ZSCAN10

Chr 16AR

zinc finger and SCAN domain containing 10

Also known as: OFNS, ZFP206, ZNF206

NCBI Gene: 84891 ENSG00000130182 UniProt: Q96SZ4 OMIM: 618365

The protein is an embryonic stem cell-specific transcription factor that maintains pluripotency by binding specific DNA sequences and regulating expression of key genes including POU5F1/OCT4. Mutations cause otofacial neurodevelopmental syndrome with autosomal recessive inheritance. The gene is highly constrained against loss-of-function variants (pLI near 1, LOEUF 0.733), indicating intolerance to complete protein loss.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

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 negative regulation of DNA-templated transcription and regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

LOFmechanismARLOEUF 0.731 OMIM phenotype

Clinical Summary— ZSCAN10

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

5 unique Pathogenic / Likely Pathogenic· 136 VUS of 165 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.73LOEUF

pLI 0.000

Z-score 2.57

OE 0.44 (0.28–0.73)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.51Z-score

OE missense 0.94 (0.87–1.01)

456 obs / 487.5 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.44 (0.28–0.73)

0≤0.351.4

Missense OE?0.94 (0.87–1.01)

0≤0.61.4

Synonymous OE?1.10

0≤1.21.6

LoF obs/exp: 11 / 24.9Missense obs/exp: 456 / 487.5Syn Z: -1.14

Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗

moderateZSCAN10-related neurodevelopmental disorder with oto-facial malformationsLOFAR

This gene — mechanism propensity

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

0.88top 5%

GOF

0.82top 10%

LOF

0.1697th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

165 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic5

VUS136

Likely Benign17

Benign4

Conflicting1

Pathogenic

136

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	5	0	0	0	5
Likely Pathogenic	0	0	0	0	0
VUS	2	134	0	0	136
Likely Benign	0	11	0	6	17
Benign	0	2	0	2	4
Conflicting	—				1
Total	7	147	0	8	163

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

View in ClinVar →

35 pathogenic / likely-pathogenic (of 50) ClinVar copy-number / structural variants overlap ZSCAN10 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →