ZNF609

protein-coding

zinc finger protein 609, the group of Zinc fingers C2H2-type

Gene summary

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and promoter-specific chromatin binding activity. Involved in regulation of myoblast proliferation. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_015042.2

Inheritance

ClinVar variants

U:218B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.06

Max pathogenic AF

—

Genomic locus

chr15:64,460,578-64,686,068

External References & Databases

Ensembl (ENSG00000180357)

Transcript & Mutation Effects

hg38 • Region Span ~225.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0700092

Submitter: PMGRC

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZNF609 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 212

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015042.2. 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			3 clinvar	1 clinvar	3 clinvar	7
missense			212 clinvar	3 clinvar	1 clinvar	216
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	218	4	4	226

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015042.2	RefSeq	NP_055857.1	8	MANE Select
ENST00000326648.5	Ensembl	ENSP00000316527.3	8	MANE Select
ENST00000416172.1	Ensembl	ENSP00000388846.1	1	Standard
ENST00000416172.2	Ensembl	ENSP00000388846.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
muscle organ development
positive regulation of transcription by RNA polymerase II
regulation of myoblast proliferation
positive regulation of neuron migration

Molecular Function

nucleic acid binding
metal ion binding

Cellular Component

nucleus
nucleoplasm
integrator complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000326648
Coding exons: 8
Length: 225324
Individuals with no LoFs: 125739
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125744
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.83	651	796	0.818	0.0000450	9203
Missense (PolyPhen)		248	326.56	0.75944		3750
Synonymous	-0.289	310	304	1.02	0.0000169	2851
Loss of Function	6.18	3	50.3	0.0596	0.00000289	639

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcription factor, which activates RAG1, and possibly RAG2, transcription. Through the regulation of RAG1/2 expression, may regulate thymocyte maturation. Along with NIPBL and the multiprotein complex Integrator, promotes cortical neuron migration during brain development by regulating the transcription of crucial genes in this process. Preferentially binds promoters containing paused RNA polymerase II. Up-regulates the expression of SEMA3A, NRP1, PLXND1 and GABBR2 genes, among others. {ECO:0000250|UniProtKB:Q8BZ47}.;

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.00751
RVIS EVS: -2.58
RVIS percentile EVS: 0.83

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.309

Gene Damage Prediction

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