ZNF362

Chr 1

zinc finger protein 362

Also known as: LIN29, RN, lin-29

NCBI Gene: 149076 ENSG00000160094 UniProt: Q5T0B9 OMIM: 621584

The ZNF362 protein is a DNA-binding transcription factor that regulates gene transcription by RNA polymerase II in the nucleus. This gene is highly constrained against loss-of-function variants (pLI 0.94, LOEUF 0.35), suggesting that mutations would likely cause significant developmental or neurological phenotypes, though specific disease associations have not yet been established in humans.

OMIM ResearchSummary from RefSeq, UniProt

Predicted to enable DNA-binding transcription factor activity and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

LOFmechanismLOEUF 0.35

Clinical Summary— ZNF362

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Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.94). One damaged copy is likely sufficient to cause disease.

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ClinVar Variants

104 VUS of 131 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?

0.35LOEUF

pLI 0.941

Z-score 3.47

OE 0.11 (0.04–0.35)

Highly constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

2.73Z-score

OE missense 0.52 (0.45–0.60)

135 obs / 258.4 exp

Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?

LoF OE?0.11 (0.04–0.35)

0≤0.351.4

Missense OE?0.52 (0.45–0.60)

0≤0.61.4

Synonymous OE?0.97

0≤1.21.6

LoF obs/exp: 2 / 17.8Missense obs/exp: 135 / 258.4Syn Z: 0.23

This gene — mechanism propensity

0.4487th %ile

GOF

0.3788th %ile

LOF

0.81top 5%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.35

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

131 submitted variants in ClinVar

ClinVar

Classification Summary

VUS104

Likely Benign7

Benign2

104

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	104	0	104
Likely Benign	1	6	7
Benign	1	1	2
Total	106	7	113

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

View in ClinVar →

9 pathogenic / likely-pathogenic (of 12) ClinVar copy-number / structural variants overlap ZNF362 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →