ZSCAN9

protein-coding

zinc finger and SCAN domain containing 9, 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 nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

ZNF193

MANE transcript

NM_006299.5

Inheritance

—

ClinVar variants

U:58B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.88

Max pathogenic AF

—

Genomic locus

chr6:28,224,886-28,233,487

External References & Databases

Ensembl (ENSG00000137185)

Transcript & Mutation Effects

hg38 • Region Span ~8.6 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 ZSCAN9 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 63

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006299.5. 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			57 clinvar	1 clinvar		58
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	58	1	0	59

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006299.5	RefSeq	NP_006290.1	3	MANE Select
ENST00000252207.10	Ensembl	ENSP00000252207.5	3	MANE Select
NM_001199479.2	RefSeq	NP_001186408.1	4	Standard
NM_001199480.2	RefSeq	NP_001186409.1	3	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: ENST00000425468
Coding exons: 4
Length: 8597
Individuals with no LoFs: 125710
Homozygous LoFs: 0
Heterozygous LoFs: 37
Defined: 125747
p: 0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.624	211	238	0.886	0.0000118	2931
Missense (PolyPhen)		78	76.344	1.0217		951
Synonymous	0.697	76	84.1	0.903	0.00000388	839
Loss of Function	0.504	18	20.5	0.880	0.00000132	205

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00027	0.00027	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.00029	0.00029	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.0773

Intolerance Scores

RVIS EVS: 0.04
RVIS percentile EVS: 57.15

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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