
Synonymous	0.992	81	93.2	0.869	0.00000448	913
Loss of Function	0.105	19	19.5	0.974	9.96e-7	250

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00077	0.00074	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.0017	0.0017	notable
Finnish	0.00051	0.00051	rare
European (Non-Finnish)	0.00030	0.00030	rare
South Asian	0.0010	0.0010	notable
Other	0.00099	0.00098	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

RVIS EVS: 0.75
RVIS percentile EVS: 86.65

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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