ZNF677

protein-coding

zinc finger protein 677, 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 cis-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_182609.4

Inheritance

—

ClinVar variants

U:89B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.71

Max pathogenic AF

—

Genomic locus

chr19:53,235,381-53,254,898

External References & Databases

Ensembl (ENSG00000197928)

Transcript & Mutation Effects

hg38 • Region Span ~19.5 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 ZNF677 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 91

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182609.4. 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	2 clinvar		3
missense			86 clinvar	6 clinvar		92
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	89	8	0	97

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 48 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182609.4	RefSeq	NP_872415.1	3	MANE Select
ENST00000598513.6	Ensembl	ENSP00000469391.1	3	MANE Select
NM_001317998.2	RefSeq	NP_001304927.1	3	Standard
NM_001385608.1	RefSeq	NP_001372537.1	3	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
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000333952
Coding exons: 3
Length: 26575
Individuals with no LoFs: 124698
Homozygous LoFs: 5
Heterozygous LoFs: 1043
Defined: 125746
p: 0.00418

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0762	303	299	1.01	0.0000142	3927
Missense (PolyPhen)		65	76.209	0.85292		1005
Synonymous	-0.482	109	103	1.06	0.00000490	977
Loss of Function	1.21	15	21.0	0.714	8.76e-7	338

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0020	0.0019	notable
Latino/Admixed American	0.0038	0.0038	notable
Ashkenazi Jewish	0.0026	0.0025	notable
East Asian	0.0018	0.0018	notable
Finnish	0.0015	0.0015	notable
European (Non-Finnish)	0.0064	0.0064	notable
South Asian	0.0016	0.0015	notable
Other	0.0046	0.0046	notable

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.943
RVIS EVS: -0.22
RVIS percentile EVS: 37.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.0955

Gene Damage Prediction

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