ZC3H6

protein-coding

zinc finger CCCH-type containing 6, the group of Zinc fingers CCCH-type

Gene summary

Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific. Predicted to be involved in negative regulation of DNA-templated transcription, elongation. Predicted to be located in chromatin. Predicted to be active in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ZC3HDC6

MANE transcript

NM_198581.3

Inheritance

—

ClinVar variants

U:150B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.24

Max pathogenic AF

—

Genomic locus

chr2:112,275,597-112,340,059

External References & Databases

Ensembl (ENSG00000188177)

Transcript & Mutation Effects

hg38 • Region Span ~64.5 kb

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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 ZC3H6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 148

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198581.3. 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			2 clinvar	3 clinvar		5
missense			148 clinvar	4 clinvar		152
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	150	7	0	157

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198581.3	RefSeq	NP_940983.2	12	MANE Select
ENST00000409871.6	Ensembl	ENSP00000386764.1	12	MANE Select
ENST00000968137.1	Ensembl	ENSP00000638196.1	13	Standard
ENST00000968137.2	Ensembl	ENSP00000638196.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
biological_process
negative regulation of transcription, DNA-templated

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding
molecular_function
DNA-binding transcription factor activity
metal ion binding

Cellular Component

cellular_component
nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409871
Coding exons: 12
Length: 64470
Individuals with no LoFs: 124604
Homozygous LoFs: 0
Heterozygous LoFs: 34
Defined: 124638
p: 0.000136

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.47	482	582	0.828	0.0000274	7808
Missense (PolyPhen)		116	181.75	0.63824		2613
Synonymous	-0.467	220	211	1.04	0.0000109	2252
Loss of Function	4.56	10	41.8	0.239	0.00000186	637

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000066	0.000065	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000056	0.000056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0948

Intolerance Scores

LoFtool: 0.519
RVIS EVS: -0.57
RVIS percentile EVS: 18.9

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.274

Gene Damage Prediction

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