ZSCAN10

protein-coding

zinc finger and SCAN domain containing 10, the group of Zinc fingers C2H2-type|SCAN domain containing

Gene summary

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]

Previous symbols:

ZNF206

MANE transcript

NM_032805.3

Inheritance

ClinVar variants

P:6U:135B:22

Top phenotype

Otofacial neurodevelopmental syndrome

gnomAD constraint

pLI —, LoF o/e 0.44

Max pathogenic AF

—

Genomic locus

chr16:3,088,890-3,099,295

External References & Databases

Ensembl (ENSG00000130182)

Transcript & Mutation Effects

hg38 • Region Span ~10.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

otofacial neurodevelopmental syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0975705

Submitter: PanelApp Australia

otofacial neurodevelopmental syndromeMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0975705

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Otofacial neurodevelopmental syndromeAR

Manifestation: Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Genitourinary; Neurologic

Intervention: Audiologic/Otolaryngologic; Cardiovascular

Rationale: Among other findings, the condition can involve hearing loss, and early recognition and treatment of hearing impairment may improve outcomes, including speech and language development; The condition can include congenital anomalies, including cardiovascular anomalies, and awareness may allow early difentificaitons and management

Refs: 38386308

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZSCAN10 variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 140

not providedTotal: 20

Otofacial neurodevelopmental syndromeTotal: 7

ZSCAN10 DeficiencyTotal: 2

Global developmental delayTotal: 2

Sensorineural hearing loss disorderTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032805.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				8 clinvar	3 clinvar	11
missense			133 clinvar	11 clinvar		144
nonsense	2 clinvar	1 clinvar				3
start loss						0
frameshift	3 clinvar		2 clinvar			5
splice donor/acceptor (+/-2bp)						0
Total	5	1	135	19	3	163

Highest pathogenic variant AF is 0.000066527275

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032805.3	RefSeq	NP_116194.2	5	MANE Select
ENST00000576985.6	Ensembl	ENSP00000458879.2	5	MANE Select
NM_001282415.2	RefSeq	NP_001269344.1	1	Standard
NM_001282416.2	RefSeq	NP_001269345.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Developmental Biology
Transcriptional regulation of pluripotent stem cells

Biological Process

regulation of transcription by RNA polymerase II
somatic stem cell population maintenance
negative regulation of transcription, DNA-templated

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA-binding transcription factor activity
sequence-specific DNA binding
metal ion binding

Cellular Component

nucleus
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000252463
Coding exons: 5
Length: 10428
Individuals with no LoFs: 125689
Homozygous LoFs: 0
Heterozygous LoFs: 58
Defined: 125747
p: 0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.506	456	487	0.935	0.0000370	4613
Missense (PolyPhen)		186	214.2	0.86836		1999
Synonymous	-1.14	247	225	1.10	0.0000177	1514
Loss of Function	2.57	11	24.9	0.443	0.00000123	248

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000070	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000057	0.000054	rare
Finnish	0.0018	0.0018	notable
European (Non-Finnish)	0.00013	0.00012	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Embryonic stem (ES) cell-specific transcription factor required to maintain ES cell pluripotency. Can both activate and /or repress expression of target genes, depending on the context. Specifically binds the 5'-[GA]CGCNNGCG[CT]-3' DNA consensus sequence. Regulates expression of POU5F1/OCT4, ZSCAN4 and ALYREF/THOC4. {ECO:0000250|UniProtKB:Q3URR7}.;

Recessive Scores

pRec: 0.105

Intolerance Scores

LoFtool: 0.490
RVIS EVS: -0.62
RVIS percentile EVS: 17.36

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.320

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium