ZNF438

protein-coding

zinc finger protein 438, the group of Zinc fingers C2H2-type

Gene summary

Enables DNA-binding transcription factor activity. Involved in negative regulation of DNA-templated transcription. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001143768.2

Inheritance

—

ClinVar variants

U:122B:15

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chr10:30,820,207-31,031,937

External References & Databases

Ensembl (ENSG00000183621)

Transcript & Mutation Effects

hg38 • Region Span ~211.7 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 ZNF438 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 130

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001143768.2. 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			2 clinvar	2 clinvar		4
missense			120 clinvar	13 clinvar		133
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	122	15	0	137

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 148 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001143768.2	RefSeq	NP_001137240.1	3	MANE Select
ENST00000436087.7	Ensembl	ENSP00000406934.2	3	MANE Select
NM_001143766.2	RefSeq	NP_001137238.1	3	Standard
NM_001143767.2	RefSeq	NP_001137239.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

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

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
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000436087
Coding exons: 3
Length: 211731
Individuals with no LoFs: 125657
Homozygous LoFs: 0
Heterozygous LoFs: 91
Defined: 125748
p: 0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.286	446	429	1.04	0.0000225	5450
Missense (PolyPhen)		106	103.8	1.0212		1370
Synonymous	-1.30	182	161	1.13	0.00000862	1645
Loss of Function	1.24	11	16.4	0.669	8.69e-7	243

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00040	0.00040	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00065	0.00065	rare
European (Non-Finnish)	0.00026	0.00025	rare
South Asian	0.00098	0.00095	rare
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Isoform 1 acts as a transcriptional repressor.;

Intolerance Scores

LoFtool: 0.866
RVIS EVS: 0.65
RVIS percentile EVS: 84.12

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0431

Gene Damage Prediction

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