ZSCAN20

protein-coding

zinc finger and SCAN domain containing 20, the group of Zinc fingers C2H2-type|Myb/SANT domain containing|SCAN domain containing

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:

ZNF360
ZNF31

MANE transcript

NM_001377376.1

Inheritance

—

ClinVar variants

U:131B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.33

Max pathogenic AF

—

Genomic locus

chr1:33,472,645-33,501,643

External References & Databases

Ensembl (ENSG00000121903)

Transcript & Mutation Effects

hg38 • Region Span ~29.0 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 ZSCAN20 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 133

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001377376.1. 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			130 clinvar	6 clinvar		136
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	131	6	0	137

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 59 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001377376.1	RefSeq	NP_001364305.1	7	MANE Select
ENST00000684572.1	Ensembl	ENSP00000507139.1	7	MANE Select
NM_001377377.1	RefSeq	NP_001364306.1	7	Standard
NM_001377378.1	RefSeq	NP_001364307.1	5	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: ENST00000361328
Coding exons: 7
Length: 23862
Individuals with no LoFs: 125183
Homozygous LoFs: 0
Heterozygous LoFs: 34
Defined: 125217
p: 0.000136

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.34	486	576	0.843	0.0000319	6877
Missense (PolyPhen)		149	228.69	0.65153		2645
Synonymous	0.425	207	215	0.963	0.0000114	1976
Loss of Function	4.08	14	42.9	0.327	0.00000216	514

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00013	rare
Latino/Admixed American	0.00016	0.00014	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00017	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.00016	0.00016	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.0898

Intolerance Scores

LoFtool: 0.578
RVIS EVS: -0.53
RVIS percentile EVS: 20.91

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.688

Gene Damage Prediction

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