ZNF135

protein-coding

zinc finger protein 135, the group of Zinc fingers C2H2-type

Gene summary

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ZNF61
ZNF78L1

MANE transcript

NM_001289401.2

Inheritance

—

ClinVar variants

U:97B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chr19:58,059,239-58,086,310

External References & Databases

Ensembl (ENSG00000176293)

Transcript & Mutation Effects

hg38 • Region Span ~27.1 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 ZNF135 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 91

not providedTotal: 9

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001289401.2. 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	5 clinvar	9
missense			94 clinvar	1 clinvar	1 clinvar	96
nonsense				1 clinvar		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	97	4	6	107

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001289401.2	RefSeq	NP_001276330.1	4	MANE Select
ENST00000313434.10	Ensembl	ENSP00000321406.5	4	MANE Select
NM_001164527.1	RefSeq	NP_001157999.1	3	Standard
NM_001164529.1	RefSeq	NP_001158001.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription

Biological Process

regulation of transcription, DNA-templated
regulation of transcription by RNA polymerase II
cytoskeleton organization
regulation of cell morphogenesis

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000401053
Coding exons: 4
Length: 27071
Individuals with no LoFs: 125004
Homozygous LoFs: 0
Heterozygous LoFs: 744
Defined: 125748
p: 0.00296

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0787	375	371	1.01	0.0000206	4508
Missense (PolyPhen)		132	135.06	0.97735		1698
Synonymous	-1.10	171	154	1.11	0.00000937	1271
Loss of Function	1.17	22	28.8	0.765	0.00000160	326

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0062	0.0061	notable
Latino/Admixed American	0.0025	0.0025	notable
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.0021	0.0021	notable
Finnish	0.00018	0.00018	rare
European (Non-Finnish)	0.0040	0.0040	notable
South Asian	0.0012	0.0012	notable
Other	0.0042	0.0042	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in the regulation of cell morphology and cytoskeletal organization. May be involved in transcriptional regulation. {ECO:0000269|PubMed:21834987}.;

Recessive Scores

pRec: 0.160

Intolerance Scores

LoFtool: 0.970
RVIS EVS: 1.16
RVIS percentile EVS: 92.63

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0133

Gene Damage Prediction

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