ZNHIT1

Chr 7

zinc finger HIT-type containing 1

Also known as: CG1I, ZNFN4A1, p18(Hamlet)

NCBI Gene: 10467ENSG00000106400UniProt: O43257

Enables histone binding activity. Involved in muscle cell differentiation and positive regulation of DNA damage response, signal transduction by p53 class mediator. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

47
ClinVar variants
19
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— ZNHIT1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
19 Pathogenic / Likely Pathogenic· 26 VUS of 47 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
Tolerant — LoF & missense variants common in population
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.
1.58LOEUF
pLI 0.000
Z-score 0.24
OE 0.92 (0.55–1.58)
Tolerant

Highly tolerant — LoF variants common in population

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.
1.12Z-score
OE missense 0.70 (0.58–0.84)
76 obs / 109.0 exp
Tolerant

Mild missense constraint

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.0.92 (0.55–1.58)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.70 (0.58–0.84)
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.1.04
0≤1.21.6
LoF obs/exp: 9 / 9.8Missense obs/exp: 76 / 109.0Syn Z: -0.20

ClinVar Variant Classifications

47 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic17
Likely Pathogenic2
VUS26
Benign2
17
Pathogenic
2
Likely Pathogenic
26
VUS
2
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
17
0
17
Likely Pathogenic
0
0
2
0
2
VUS
0
23
3
0
26
Likely Benign
0
0
0
0
0
Benign
0
0
2
0
2
Total02324047

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

View in ClinVar →

Protein Context — Lollipop Plot

ZNHIT1 · 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
Deficient H2A.Z deposition is associated with genesis of uterine leiomyoma.
Berta DG et al.·Nature
2021
Cellular hierarchy framework based on single-cell and bulk RNA sequencing reveals fatty acid metabolic biomarker MYDGF as a therapeutic target for ccRCC.
Wang N et al.·Front Immunol
2025
Znhit1 and HIF-2α are correlated with cancer stem cell markers in breast cancer patients.
Ebeid SA et al.·Sci Rep
2022Cohort
Inherited mutations affecting the SRCAP complex are central in moderate-penetrance predisposition to uterine leiomyomas.
Välimäki N et al.·Am J Hum Genet
2023
Gene Co-expression Analysis of the Human Substantia Nigra Identifies ZNHIT1 as an SNCA Co-expressed Gene that Protects Against α-Synuclein-Induced Impairments in Neurite Growth and Mitochondrial Dysfunction in SH-SY5Y Cells.
McCarthy E et al.·Mol Neurobiol
2022
Suppression of SRCAP chromatin remodelling complex and restriction of lymphoid lineage commitment by Pcid2.
Ye B et al.·Nat Commun
2017Functional
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