ZNF35

protein-coding

zinc finger protein 35, the group of Zinc fingers C2H2-type

Gene summary

Enables DNA-binding transcription factor activity and sequence-specific DNA binding activity. Predicted to be involved in cellular response to retinoic acid; regulation of transcription by RNA polymerase II; and spermatogenesis. Located in nucleus and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_003420.4

Inheritance

—

ClinVar variants

U:65

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.31

Max pathogenic AF

—

Genomic locus

chr3:44,648,732-44,660,791

External References & Databases

Ensembl (ENSG00000169981)

Transcript & Mutation Effects

hg38 • Region Span ~12.1 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 ZNF35 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 65

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003420.4. 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						0
missense			65 clinvar			65
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	65	0	0	65

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003420.4	RefSeq	NP_003411.3	3	MANE Select
ENST00000396056.7	Ensembl	ENSP00000379368.2	3	MANE Select
ENST00000296092.7	Ensembl	ENSP00000296092.3	2	Standard
ENST00000296092.8	Ensembl	ENSP00000296092.3	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription, DNA-templated
regulation of transcription by RNA polymerase II
spermatogenesis
cellular response to retinoic acid

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
DNA-binding transcription factor activity
sequence-specific DNA binding
metal ion binding

Cellular Component

cell
nucleus
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000396056
Coding exons: 3
Length: 12065
Individuals with no LoFs: 125705
Homozygous LoFs: 0
Heterozygous LoFs: 42
Defined: 125747
p: 0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.36	212	275	0.770	0.0000132	3499
Missense (PolyPhen)		58	100.92	0.5747		1308
Synonymous	-0.612	109	101	1.08	0.00000531	952
Loss of Function	2.85	6	19.6	0.305	9.94e-7	266

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00044	0.00043	rare
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00027	0.00027	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.00046	0.00046	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation. Involved in cell differentiation and/or proliferation.;

Recessive Scores

pRec: 0.0987

Intolerance Scores

LoFtool: 0.693
RVIS EVS: -0.49
RVIS percentile EVS: 22.36

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.992

Gene Damage Prediction

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