ZSCAN1

protein-coding

zinc finger and SCAN domain containing 1, the group of SCAN domain containing|Zinc fingers C2H2-type

Gene summary

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in chromatin. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_182572.4

Inheritance

—

ClinVar variants

U:76B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.95

Max pathogenic AF

—

Genomic locus

chr19:58,034,025-58,054,631

External References & Databases

Ensembl (ENSG00000152467)

Transcript & Mutation Effects

hg38 • Region Span ~20.6 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 ZSCAN1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 80

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182572.4. 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					1 clinvar	1
missense			76 clinvar	5 clinvar		81
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	76	5	1	82

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182572.4	RefSeq	NP_872378.3	4	MANE Select
ENST00000282326.6	Ensembl	ENSP00000282326.1	4	MANE Select
ENST00000391700.5	Ensembl	ENSP00000375581.1	1	Standard
ENST00000391700.6	Ensembl	ENSP00000375581.1	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
protein binding
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000282326
Coding exons: 4
Length: 20600
Individuals with no LoFs: 125647
Homozygous LoFs: 0
Heterozygous LoFs: 94
Defined: 125741
p: 0.000374

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.00992	258	258	0.998	0.0000171	2620
Missense (PolyPhen)		61	59.89	1.0185		676
Synonymous	-0.0930	115	114	1.01	0.00000796	848
Loss of Function	0.141	10	10.5	0.953	5.02e-7	99

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00014	0.00012	rare
Latino/Admixed American	0.00058	0.00052	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00049	0.00049	rare
Finnish	0.000072	0.000046	rare
European (Non-Finnish)	0.00053	0.00050	rare
South Asian	0.00013	0.00013	rare
Other	0.00051	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.847
RVIS EVS: 0.02
RVIS percentile EVS: 55.69

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.413

Gene Damage Prediction

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