ZGPAT

protein-coding

zinc finger CCCH-type and G-patch domain containing, the group of Zinc fingers CCCH-type|G-patch domain containing

Gene summary

Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of epidermal growth factor-activated receptor activity and negative regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

KIAA1847

MANE transcript

NM_181485.3

Inheritance

—

ClinVar variants

U:84B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.45

Max pathogenic AF

—

Genomic locus

chr20:63,707,465-63,736,142

External References & Databases

Ensembl (ENSG00000197114)

Transcript & Mutation Effects

hg38 • Region Span ~28.7 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 ZGPAT variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 88

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_181485.3. 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	1 clinvar		3
missense			80 clinvar	7 clinvar		87
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	84	8	0	92

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 67 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_181485.3	RefSeq	NP_852150.2	6	MANE Select
ENST00000355969.11	Ensembl	ENSP00000348242.6	6	MANE Select
NM_001083113.2	RefSeq	NP_001076582.1	6	Standard
NM_001195653.2	RefSeq	NP_001182582.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of transcription by RNA polymerase II
negative regulation of epidermal growth factor-activated receptor activity
negative regulation of transcription, DNA-templated

Molecular Function

RNA polymerase II proximal promoter sequence-specific DNA binding
DNA-binding transcription factor activity, RNA polymerase II-specific
DNA-binding transcription repressor activity, RNA polymerase II-specific
DNA-binding transcription factor activity
protein binding

Cellular Component

nucleus
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000328969
Coding exons: 6
Length: 28678
Individuals with no LoFs: 125709
Homozygous LoFs: 0
Heterozygous LoFs: 38
Defined: 125747
p: 0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.208	310	320	0.967	0.0000199	3364
Missense (PolyPhen)		87	107.48	0.80948		1222
Synonymous	-0.275	149	145	1.03	0.00000982	1124
Loss of Function	2.31	9	20.2	0.445	0.00000107	226

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00015	0.00014	rare
European (Non-Finnish)	0.00021	0.00020	rare
South Asian	0.00014	0.00013	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcription repressor that specifically binds the 5'- GGAG[GA]A[GA]A-3' consensus sequence. Represses transcription by recruiting the chromatin multiprotein complex NuRD to target promoters. Negatively regulates expression of EGFR, a gene involved in cell proliferation, survival and migration. Its ability to repress genes of the EGFR pathway suggest it may act as a tumor suppressor. Able to suppress breast carcinogenesis. {ECO:0000269|PubMed:19644445}.;

Recessive Scores

pRec: 0.107

Intolerance Scores

RVIS EVS: -0.71
RVIS percentile EVS: 14.67

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.973

Gene Damage Prediction

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