ZSCAN29

protein-coding

zinc finger and SCAN domain containing 29, the group of SCAN domain containing|Zinc fingers C2H2-type

Gene summary

Enables sequence-specific double-stranded 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]

Previous symbols:

ZNF690

MANE transcript

NM_001372080.1

Inheritance

—

ClinVar variants

U:118B:10

Top phenotype

ZSCAN29-related disorder

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr15:43,358,172-43,371,043

External References & Databases

Ensembl (ENSG00000140265)

Transcript & Mutation Effects

hg38 • Region Span ~12.9 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZSCAN29 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 118

ZSCAN29-related disorderTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001372080.1. 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			2 clinvar	4 clinvar		6
missense			115 clinvar	6 clinvar		121
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	118	10	0	128

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001372080.1	RefSeq	NP_001359009.1	5	MANE Select
ENST00000684362.1	Ensembl	ENSP00000507363.1	5	MANE Select
NM_152455.4	RefSeq	NP_689668.3	5	Standard
ENST00000396976.6	Ensembl	ENSP00000380174.2	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000396976
Coding exons: 5
Length: 12854
Individuals with no LoFs: 125642
Homozygous LoFs: 0
Heterozygous LoFs: 106
Defined: 125748
p: 0.000422

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0638	470	474	0.992	0.0000264	5611
Missense (PolyPhen)		175	187.26	0.93454		2259
Synonymous	0.243	165	169	0.976	0.00000849	1617
Loss of Function	1.93	21	32.9	0.638	0.00000169	425

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00074	0.00074	rare
Latino/Admixed American	0.00067	0.00055	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00033	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00048	0.00047	rare
South Asian	0.00053	0.00052	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation.;

Intolerance Scores

LoFtool: 0.904
RVIS EVS: -0.15
RVIS percentile EVS: 42.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0251

Gene Damage Prediction

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