ZKSCAN1

Chr 7

zinc finger with KRAB and SCAN domains 1

Also known as: KOX18, PHZ-37, ZNF139, ZNF36, ZSCAN33

NCBI Gene: 7586ENSG00000106261UniProt: P17029

This gene encodes a member of the Kruppel C2H2-type zinc-finger family of proteins. This encoded protein may function as a transcription factor that regulates the expression of GABA type-A receptors in the brain. Transcripts from this gene have been shown to form stable and abundant circular RNAs. Elevated expression of this gene has been observed in gastric cancer and the encoded protein may stimulate migration and invasion of human gastric cancer cells. [provided by RefSeq, Oct 2016]

92
ClinVar variants
21
Pathogenic / LP
0.97
pLI score· haploinsufficient
0
Active trials
Clinical Summary— ZKSCAN1
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.97). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
21 Pathogenic / Likely Pathogenic· 67 VUS of 92 total submissions
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.32LOEUF
pLI 0.969
Z-score 3.97
OE 0.12 (0.06–0.32)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
2.12Z-score
OE missense 0.67 (0.60–0.75)
224 obs / 332.6 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.12 (0.06–0.32)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.67 (0.60–0.75)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.94
0≤1.21.6
LoF obs/exp: 3 / 24.0Missense obs/exp: 224 / 332.6Syn Z: 0.51

ClinVar Variant Classifications

92 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic19
Likely Pathogenic2
VUS67
Likely Benign4
19
Pathogenic
2
Likely Pathogenic
67
VUS
4
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
19
0
19
Likely Pathogenic
0
0
2
0
2
VUS
0
60
7
0
67
Likely Benign
0
2
1
1
4
Benign
0
0
0
0
0
Total06229192

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

ZKSCAN1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype

OMIM

No OMIM entries found.

Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Exploring the Immunogenicity of Noncanonical HLA-I Tumor Ligands Identified through Proteogenomics.
Lozano-Rabella M et al.·Clin Cancer Res
2023
MUC5B Genotype and Other Common Variants Are Associated with Computational Imaging Features of Usual Interstitial Pneumonia.
Blumhagen RZ et al.·Ann Am Thorac Soc
2025
Clinical, Morphologic, and Molecular Findings in MET Fusion Spitz Neoplasms.
Jeyakumar JE et al.·Am J Dermatopathol
2025
Somatic Genomics and Clinical Features of Lung Adenocarcinoma: A Retrospective Study.
Shi J et al.·PLoS Med
2016
Driver and targetable alterations in Chinese patients with small bowel carcinoma.
Li J et al.·J Cancer Res Clin Oncol
2023Cohort
KLF2-induced circZKSCAN1 potentiates the tumorigenic properties of clear cell renal cell carcinoma by targeting the miR-1294/PIM1 axis.
Li M et al.·Cell Cycle
2022
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools