ZKSCAN7

protein-coding

zinc finger with KRAB and SCAN domains 7, the group of SCAN domain containing|Zinc fingers C2H2-type

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. Located in cytosol. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ZNF64
ZNF448
ZNF167

MANE transcript

NM_001288590.2

Inheritance

—

ClinVar variants

U:98B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.45

Max pathogenic AF

—

Genomic locus

chr3:44,555,193-44,594,173

External References & Databases

Ensembl (ENSG00000196345)

Transcript & Mutation Effects

hg38 • Region Span ~39.0 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 ZKSCAN7 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 103

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001288590.2. 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			1 clinvar	2 clinvar		3
missense			96 clinvar	8 clinvar		104
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	98	10	0	108

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 42 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001288590.2	RefSeq	NP_001275519.1	5	MANE Select
ENST00000426540.6	Ensembl	ENSP00000395524.1	5	MANE Select
NM_001288591.2	RefSeq	NP_001275520.1	5	Standard
NM_001288592.2	RefSeq	NP_001275521.1	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
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000273320
Coding exons: 5
Length: 28291
Individuals with no LoFs: 125579
Homozygous LoFs: 0
Heterozygous LoFs: 169
Defined: 125748
p: 0.000672

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.146	381	389	0.979	0.0000198	4968
Missense (PolyPhen)		125	135.66	0.9214		1804
Synonymous	-1.46	163	141	1.16	0.00000677	1412
Loss of Function	2.74	13	28.9	0.450	0.00000170	372

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00099	0.00098	rare
Latino/Admixed American	0.00040	0.00040	rare
Ashkenazi Jewish	0.0047	0.0047	notable
East Asian	0.00022	0.00022	rare
Finnish	0.00060	0.00060	rare
European (Non-Finnish)	0.00059	0.00059	rare
South Asian	0.00016	0.00016	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.279

Intolerance Scores

RVIS EVS: 0.94
RVIS percentile EVS: 89.86

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