ZNF839

protein-coding

zinc finger protein 839

Gene summary

Predicted to enable zinc ion binding activity. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C14orf131

MANE transcript

NM_018335.6

Inheritance

—

ClinVar variants

U:140B:29

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.48

Max pathogenic AF

—

Genomic locus

chr14:102,317,377-102,342,702

External References & Databases

Ensembl (ENSG00000022976)

Transcript & Mutation Effects

hg38 • Region Span ~25.3 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 ZNF839 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 158

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018335.6. 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	5 clinvar		7
missense			138 clinvar	23 clinvar	1 clinvar	162
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	140	28	1	169

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 53 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018335.6	RefSeq	NP_060805.3	8	MANE Select
ENST00000442396.7	Ensembl	ENSP00000399863.2	8	MANE Select
NM_001267827.2	RefSeq	NP_001254756.1	7	Standard
NM_001267828.2	RefSeq	NP_001254757.1	7	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

Molecular Function

nucleic acid binding
metal ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000442396
Coding exons: 8
Length: 25331
Individuals with no LoFs: 124601
Homozygous LoFs: 1
Heterozygous LoFs: 37
Defined: 124639
p: 0.000152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.921	420	477	0.881	0.0000270	5874
Missense (PolyPhen)		91	135.14	0.67336		1748
Synonymous	-0.468	209	201	1.04	0.0000122	2005
Loss of Function	2.30	11	22.9	0.481	0.00000129	300

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00017	0.00017	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00021	0.00019	rare
South Asian	0.00027	0.00026	rare
Other	0.00017	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.897
RVIS EVS: 1.5
RVIS percentile EVS: 95.38

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.475

Gene Damage Prediction

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