ZNF302

protein-coding

zinc finger protein 302, the group of Zinc fingers C2H2-type

Gene summary

This gene encodes a member of the zinc-finger protein family. The encoded protein contains seven C2H2-type zinc fingers and a KRAB domain, but its function has yet to be determined. Alternatively spliced transcript variants have been described. [provided by RefSeq, Mar 2014]

MANE transcript

NM_001289187.2

Inheritance

—

ClinVar variants

U:67B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.56

Max pathogenic AF

—

Genomic locus

chr19:34,677,639-34,686,397

External References & Databases

Ensembl (ENSG00000089335)

Transcript & Mutation Effects

hg38 • Region Span ~8.8 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 ZNF302 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 70

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001289187.2. 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
missense			65 clinvar	5 clinvar	2 clinvar	72
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	67	5	2	74

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 148 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001289187.2	RefSeq	NP_001276116.1	4	MANE Select
ENST00000505242.6	Ensembl	ENSP00000421028.1	4	MANE Select
NM_001012320.3	RefSeq	NP_001012320.1	4	Standard
NM_001289181.2	RefSeq	NP_001276110.1	5	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
protein binding
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000505242
Coding exons: 4
Length: 8759
Individuals with no LoFs: 125318
Homozygous LoFs: 5
Heterozygous LoFs: 423
Defined: 125746
p: 0.00170

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.511	232	211	1.10	0.0000103	2665
Missense (PolyPhen)		83	67.759	1.2249		848
Synonymous	-2.52	100	72.7	1.38	0.00000378	667
Loss of Function	1.53	8	14.2	0.563	6.93e-7	197

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00091	0.00086	rare
Latino/Admixed American	0.00035	0.00035	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.018	0.017	notable
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00032	0.00032	rare
South Asian	0.0013	0.0012	notable
Other	0.0013	0.0013	notable

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.0884

Intolerance Scores

LoFtool: 0.709
RVIS EVS: 0.95
RVIS percentile EVS: 90.09

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.861

Gene Damage Prediction

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