ZKSCAN4

protein-coding

zinc finger with KRAB and SCAN domains 4, the group of Zinc fingers C2H2-type|SCAN domain containing

Gene summary

Enables identical protein binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

ZNF307
ZNF427

MANE transcript

NM_019110.5

Inheritance

—

ClinVar variants

U:63B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.46

Max pathogenic AF

—

Genomic locus

chr6:28,241,697-28,252,269

External References & Databases

Ensembl (ENSG00000187626)

Transcript & Mutation Effects

hg38 • Region Span ~10.6 kb

Loading mutation effect viewer...

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 ZKSCAN4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 66

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_019110.5. 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				2 clinvar		2
missense			63 clinvar	3 clinvar		66
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	63	5	0	68

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_019110.5	RefSeq	NP_061983.2	5	MANE Select
ENST00000377294.3	Ensembl	ENSP00000366509.2	5	MANE Select
NM_001304506.2	RefSeq	NP_001291435.1	4	Standard
ENST00000901698.1	Ensembl	ENSP00000571757.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription

Biological Process

regulation of transcription by RNA polymerase II

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
protein binding
identical protein binding
metal ion binding

Cellular Component

nucleoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000377294
Coding exons: 5
Length: 14611
Individuals with no LoFs: 125631
Homozygous LoFs: 1
Heterozygous LoFs: 116
Defined: 125748
p: 0.000465

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.07	238	289	0.822	0.0000137	3580
Missense (PolyPhen)		67	100.81	0.66461		1299
Synonymous	1.30	97	115	0.845	0.00000569	1033
Loss of Function	2.37	10	22.0	0.455	0.00000104	267

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00040	0.00040	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0012	0.0011	notable
Finnish	0.0025	0.0025	notable
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.000065	0.000065	rare
Other	0.0011	0.0011	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in the transcriptional activation of MDM2 and EP300 genes. {ECO:0000269|PubMed:17910948}.;

Recessive Scores

pRec: 0.0911

Intolerance Scores

LoFtool: 0.902
RVIS EVS: -0.53
RVIS percentile EVS: 20.7

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.891

Gene Damage Prediction

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