ZNF875

protein-coding

zinc finger protein 875, 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]

Previous symbols:

HKR1

MANE transcript

NM_001353803.2

Inheritance

—

ClinVar variants

U:101B:7

Top phenotype

Fetal akinesia deformation sequence 1

gnomAD constraint

pLI —, LoF o/e 1.05

Max pathogenic AF

—

Genomic locus

chr19:37,312,837-37,369,365

External References & Databases

Ensembl (ENSG00000181666)

Transcript & Mutation Effects

hg38 • Region Span ~56.5 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 ZNF875 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 105

not providedTotal: 7

Fetal akinesia deformation sequence 1Total: 1

Arthrogryposis multiplex congenitaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001353803.2. 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				1 clinvar	1 clinvar	2
missense			99 clinvar	4 clinvar	1 clinvar	104
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	101	5	2	108

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 102 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001353803.2	RefSeq	NP_001340732.1	4	MANE Select
ENST00000392153.8	Ensembl	ENSP00000375994.3	4	MANE Select
NM_001329761.2	RefSeq	NP_001316690.1	4	Standard
NM_001329762.2	RefSeq	NP_001316691.1	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
multicellular organism development

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: ENST00000324411
Coding exons: 4
Length: 56529
Individuals with no LoFs: 125111
Homozygous LoFs: 0
Heterozygous LoFs: 636
Defined: 125747
p: 0.00253

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.349	378	359	1.05	0.0000187	4318
Missense (PolyPhen)		96	84.888	1.1309		1145
Synonymous	-1.10	150	134	1.12	0.00000665	1262
Loss of Function	-0.244	28	26.6	1.05	0.00000150	317

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0015	0.0015	notable
Latino/Admixed American	0.0016	0.0016	notable
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.0015	0.0015	notable
Finnish	0.0061	0.0061	notable
European (Non-Finnish)	0.0030	0.0030	notable
South Asian	0.0014	0.0013	notable
Other	0.0020	0.0020	notable

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.886
RVIS EVS: 0.27
RVIS percentile EVS: 70.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.539

Gene Damage Prediction

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