ZNF675

protein-coding

zinc finger protein 675, the group of Zinc fingers C2H2-type

Gene summary

Enables ubiquitin protein ligase binding activity. Involved in negative regulation of osteoclast differentiation; negative regulation of signal transduction; and negative regulation of transcription by RNA polymerase II. Located in nucleus and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_138330.3

Inheritance

—

ClinVar variants

U:74

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.37

Max pathogenic AF

—

Genomic locus

chr19:23,525,631-23,687,220

External References & Databases

Ensembl (ENSG00000197372)

Transcript & Mutation Effects

hg38 • Region Span ~161.6 kb

Loading mutation effect viewer...

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 ZNF675 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 72

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138330.3. 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			72 clinvar			72
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	74	0	0	74

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138330.3	RefSeq	NP_612203.2	4	MANE Select
ENST00000359788.9	Ensembl	ENSP00000352836.3	4	MANE Select
ENST00000596211.5	Ensembl	ENSP00000473217.1	4	Standard
ENST00000596211.6	Ensembl	ENSP00000473217.1	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

negative regulation of transcription by RNA polymerase II
I-kappaB kinase/NF-kappaB signaling
negative regulation of tumor necrosis factor-mediated signaling pathway
cytokine-mediated signaling pathway
negative regulation of NF-kappaB transcription factor activity

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
protein binding
zinc ion binding
ubiquitin protein ligase binding

Cellular Component

nucleus
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000359788
Coding exons: 4
Length: 161590
Individuals with no LoFs: 125116
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125119
p: 0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.225	292	281	1.04	0.0000128	3752
Missense (PolyPhen)		114	112.02	1.0176		1463
Synonymous	0.404	93	98.1	0.948	0.00000451	962
Loss of Function	1.35	2	5.39	0.371	2.28e-7	63

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000090	0.0000088	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation. May play a role during osteoclast differentiation by modulating TRAF6 signaling activity.;

Recessive Scores

pRec: 0.0855

Intolerance Scores

LoFtool: 0.687
RVIS EVS: 0
RVIS percentile EVS: 53.85

Essentials

Essential (CRISPR): N
Essential (gene trap): H
Indispensability pred.: E
Indispensability score: 1.00

Gene Damage Prediction

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