ZNF496

Chr 1

zinc finger protein 496

Also known as: NIZP1, ZFP496, ZKSCAN17, ZSCAN49

NCBI Gene: 84838ENSG00000162714UniProt: Q96IT1OMIM: 613911

This gene encodes a DNA-binding transcription factor that functions as both a transcriptional activator and repressor. ZNF496 is highly constrained against loss-of-function variants (pLI=1.00, LOEUF=0.25), suggesting that mutations likely cause severe developmental disorders, though specific associated diseases have not yet been established in the literature.

OMIMResearchSummary from RefSeq, UniProt
LOEUF 0.25
Clinical Summary— ZNF496
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
72 unique Pathogenic / Likely Pathogenic· 93 VUS of 180 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.25LOEUF
pLI 0.996
Z-score 4.29
OE 0.08 (0.03–0.25)
Highly constrained

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

Missense Constraint
1.40Z-score
OE missense 0.80 (0.73–0.88)
314 obs / 391.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.08 (0.03–0.25)
0≤0.351.4
Missense OE0.80 (0.73–0.88)
0≤0.61.4
Synonymous OE1.06
0≤1.21.6
LoF obs/exp: 2 / 25.3Missense obs/exp: 314 / 391.7Syn Z: -0.59

ClinVar Variant Classifications

180 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic66
Likely Pathogenic6
VUS93
Likely Benign4
66
Pathogenic
6
Likely Pathogenic
93
VUS
4
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
1
0
65
0
66
Likely Pathogenic
0
0
6
0
6
VUS
0
83
10
0
93
Likely Benign
0
4
0
0
4
Benign
0
0
0
0
0
Total187810169

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

View in ClinVar →

Protein Context — Lollipop Plot

ZNF496 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
The pattern of gene copy number alteration (CNAs) in hepatocellular carcinoma: an in silico analysis
Shahrisa A et al.·Mol Cytogenet
2021
A de novo PAK1 likely pathogenic variant and a de novo terminal 1q microdeletion in a Chinese girl with global developmental delay, severe intellectual disability, and seizures
Zhuang J et al.·BMC Med Genomics
2023
Genome-wide association analysis of milk production, somatic cell score, and body conformation traits in Holstein cows
Wang P et al.·Front Vet Sci
2022
Low Levels of TRIM28-Interacting KRAB-ZNF Genes Associate with Cancer Stemness and Predict Poor Prognosis of Kidney Renal Clear Cell Carcinoma Patients
Czerwinska P et al.·Cancers (Basel)
2021Cohort
KRAB-ZFP Transcriptional Regulators Acting as Oncogenes and Tumor Suppressors: An Overview
Sobocińska J et al.·Int J Mol Sci
2021Review
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 1 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients