ZNF169

protein-coding

zinc finger protein 169, 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 transcription 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, Jul 2025]

MANE transcript

NM_194320.4

Inheritance

—

ClinVar variants

U:84B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.91

Max pathogenic AF

—

Genomic locus

chr9:94,259,298-94,303,967

External References & Databases

Ensembl (ENSG00000175787)

Transcript & Mutation Effects

hg38 • Region Span ~44.7 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 ZNF169 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 86

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_194320.4. 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			1 clinvar			1
missense			83 clinvar	4 clinvar		87
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	84	4	0	88

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_194320.4	RefSeq	NP_919301.2	4	MANE Select
ENST00000395395.7	Ensembl	ENSP00000378792.2	4	MANE Select
NM_001301275.2	RefSeq	NP_001288204.1	1	Standard
NM_003448.3	RefSeq	NP_003439.2	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 by RNA polymerase II

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000395395
Coding exons: 4
Length: 42144
Individuals with no LoFs: 125605
Homozygous LoFs: 0
Heterozygous LoFs: 143
Defined: 125748
p: 0.000569

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.216	331	342	0.967	0.0000188	3941
Missense (PolyPhen)		103	113.69	0.90596		1309
Synonymous	-0.812	148	136	1.09	0.00000758	1189
Loss of Function	0.370	18	19.8	0.910	0.00000101	243

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0024	0.0024	notable
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00082	0.00082	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00053	0.00053	rare
South Asian	0.00049	0.00049	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation.;

Recessive Scores

pRec: 0.116

Intolerance Scores

LoFtool: 0.911
RVIS EVS: 0.62
RVIS percentile EVS: 83.47

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.292

Gene Damage Prediction

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