ZNF311

protein-coding

zinc finger protein 311, 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_001382360.1

Inheritance

—

ClinVar variants

U:78B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.61

Max pathogenic AF

—

Genomic locus

chr6:28,994,785-29,005,316

External References & Databases

Ensembl (ENSG00000197935)

Transcript & Mutation Effects

hg38 • Region Span ~10.5 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 ZNF311 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 79

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001382360.1. 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			78 clinvar	3 clinvar		81
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	78	3	0	81

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 74 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001382360.1	RefSeq	NP_001369289.1	6	MANE Select
ENST00000377179.4	Ensembl	ENSP00000366384.3	6	MANE Select
NM_001010877.5	RefSeq	NP_001010877.2	6	Standard
NM_001350637.4	RefSeq	NP_001337566.1	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 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: ENST00000377179
Coding exons: 6
Length: 10532
Individuals with no LoFs: 124882
Homozygous LoFs: 1
Heterozygous LoFs: 118
Defined: 125001
p: 0.000476

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.828	307	351	0.876	0.0000178	4437
Missense (PolyPhen)		83	101.35	0.81892		1323
Synonymous	2.18	93	124	0.751	0.00000599	1181
Loss of Function	1.92	17	27.9	0.609	0.00000175	345

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0023	0.0021	notable
Latino/Admixed American	0.0011	0.0011	notable
Ashkenazi Jewish	0.00010	0.00010	rare
East Asian	0.00033	0.00033	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00021	0.00020	rare
South Asian	0.00036	0.00036	rare
Other	0.00083	0.00082	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.768
RVIS EVS: 0.64
RVIS percentile EVS: 83.98

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.175

Gene Damage Prediction

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