ZFP42

protein-coding

ZFP42 zinc finger protein, the group of Zinc fingers C2H2-type

Gene summary

Enables sequence-specific double-stranded DNA binding activity. Involved in female gonad development and male gonad development. Located in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_174900.5

Inheritance

—

ClinVar variants

U:46B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e —

Max pathogenic AF

—

Genomic locus

chr4:187,995,771-188,005,046

External References & Databases

Ensembl (ENSG00000179059)

Transcript & Mutation Effects

hg38 • Region Span ~9.3 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 ZFP42 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 48

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_174900.5. 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					1 clinvar	1
missense			46 clinvar	4 clinvar		50
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	46	4	1	51

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 58 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_174900.5	RefSeq	NP_777560.2	1	MANE Select
ENST00000326866.5	Ensembl	ENSP00000317686.4	1	MANE Select
NM_001304358.2	RefSeq	NP_001291287.1	1	Standard
ENST00000509524.5	Ensembl	ENSP00000424662.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Cardiac Progenitor Differentiation
Preimplantation Embryo

Biological Process

negative regulation of transcription by RNA polymerase II
male gonad development
female gonad development
meiotic cell cycle

Molecular Function

RNA polymerase II proximal promoter sequence-specific DNA binding
RNA polymerase II distal enhancer sequence-specific DNA binding
DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
DNA-binding transcription factor activity

Cellular Component

nuclear chromatin
nucleus
transcription factor complex
cytoplasm
PcG protein complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000326866
Coding exons: 1
Length: 9280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.448	194	177	1.09	0.0000106	2022
Missense (PolyPhen)		43	51.924	0.82813		557
Synonymous	0.263	71	73.9	0.961	0.00000512	599
Loss of Function

Population LoF Frequency

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

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in the reprogramming of X-chromosome inactivation during the acquisition of pluripotency. Required for efficient elongation of TSIX, a non-coding RNA antisense to XIST. Binds DXPas34 enhancer within the TSIX promoter. Involved in ES cell self-renewal (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.465
RVIS EVS: 0.17
RVIS percentile EVS: 65.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.265

Gene Damage Prediction

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