ZSCAN12

protein-coding

zinc finger and SCAN domain containing 12, the group of Zinc fingers C2H2-type|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:

ZNF305
ZNF96

MANE transcript

NM_001163391.2

Inheritance

—

ClinVar variants

U:76B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.56

Max pathogenic AF

—

Genomic locus

chr6:28,378,821-28,399,747

External References & Databases

Ensembl (ENSG00000158691)

Transcript & Mutation Effects

hg38 • Region Span ~20.9 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 ZSCAN12 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 78

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001163391.2. 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			76 clinvar	2 clinvar		78
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	76	2	0	78

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001163391.2	RefSeq	NP_001156863.1	3	MANE Select
ENST00000684592.1	Ensembl	ENSP00000507347.1	3	MANE Select
NM_001368124.1	RefSeq	NP_001355053.1	3	Standard
ENST00000361028.5	Ensembl	ENSP00000354305.1	4	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: ENST00000361028
Coding exons: 4
Length: 20780
Individuals with no LoFs: 125702
Homozygous LoFs: 0
Heterozygous LoFs: 29
Defined: 125731
p: 0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.90	222	317	0.699	0.0000163	3995
Missense (PolyPhen)		86	110.36	0.77923		1425
Synonymous	2.56	78	113	0.693	0.00000582	1073
Loss of Function	2.09	15	26.7	0.562	0.00000154	320

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00039	0.00037	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000089	0.000088	rare
South Asian	0.00020	0.00020	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.0915

Essentials

Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.743

Gene Damage Prediction

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