ZNF841

protein-coding

zinc finger protein 841, the group of Zinc fingers C2H2-type

Gene summary

Predicted to enable transcription cis-regulatory region binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nuclear lumen. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001136499.2

Inheritance

—

ClinVar variants

U:120B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.55

Max pathogenic AF

—

Genomic locus

chr19:52,064,465-52,095,765

External References & Databases

Ensembl (ENSG00000197608)

Transcript & Mutation Effects

hg38 • Region Span ~31.3 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 ZNF841 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 123

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001136499.2. 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						0
missense			118 clinvar	6 clinvar		124
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	120	6	0	126

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 37 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001136499.2	RefSeq	NP_001129971.1	4	MANE Select
ENST00000594440.6	Ensembl	ENSP00000470100.2	4	MANE Select
NM_001321349.2	RefSeq	NP_001308278.1	1	Standard
NM_001352298.2	RefSeq	NP_001339227.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000389534
Coding exons: 4
Length: 31300
Individuals with no LoFs: 125659
Homozygous LoFs: 0
Heterozygous LoFs: 20
Defined: 125679
p: 0.0000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.794	453	503	0.900	0.0000269	6120
Missense (PolyPhen)		131	165.34	0.79231		2132
Synonymous	0.694	159	171	0.932	0.00000873	1668
Loss of Function	0.968	3	5.44	0.552	2.30e-7	66

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	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00015	0.00015	rare
South Asian	0	0.0	absent
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation. {ECO:0000250}.;

Intolerance Scores

RVIS EVS: 0.62
RVIS percentile EVS: 83.36

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.179

Gene Damage Prediction

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