ZSCAN21

protein-coding

zinc finger and SCAN domain containing 21, the group of Zinc fingers C2H2-type|SCAN domain containing

Gene summary

Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

ZNF38

MANE transcript

NM_145914.3

Inheritance

—

ClinVar variants

U:72B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.97

Max pathogenic AF

—

Genomic locus

chr7:100,049,774-100,065,040

External References & Databases

Ensembl (ENSG00000166529)

Transcript & Mutation Effects

hg38 • Region Span ~15.3 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 ZSCAN21 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 77

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_145914.3. 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			70 clinvar	7 clinvar		77
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	72	8	0	80

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_145914.3	RefSeq	NP_666019.1	3	MANE Select
ENST00000292450.9	Ensembl	ENSP00000292450.4	3	MANE Select
NM_001362779.2	RefSeq	NP_001349708.1	3	Standard
NM_001362780.2	RefSeq	NP_001349709.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription, DNA-templated
positive regulation of transcription by RNA polymerase II

Molecular Function

RNA polymerase II proximal promoter sequence-specific DNA binding
DNA-binding transcription factor activity, RNA polymerase II-specific
DNA-binding transcription activator activity, RNA polymerase II-specific
protein binding
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000292450
Coding exons: 3
Length: 15272
Individuals with no LoFs: 125667
Homozygous LoFs: 0
Heterozygous LoFs: 80
Defined: 125747
p: 0.000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.246	258	269	0.958	0.0000147	3107
Missense (PolyPhen)		93	97.897	0.94998		1160
Synonymous	-0.146	107	105	1.02	0.00000620	878
Loss of Function	0.133	18	18.6	0.967	9.45e-7	229

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00049	0.00049	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00060	0.00060	rare
Finnish	0.000048	0.000046	rare
European (Non-Finnish)	0.00032	0.00032	rare
South Asian	0.00044	0.00042	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Strong transcriptional activator. {ECO:0000250}.;

Recessive Scores

pRec: 0.102

Intolerance Scores

LoFtool: 0.707
RVIS EVS: -0.38
RVIS percentile EVS: 27.88

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.460

Gene Damage Prediction

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